Bio


Born in Scotland, Dr. Ashley graduated with 1st class Honors in Physiology and Medicine from the University of Glasgow. He completed medical residency and a PhD at the University of Oxford before moving to Stanford University where he trained in cardiology, joining the faculty in 2006. His group is focused on the science of precision medicine. He is best known for his work helping establish the field of medical genomics. His team developed some of the earliest tools for the interpretation of the human genome in the context of human health. He founded the Clinical Genomics Program and the Center for Inherited Cardiovascular Disease at Stanford. He was the first co-chair of the steering committee of the national Undiagnosed Diseases Network. He was a recipient of the National Innovation Award from the American Heart Association and the NIH Director’s New Innovator Award. He was recognized by the Obama White House for his contributions to Personalized Medicine. In 2018, he was awarded the American Heart Association Medal of Honor for Genomic and Precision Medicine. He was appointed Stanford Associate Dean in 2019 and became the inaugural holder of the Roger and Joelle Burnell Chair in Genomics and Precision Health in 2021. In 2023, he became a Fellow of the John Simon Guggenheim Memorial Foundation. He is co-founder of several companies including Personalis, Deepcell, and Svexa. His first book The Genome Odyssey - Medical Mysteries and the Incredible Quest to Solve Them was released in 2021. Father to three Americans, in his spare time, he pilots planes, tries to understand American football, plays jazz saxophone, and conducts research on the health benefits of single malt Scotch whisky.

Clinical Focus


  • Cardiology
  • Inherited cardiovascular disease
  • Hypertrophic Cardiomyopathy
  • Cardiomyopathy, Dilated
  • Sports Cardiology
  • Heart Failure
  • Arrhythmogenic Right Ventricular Dysplasia
  • Left ventricular non-compaction cardiomyopathy
  • Genomic medicine
  • Undiagnosed disease

Academic Appointments


Administrative Appointments


  • Founding Director, Stanford Center for Inherited Cardiovascular Disease (2010 - Present)
  • Chair, Stanford Medicine Clinical Genomics Advisory Committee (2020 - Present)
  • Co-Director, Stanford Center for Digital Health (2017 - Present)
  • Director, Stanford Cardiopulmonary Exercise Testing Laboratory (2007 - Present)
  • Executive Committee, Wu Tsai Human Performance Alliance (2021 - Present)
  • Executive Committee, Molecular Transducers of Physical Activity Consortium (MoTrPAC) (2018 - Present)
  • Co-Director, Stanford Research Training Program in Myocardial Biology (T32) (2010 - Present)
  • Medical Director, Clinical Genomics Program (2013 - 2020)
  • Co-Director, Stanford Data Science Initiative (2016 - 2021)
  • Co-chair, NIH Undiagnosed Diseases Network (2014 - 2017)
  • Co-chair, Cardiovascular Working Group, Clinical Genome Resource (Clingen) (2014 - 2016)
  • Leadership committee, AHA Council on Functional Genomics and Translational Biology (2009 - 2014)
  • Member, Institute of Medicine Roundtable on Translating Genomic-based Research for Health (2012 - 2015)

Honors & Awards


  • Guggenheim Fellowship, John Simon Guggenheim Memorial Foundation (2023)
  • Roger and Joelle Burnell Chair of Genomics and Precision Health, Stanford University (2021)
  • Medal of Honor (Genomic and Precision Medicine), American Heart Association (2018)
  • One Brave Idea, American Heart Association (2017)
  • Fellow, Royal College of Physicians (London) (2017)
  • Fellow, American Society of Clinical Investigation (2016)
  • NIH Director's New Innovator Award, National Institutes of Health (2009)
  • Faculty Scholar, Donald E. and Delia B. Baxter Foundation (2009)
  • Fellow, American Heart Association (2009)
  • Innovative Research Award, American Heart Association (2008)
  • Career Development Award (K08), National Institutes of Health (2006)
  • Western Affiliates Young Investigator Award, American Heart Association (2004)
  • Cardiovascular Medicine Basic Science Award, Stanford University (2004)
  • Young Investigator Award (Basic), Astra-Zeneca (2003)
  • Young Investigator Prize in Cardiovascular Medicine, UK Medical Research Society (2002)
  • Young Investigator Award, European Society of Cardiology (2002)

Boards, Advisory Committees, Professional Organizations


  • Advisor, Apple (2020 - 2023)
  • Non-executive director, AstraZeneca PLC (2020 - Present)
  • Founder and Advisor, Deepcell Inc (2018 - Present)
  • Advisor, Foresite Labs (2020 - Present)
  • Advisor, Medical Excellence Capital (2022 - Present)
  • Advisor, Galatea Bio (2022 - Present)
  • Founder & Advisor, Personalis Inc (2013 - Present)
  • Advisor, Sequence Bio (2019 - Present)
  • Founder and Board Chair, Svexa Inc (2019 - Present)

Professional Education


  • Board Certification: Royal College of Physicians-U.K., Cardiology (1999)
  • Residency: University of Oxford (1996) UK
  • Internship: University of Glasgow (1997) Scotland
  • Medical Education: University of Glasgow (1996) Scotland
  • Fellowship: University of Oxford (2002) UK
  • Fellowship: Stanford University Medical Center (2006) CA
  • DPhil, University of Oxford, Molecular Cardiology (2002)
  • MRCP (UK), Royal College of Physicians (UK), Medicine (1999)
  • MB ChB, University of Glasgow, Medicine (1996)
  • BSc (Hons), University of Glasgow, Physiology (1993)

Community and International Work


  • Arbor Free Cardiology Clinic

    Location

    Bay Area

    Ongoing Project

    Yes

    Opportunities for Student Involvement

    Yes

Patents


  • Ashley EA, Quertermous T, Grube E. "United States Patent 12,074,964 Developing biologically active agents that modulate activity of restenosis target gene, comprises combining candidate biologically active agent, and determining the effect of agent on restenosis associated molecular and cellular changes", The Board of Trustees of the Leland Stanford Junior University, Mar 7, 2008
  • Ashley EA, Chen MM, Quertermous T. "United States Patent 11,985,460 Apelin and uses thereof", The Board of Trustees of the Leland Stanford Junior University, Nov 14, 2007
  • Vailaya A, Kuchinsky A, King JY, Ferrara R, Quertermous T, Vairaya A, Ashley IA, Katermas T, Ashley EA. "United States Patent 10,641,492 Significant molecules identification method for biological network used in disease analysis, involves calculating connectivity score for molecule represented by identified node based on significance scores of each node", Agilent Technologies, Inc., Jul 26, 2007
  • Deng D, Tsalenko A, Ben-Dor A, Yakhini ZH, Quertermous T, Ashley EA, Yang E, Tabibiazar R, Tsao P. "United States Patent 11,412,437 New composition comprising a targeting agent that is conjugated to a functional moiety and that selectively binds to a polypeptide encoded by a DEA gene, useful in treating or preventing atherosclerosis", Agilent Technologies, Inc., Apr 27, 2006
  • Ben-Dor A, Bruhn L, Deng D, Tsalenko A, Ashley EA, Chen MC, Quertermous T, Yakhini Z, Chen MM, Deng DX. "United States Patent 7,947,280 New composition having a targeting agent selectively binding to a polypeptide encoded by an upregulated-in-recovery (UIR) or downregulated-in-recovery (DIR) gene, useful for diagnosing, preventing and/or treating heart failure", The Board of Trustees of the Leland Stanford Junior University, Jul 14, 2005

Current Research and Scholarly Interests


The Ashley lab is focused on precision medicine. We develop methods for the interpretation of whole genome sequencing data to improve diagnosis of genetic disease and to personalize the practice of medicine. We love big data questions and systems approaches to biology especially analysis of network graphs. The wet bench is where we test causality of key genes and investigate the biology of network modules. It is also the focus of our translational efforts. Therapeutic development is a near term goal and several of our discoveries are the focus of patents or are being actively pursued by pharmaceutical and biotechnology partners.

Clinical Trials


  • Clinical and Genetic Evaluation of Individuals With Undiagnosed Disorders Through the Undiagnosed Diseases Network Recruiting

    Without an explanation for severe and sometimes life-threatening symptoms, patients and their families are left in a state of unknown. Many individuals find themselves being passed from physician to physician, undergoing countless and often repetitive tests in the hopes of finding answers and insight about what the future may hold. This long and arduous journey to find a diagnosis does not end for many patients- the Office of Rare Diseases Research (ORDR) notes that 6% of individuals seeking their assistance have an undiagnosed disorder. In 2008, the National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) was established with the goal of providing care and answers for these individuals with mysterious conditions who have long eluded diagnosis. The NIH UDP is a joint venture of the NIH ORDR, the National Human Genome Research Institute Intramural Research Program (NHGRI-IRP), and the NIH Clinical Research Center (CRC) (1-3). The goals of the NIH UDP are to: (1) provide answers for patients with undiagnosed diseases; (2) generate new knowledge about disease mechanisms; (3) assess the application of new approaches to phenotyping and the use of genomic technologies; and (4) identify potential therapeutic targets, if possible. To date, the UDP has evaluated 3300 medical records and admitted 750 individuals with rare and undiagnosed conditions to the NIH Clinical Center. The NIH UDP has identified more than 70 rare disease diagnoses and several new conditions. The success of the NIH UDP prompted the NIH Common Fund to support the establishment of a network of medical research centers, the Undiagnosed Diseases Network (UDN), for fiscal years 2013-2020. The clinical sites will perform extensive phenotyping, genetic analyses, and functional studies of potential disease-causing variants. The testing performed on patients involves medically indicated studies intended to help reach a diagnosis, as well as research investigations that include a skin biopsy, blood draws, and DNA analysis. In addition, the UDN will further the goals of the UDP by permitting the sharing of personally identifiable phenotypic and genotypic information within the network. By sharing participant information and encouraging collaboration, the UDN hopes to improve the understanding of rare conditions and advance the diagnostic process and care for individuals with undiagnosed diseases....

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  • Exercise in Genetic Cardiovascular Conditions Recruiting

    The goal is to determine how lifestyle and exercise impact the well-being of individuals with hypertrophic cardiomyopathy (HCM) and long QT syndrome (LQTS). Ancillary study Aim: To understand how the coronavirus epidemic is impacting psychological health and quality of life in the LIVE population

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  • MyHeart Counts Cardiovascular Health Study Recruiting

    The MyHeart Counts Cardiovascular Health Study will utilize mobile health capabilities of smartphones and wearables to assess daily activity measures of the general population and compare these to measures of cardiovascular health risk factors and fitness. How people divide their time among exercise, sedentary behavior, and sleep all affect cardiovascular health, yet to date these have largely gone unmeasured. With the advancement of phone sensors and wearable fitness tracking devices these factors are now more straightforward to gather and measure. The use of smartphones by a large segment of the population allows for data collection on an unprecedented scale. The investigators aim to amass activity and cardiovascular health data on thousands of participants as well as provide significantly more quantitative data on type,duration, and intensity of daily activities. In the second phase of the MyHeart Counts Cardiovascular Health Study (Randomized Assessment of Physical Activity Prompts In A Large Ambulatory Population) the researchers will conduct a randomized controlled clinical trial of four different physical activity prompts (intervention) and their effect on the level of physical activity in the study population as measured by change in step count.

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  • Open-Label Study of Perhexiline in Patients With Hypertrophic Cardiomyopathy and Moderate to Severe Heart Failure Recruiting

    The purpose of this study is to evaluate the effect of perhexiline on exercise performance (efficacy) and safety in patients with hypertrophic cardiomyopathy and moderate-to-severe heart failure following dosing for 16 weeks.

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  • DCM Precision Medicine Study Not Recruiting

    The aims of the DCM Precision Medicine Study are to test the hypothesis that DCM has substantial genetic basis and to evaluate the effectiveness of a family communication intervention in improving the uptake and impact of family member clinical screening.

    Stanford is currently not accepting patients for this trial. For more information, please contact DCM Coordinators, 650 725-6911.

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  • MyHeart Counts: Stanford Mobile Cardiovascular Health Study 3.0 Not Recruiting

    MyHeart Counts is a smartphone-based mobile cardiovascular health research study. It will use the mobile health capabilities of smartphones and wearables to assess daily activity measures of the general public and compare these to measures of cardiovascular health - risk factors and fitness. How people divide their time among exercise, sedentary behavior, and sleep all affect cardiovascular health, yet largely go unmeasured. These can now be measured with sensors in phones or wearable devices as we have shown on iOS. With the large number of smartphone users addressable with a HIPAA complaint iOS & Android platform, the investigators aim to collect activity and cardiovascular health data on many more subjects than in prior studies as well as provide much more quantitative data on type, duration, and intensity of daily activities. It also provides a platform to investigate methods to help participants increase heart-healthy activities. The study also includes a randomized controlled trial on physical activity. The overall goal is to develop an extensive source of data to help inform future cardiovascular health guidelines.

    Stanford is currently not accepting patients for this trial. For more information, please contact Anna Shcherbina, MEng, 310-689-6688.

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  • Personal Genomics for Preventive Cardiology Not Recruiting

    The purpose of this study is to see if providing information to a person on their inherited (genetic) risk of cardiovascular disease (CVD) helps to motivate that person to change their diet, lifestyle or medication regimen to alter their risk.

    Stanford is currently not accepting patients for this trial. For more information, please contact Josh Knowles, 650-804-2526.

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  • Rapid Turnaround, Home-based Saliva Testing for COVID-19 Not Recruiting

    The aim of the study is to demonstrate the feasibility and validity of a saliva based home surveillance monitoring test for SARS-CoV-2 infection. Participants will be asked to carry out as many tests as are included in the bag they are provided, on a daily basis until they are used up.

    Stanford is currently not accepting patients for this trial. For more information, please contact Study Team, 650-374-0085.

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  • Study of Exercise Training in Hypertrophic Cardiomyopathy Not Recruiting

    The investigators propose a pilot randomized controlled trial to determine the safety and potential benefits of moderate intensity exercise in patients with hypertrophic cardiomyopathy. The investigators hypotheses are that exercise parameters derived from a baseline cardiopulmonary exercise test will target an appropriately safe level of exercise intensity that will not cause significant arrhythmias or exacerbate symptoms and that exercise training for 4 months will result in significant improvements in peak oxygen consumption (peak VO2) and quality of life, with neutral effects on the clinical characteristics.

    Stanford is currently not accepting patients for this trial. For more information, please contact Heidi Salisbury, BS, RN, MSN, 650-736-7878.

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  • Valsartan for Attenuating Disease Evolution In Early Sarcomeric HCM Not Recruiting

    The purpose of this trial is to determine whether treatment with valsartan will have beneficial effect in early hypertrophic cardiomyopathy (HCM) by assessing many domains that reflect myocardial structure, function and biochemistry.

    Stanford is currently not accepting patients for this trial. For more information, please contact Euan Ashley, MD, PhD, 650-498-4900.

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  • Exercise Study Including Patients With Hypertrophic Cardiomyopathy Not Recruiting

    The long term health and cardiovascular benefits of a regular exercise program have been well-established. National guidelines recommend involvement in moderate aerobic fitness (i.e. walking, bicycling, light jogging, swimming) for patients with hypertrophic cardiomyopathy (HCM). However, data on potential benefits of recreational exercise, useful parameters for risk stratification, and methods of devising individual exercise prescriptions are completely lacking. The specific aims of this study are: 1) to devise a safe moderate intensity exercise training program in patients with HCM, and 2) to determine whether exercise training improves ability to perform activities and tasks, heart size and function, and quality of life in patients with HCM.

    Stanford is currently not accepting patients for this trial. For more information, please contact Lisa Garrett, 650-736-7878.

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2023-24 Courses


Stanford Advisees


Graduate and Fellowship Programs


All Publications


  • Temporal dynamics of the multi-omic response to endurance exercise training. Nature 2024; 629 (8010): 174-183

    Abstract

    Regular exercise promotes whole-body health and prevents disease, but the underlying molecular mechanisms are incompletely understood1-3. Here, the Molecular Transducers of Physical Activity Consortium4 profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome and immunome in whole blood, plasma and 18 solid tissues in male and female Rattus norvegicus over eight weeks of endurance exercise training. The resulting data compendium encompasses 9,466 assays across 19 tissues, 25 molecular platforms and 4 training time points. Thousands of shared and tissue-specific molecular alterations were identified, with sex differences found in multiple tissues. Temporal multi-omic and multi-tissue analyses revealed expansive biological insights into the adaptive responses to endurance training, including widespread regulation of immune, metabolic, stress response and mitochondrial pathways. Many changes were relevant to human health, including non-alcoholic fatty liver disease, inflammatory bowel disease, cardiovascular health and tissue injury and recovery. The data and analyses presented in this study will serve as valuable resources for understanding and exploring the multi-tissue molecular effects of endurance training and are provided in a public repository ( https://motrpac-data.org/ ).

    View details for DOI 10.1038/s41586-023-06877-w

    View details for PubMedID 38693412

    View details for PubMedCentralID PMC11062907

  • Almanac - Retrieval-Augmented Language Models for Clinical Medicine. NEJM AI Zakka, C., Shad, R., Chaurasia, A., Dalal, A. R., Kim, J. L., Moor, M., Fong, R., Phillips, C., Alexander, K., Ashley, E., Boyd, J., Boyd, K., Hirsch, K., Langlotz, C., Lee, R., Melia, J., Nelson, J., Sallam, K., Tullis, S., Vogelsong, M. A., Cunningham, J. P., Hiesinger, W. 2024; 1 (2)

    Abstract

    Large language models (LLMs) have recently shown impressive zero-shot capabilities, whereby they can use auxiliary data, without the availability of task-specific training examples, to complete a variety of natural language tasks, such as summarization, dialogue generation, and question answering. However, despite many promising applications of LLMs in clinical medicine, adoption of these models has been limited by their tendency to generate incorrect and sometimes even harmful statements.We tasked a panel of eight board-certified clinicians and two health care practitioners with evaluating Almanac, an LLM framework augmented with retrieval capabilities from curated medical resources for medical guideline and treatment recommendations. The panel compared responses from Almanac and standard LLMs (ChatGPT-4, Bing, and Bard) versus a novel data set of 314 clinical questions spanning nine medical specialties.Almanac showed a significant improvement in performance compared with the standard LLMs across axes of factuality, completeness, user preference, and adversarial safety.Our results show the potential for LLMs with access to domain-specific corpora to be effective in clinical decision-making. The findings also underscore the importance of carefully testing LLMs before deployment to mitigate their shortcomings. (Funded by the National Institutes of Health, National Heart, Lung, and Blood Institute.).

    View details for DOI 10.1056/aioa2300068

    View details for PubMedID 38343631

    View details for PubMedCentralID PMC10857783

  • Genetic architecture of cardiac dynamic flow volumes. Nature genetics Gomes, B., Singh, A., O'Sullivan, J. W., Schnurr, T. M., Goddard, P. C., Loong, S., Amar, D., Hughes, J. W., Kostur, M., Haddad, F., Salerno, M., Foo, R., Montgomery, S. B., Parikh, V. N., Meder, B., Ashley, E. A. 2023

    Abstract

    Cardiac blood flow is a critical determinant of human health. However, the definition of its genetic architecture is limited by the technical challenge of capturing dynamic flow volumes from cardiac imaging at scale. We present DeepFlow, a deep-learning system to extract cardiac flow and volumes from phase-contrast cardiac magnetic resonance imaging. A mixed-linear model applied to 37,653 individuals from the UK Biobank reveals genome-wide significant associations across cardiac dynamic flow volumes spanning from aortic forward velocity to aortic regurgitation fraction. Mendelian randomization reveals a causal role for aortic root size in aortic valve regurgitation. Among the most significant contributing variants, localizing genes (near ELN, PRDM6 and ADAMTS7) are implicated in connective tissue and blood pressure pathways. Here we show that DeepFlow cardiac flow phenotyping at scale, combined with genotyping data, reinforces the contribution of connective tissue genes, blood pressure and root size to aortic valve function.

    View details for DOI 10.1038/s41588-023-01587-5

    View details for PubMedID 38082205

    View details for PubMedCentralID 7612636

  • Improved Cardiac Performance and Decreased Arrhythmia in Hypertrophic Cardiomyopathy With Non-β-Blocking R-Enantiomer Carvedilol. Circulation Seo, K., Yamamoto, Y., Kirillova, A., Kawana, M., Yadav, S., Huang, Y., Wang, Q., Lane, K. V., Pruitt, B. L., Perez, M. V., Bernstein, D., Wu, J. C., Wheeler, M. T., Parikh, V. N., Ashley, E. A. 2023

    Abstract

    Hypercontractility and arrhythmia are key pathophysiologic features of hypertrophic cardiomyopathy (HCM), the most common inherited heart disease. β-Adrenergic receptor antagonists (β-blockers) are the first-line therapy for HCM. However, β-blockers commonly selected for this disease are often poorly tolerated in patients, where heart-rate reduction and noncardiac effects can lead to reduced cardiac output and fatigue. Mavacamten, myosin ATPase inhibitor recently approved by the US Food and Drug Administration, has demonstrated the ability to ameliorate hypercontractility without lowering heart rate, but its benefits are so far limited to patients with left ventricular (LV) outflow tract obstruction, and its effect on arrhythmia is unknown.We screened 21 β-blockers for their impact on myocyte contractility and evaluated the antiarrhythmic properties of the most promising drug in a ventricular myocyte arrhythmia model. We then examined its in vivo effect on LV function by hemodynamic pressure-volume loop analysis. The efficacy of the drug was tested in vitro and in vivo compared with current therapeutic options (metoprolol, verapamil, and mavacamten) for HCM in an established mouse model of HCM (Myh6R403Q/+ [myosin heavy chain 6]) and iPSC cardiomyocytes derived from patients with HCM (MYH7R403Q/+) [myosin heavy chain 7]).We identified that carvedilol, a β-blocker not commonly used in HCM, suppresses contractile function and arrhythmia by inhibiting RyR2 (ryanodine receptor type 2). Unlike metoprolol (a β1-blocker), carvedilol markedly reduced LV contractility through RyR2 inhibition, while maintaining stroke volume through α1-adrenergic receptor inhibition in vivo. Clinically available carvedilol is a racemic mixture, and the R-enantiomer, devoid of β-blocking effect, retains the ability to inhibit both α1-receptor and RyR2, thereby suppressing contractile function and arrhythmias without lowering heart rate and cardiac output. In Myh6R403Q/+ mice, R-carvedilol normalized hyperdynamic contraction, suppressed arrhythmia, and increased cardiac output better than metoprolol, verapamil, and mavacamten. The ability of R-carvedilol to suppress contractile function was well retained in MYH7R403Q/+ induced pluripotent stem cell cardiomyocytes.R-enantiomer carvedilol attenuates hyperdynamic contraction, suppresses arrhythmia, and at the same time, improves cardiac output without lowering heart rate by dual blockade of α1-adrenergic receptor and RyR2 in mouse and human models of HCM. This combination of therapeutic effects is unique among current therapeutic options for HCM and may particularly benefit patients without LV outflow tract obstruction.

    View details for DOI 10.1161/CIRCULATIONAHA.123.065017

    View details for PubMedID 37850394

  • Rare variant associations with plasma protein levels in the UK Biobank. Nature Dhindsa, R. S., Burren, O. S., Sun, B. B., Prins, B. P., Matelska, D., Wheeler, E., Mitchell, J., Oerton, E., Hristova, V. A., Smith, K. R., Carss, K., Wasilewski, S., Harper, A. R., Paul, D. S., Fabre, M. A., Runz, H., Viollet, C., Challis, B., Platt, A., Vitsios, D., Ashley, E. A., Whelan, C. D., Pangalos, M. N., Wang, Q., Petrovski, S. 2023

    Abstract

    Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.

    View details for DOI 10.1038/s41586-023-06547-x

    View details for PubMedID 37794183

    View details for PubMedCentralID 7610464

  • COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning. Communications biology Salek, M., Li, N., Chou, H., Saini, K., Jovic, A., Jacobs, K. B., Johnson, C., Lu, V., Lee, E. J., Chang, C., Nguyen, P., Mei, J., Pant, K. P., Wong-Thai, A. Y., Smith, Q. F., Huang, S., Chow, R., Cruz, J., Walker, J., Chan, B., Musci, T. J., Ashley, E. A., Masaeli, M. M. 2023; 6 (1): 971

    Abstract

    Cells are the singular building blocks of life, and a comprehensive understanding of morphology, among other properties, is crucial to the assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without the need for biomarker labels and stains/dyes. We demonstrate COSMOS capabilities with multiple human cell lines and tissue samples. These early results suggest that our neural networks embedding space can capture and recapitulate deep visual characteristics and can be used to efficiently purify unlabeled viable cells with desired morphological traits. Our approach resolves a technical gap in the ability to perform real-time deep learning assessment and sorting of cells based on high-resolution brightfield images.

    View details for DOI 10.1038/s42003-023-05325-9

    View details for PubMedID 37740030

  • Artificial Intelligence in Molecular Medicine. The New England journal of medicine Gomes, B., Ashley, E. A. 2023; 388 (26): 2456-2465

    View details for DOI 10.1056/NEJMra2204787

    View details for PubMedID 37379136

  • Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature biotechnology Goenka, S. D., Gorzynski, J. E., Shafin, K., Fisk, D. G., Pesout, T., Jensen, T. D., Monlong, J., Chang, P. C., Baid, G., Bernstein, J. A., Christle, J. W., Dalton, K. P., Garalde, D. R., Grove, M. E., Guillory, J., Kolesnikov, A., Nattestad, M., Ruzhnikov, M. R., Samadi, M., Sethia, A., Spiteri, E., Wright, C. J., Xiong, K., Zhu, T., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022

    Abstract

    Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.

    View details for DOI 10.1038/s41587-022-01221-5

    View details for PubMedID 35347328

  • Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England journal of medicine Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., Spiteri, E., Pesout, T., Monlong, J., Baid, G., Bernstein, J. A., Ceresnak, S., Chang, P. C., Christle, J. W., Chubb, H., Dalton, K. P., Dunn, K., Garalde, D. R., Guillory, J., Knowles, J. W., Kolesnikov, A., Ma, M., Moscarello, T., Nattestad, M., Perez, M., Ruzhnikov, M. R., Samadi, M., Setia, A., Wright, C., Wusthoff, C. J., Xiong, K., Zhu, T., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022

    View details for DOI 10.1056/NEJMc2112090

    View details for PubMedID 35020984

  • The genetics of human performance. Nature reviews. Genetics Kim, D. S., Wheeler, M. T., Ashley, E. A. 2021

    Abstract

    Human physiology is likely to have been selected for endurance physical activity. However, modern humans have become largely sedentary, with physical activity becoming a leisure-time pursuit for most. Whereas inactivity is a strong risk factor for disease, regular physical activity reduces the risk of chronic disease and mortality. Although substantial epidemiological evidence supports the beneficial effects of exercise, comparatively little is known about the molecular mechanisms through which these effects operate. Genetic and genomic analyses have identified genetic variation associated with human performance and, together with recent proteomic, metabolomic and multi-omic analyses, are beginning to elucidate the molecular genetic mechanisms underlying the beneficial effects of physical activity on human health.

    View details for DOI 10.1038/s41576-021-00400-5

    View details for PubMedID 34522035

  • Mapping the human genetic architecture of COVID-19. Nature COVID-19 Host Genetics Initiative 2021

    Abstract

    The genetic makeup of an individual contributes to susceptibility and response to viral infection. While environmental, clinical and social factors play a role in exposure to SARS-CoV-2 and COVID-19 disease severity1,2, host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. We describe the results of three genome-wide association meta-analyses comprised of up to 49,562 COVID-19 patients from 46 studies across 19 countries. We reported 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases3-7. They also represent potentially actionable mechanisms in response to infection. Mendelian Randomization analyses support a causal role for smoking and body mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19, with unprecedented speed, was made possible by the community of human genetic researchers coming together to prioritize sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.

    View details for DOI 10.1038/s41586-021-03767-x

    View details for PubMedID 34237774

  • Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise. Cell Sanford, J. A., Nogiec, C. D., Lindholm, M. E., Adkins, J. N., Amar, D., Dasari, S., Drugan, J. K., Fernandez, F. M., Radom-Aizik, S., Schenk, S., Snyder, M. P., Tracy, R. P., Vanderboom, P., Trappe, S., Walsh, M. J., Molecular Transducers of Physical Activity Consortium, Adkins, J. N., Amar, D., Dasari, S., Drugan, J. K., Evans, C. R., Fernandez, F. M., Li, Y., Lindholm, M. E., Nogiec, C. D., Radom-Aizik, S., Sanford, J. A., Schenk, S., Snyder, M. P., Tomlinson, L., Tracy, R. P., Trappe, S., Vanderboom, P., Walsh, M. J., Alekel, D. L., Bekirov, I., Boyce, A. T., Boyington, J., Fleg, J. L., Joseph, L. J., Laughlin, M. R., Maruvada, P., Morris, S. A., McGowan, J. A., Nierras, C., Pai, V., Peterson, C., Ramos, E., Roary, M. C., Williams, J. P., Xia, A., Cornell, E., Rooney, J., Miller, M. E., Ambrosius, W. T., Rushing, S., Stowe, C. L., Rejeski, W. J., Nicklas, B. J., Pahor, M., Lu, C., Trappe, T., Chambers, T., Raue, U., Lester, B., Bergman, B. C., Bessesen, D. H., Jankowski, C. M., Kohrt, W. M., Melanson, E. L., Moreau, K. L., Schauer, I. E., Schwartz, R. S., Kraus, W. E., Slentz, C. A., Huffman, K. M., Johnson, J. L., Willis, L. H., Kelly, L., Houmard, J. A., Dubis, G., Broskey, N., Goodpaster, B. H., Sparks, L. M., Coen, P. M., Cooper, D. M., Haddad, F., Rankinen, T., Ravussin, E., Johannsen, N., Harris, M., Jakicic, J. M., Newman, A. B., Forman, D. D., Kershaw, E., Rogers, R. J., Nindl, B. C., Page, L. C., Stefanovic-Racic, M., Barr, S. L., Rasmussen, B. B., Moro, T., Paddon-Jones, D., Volpi, E., Spratt, H., Musi, N., Espinoza, S., Patel, D., Serra, M., Gelfond, J., Burns, A., Bamman, M. M., Buford, T. W., Cutter, G. R., Bodine, S. C., Esser, K., Farrar, R. P., Goodyear, L. J., Hirshman, M. F., Albertson, B. G., Qian, W., Piehowski, P., Gritsenko, M. A., Monore, M. E., Petyuk, V. A., McDermott, J. E., Hansen, J. N., Hutchison, C., Moore, S., Gaul, D. A., Clish, C. B., Avila-Pacheco, J., Dennis, C., Kellis, M., Carr, S., Jean-Beltran, P. M., Keshishian, H., Mani, D. R., Clauser, K., Krug, K., Mundorff, C., Pearce, C., Ivanova, A. A., Ortlund, E. A., Maner-Smith, K., Uppal, K., Zhang, T., Sealfon, S. C., Zavlasky, E., Nair, V., Li, S., Jain, N., Ge, Y., Sun, Y., Nudelman, G., Ruf-Zamojski, F., Smith, G., Pincas, N., Rubenstein, A., Amper, M. A., Seenarine, N., Lappalainen, T., Lanza, I. R., Nair, K. S., Klaus, K., Montgomery, S. B., Smith, K. S., Gay, N. R., Zhao, B., Hung, C. J., Zebarjadi, N., Balliu, B., Fresard, L., Burant, C. F., Li, J. Z., Kachman, M., Soni, T., Raskind, A. B., Gerszten, R., Robbins, J., Ilkayeva, O., Muehlbauer, M. J., Newgard, C. B., Ashley, E. A., Wheeler, M. T., Jimenez-Morales, D., Raja, A., Dalton, K. P., Zhen, J., Kim, Y. S., Christle, J. W., Marwaha, S., Chin, E. T., Hershman, S. G., Hastie, T., Tibshirani, R., Rivas, M. A. 2020; 181 (7): 1464–74

    Abstract

    Exercise provides a robust physiological stimulus that evokes cross-talk among multiple tissues that when repeated regularly (i.e., training) improves physiological capacity, benefits numerous organ systems, and decreases the risk for premature mortality. However, a gap remains in identifying the detailed molecular signals induced by exercise that benefits health and prevents disease. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to address this gap and generate a molecular map of exercise. Preclinical and clinical studies will examine the systemic effects of endurance and resistance exercise across a range of ages and fitness levels by molecular probing of multiple tissues before and after acute and chronic exercise. From this multi-omic and bioinformatic analysis, a molecular map of exercise will be established. Altogether, MoTrPAC will provide a public database that is expected to enhance our understanding of the health benefits of exercise and to provide insight into how physical activity mitigates disease.

    View details for DOI 10.1016/j.cell.2020.06.004

    View details for PubMedID 32589957

  • Video-based AI for beat-to-beat assessment of cardiac function NATURE Ouyang, D., He, B., Ghorbani, A., Yuan, N., Ebinger, J., Langlotz, C. P., Heidenreich, P. A., Harrington, R. A., Liang, D. H., Ashley, E. A., Zou, J. Y. 2020
  • Molecular Choreography of Acute Exercise. Cell Contrepois, K. n., Wu, S. n., Moneghetti, K. J., Hornburg, D. n., Ahadi, S. n., Tsai, M. S., Metwally, A. A., Wei, E. n., Lee-McMullen, B. n., Quijada, J. V., Chen, S. n., Christle, J. W., Ellenberger, M. n., Balliu, B. n., Taylor, S. n., Durrant, M. G., Knowles, D. A., Choudhry, H. n., Ashland, M. n., Bahmani, A. n., Enslen, B. n., Amsallem, M. n., Kobayashi, Y. n., Avina, M. n., Perelman, D. n., Schüssler-Fiorenza Rose, S. M., Zhou, W. n., Ashley, E. A., Montgomery, S. B., Chaib, H. n., Haddad, F. n., Snyder, M. P. 2020; 181 (5): 1112–30.e16

    Abstract

    Acute physical activity leads to several changes in metabolic, cardiovascular, and immune pathways. Although studies have examined selected changes in these pathways, the system-wide molecular response to an acute bout of exercise has not been fully characterized. We performed longitudinal multi-omic profiling of plasma and peripheral blood mononuclear cells including metabolome, lipidome, immunome, proteome, and transcriptome from 36 well-characterized volunteers, before and after a controlled bout of symptom-limited exercise. Time-series analysis revealed thousands of molecular changes and an orchestrated choreography of biological processes involving energy metabolism, oxidative stress, inflammation, tissue repair, and growth factor response, as well as regulatory pathways. Most of these processes were dampened and some were reversed in insulin-resistant participants. Finally, we discovered biological pathways involved in cardiopulmonary exercise response and developed prediction models revealing potential resting blood-based biomarkers of peak oxygen consumption.

    View details for DOI 10.1016/j.cell.2020.04.043

    View details for PubMedID 32470399

  • The effect of digital physical activity interventions on daily step count: a randomised controlled crossover substudy of the MyHeart Counts Cardiovascular Health Study LANCET DIGITAL HEALTH Shcherbina, A., Hershman, S. G., Lazzeroni, L., King, A. C., O'Sullivan, J. W., Hekler, E., Moayedi, Y., Pavlovic, A., Waggott, D., Sharma, A., Yeung, A., Christle, J. W., Wheeler, M. T., McConnell, M. V., Harrington, R. A., Ashley, E. A. 2019; 1 (7): E344–E352
  • Allele-Specific Silencing Ameliorates Restrictive Cardiomyopathy Due to a Human Myosin Regulatory Light Chain Mutation. Circulation Zaleta-Rivera, K., Dainis, A., Ribeiro, A. J., Sanchez Cordero, P., Rubio, G., Shang, C., Liu, J., Finsterbach, T., Parikh, V. N., Sutton, S., Seo, K., Sinha, N., Jain, N., Huang, Y., Hajjar, R. J., Kay, M. A., Szczesna-Cordary, D., Pruitt, B. L., Wheeler, M. T., Ashley, E. A. 2019

    Abstract

    BACKGROUND: Restrictive cardiomyopathy (RCM) is a rare heart disease associated with mutations in sarcomeric genes and with phenotypic overlap with hypertrophic cardiomyopathy. There is no approved therapy. Here, we explore the potential of an interfering RNA (RNAi) therapeutic for a human sarcomeric mutation in MYL2 causative of restrictive cardiomyopathy in a mouse model.METHODS: AAV9-M7.8L shRNA was selected from a pool of RNAi oligonucleotides containing the SNV in different positions to specifically target the mutated allele causative of RCM by FACS screening. Two groups of RLC-N47K transgenic mice were injected with a single dose of AAV9-M7.8L shRNA at 3 days of age and at 60 days of age. Mice were subjected to treadmill exercise and echocardiography after treatment to determine VO2max and left ventricular mass. At the end of treatment, heart, lung, liver and kidney tissue was harvested to determine viral tropism and for transcriptome and proteomic analysis. Cardiomyocytes were isolated for single cell studies.RESULTS: One time injection of AAV9-M7.8L RNAi in 3-day-old humanized RLC mutant transgenic mice silenced the mutated allele (RLC-47K) with minimal effects on the normal allele (RLC-47N) assayed 16 weeks post-injection. AAV9-M7.8L RNAi suppressed the expression of hypertrophic biomarkers, reduced heart weight and attenuated a pathological increase in left ventricular mass (LVM). Single adult cardiac myocytes from mice treated with AAV9-M7.8L showed partial restoration of the maximal contraction velocity with marked reduction in hypercontractility as well as relaxation kinetics and improved time to maximal calcium reuptake velocity. In addition, cardiac stress protein biomarkers, such as calmodulin-dependent protein kinase II (CAMKII) and the transcription activator Brg1 were reduced suggesting recovery towards a healthy myocardium. Transcriptome analyses further revealed no significant changes of argonaute (AGO1, AGO2) and endoribonuclease dicer (DICER1) transcripts while endogenous microRNAs were preserved suggesting the RNAi pathway was not saturated.CONCLUSIONS: Our results show the feasibility, efficacy, and safety of RNAi therapeutics directed at human restrictive cardiomyopathy. This is a promising step towards targeted therapy for a prevalent human disease.

    View details for DOI 10.1161/CIRCULATIONAHA.118.036965

    View details for PubMedID 31315475

  • Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nature medicine Frésard, L. n., Smail, C. n., Ferraro, N. M., Teran, N. A., Li, X. n., Smith, K. S., Bonner, D. n., Kernohan, K. D., Marwaha, S. n., Zappala, Z. n., Balliu, B. n., Davis, J. R., Liu, B. n., Prybol, C. J., Kohler, J. N., Zastrow, D. B., Reuter, C. M., Fisk, D. G., Grove, M. E., Davidson, J. M., Hartley, T. n., Joshi, R. n., Strober, B. J., Utiramerur, S. n., Lind, L. n., Ingelsson, E. n., Battle, A. n., Bejerano, G. n., Bernstein, J. A., Ashley, E. A., Boycott, K. M., Merker, J. D., Wheeler, M. T., Montgomery, S. B. 2019

    Abstract

    It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.

    View details for DOI 10.1038/s41591-019-0457-8

    View details for PubMedID 31160820

  • Pathologic gene network rewiring implicates PPP1R3A as a central regulator in pressure overload heart failure. Nature communications Cordero, P., Parikh, V. N., Chin, E. T., Erbilgin, A., Gloudemans, M. J., Shang, C., Huang, Y., Chang, A. C., Smith, K. S., Dewey, F., Zaleta, K., Morley, M., Brandimarto, J., Glazer, N., Waggott, D., Pavlovic, A., Zhao, M., Moravec, C. S., Tang, W. H., Skreen, J., Malloy, C., Hannenhalli, S., Li, H., Ritter, S., Li, M., Bernstein, D., Connolly, A., Hakonarson, H., Lusis, A. J., Margulies, K. B., Depaoli-Roach, A. A., Montgomery, S. B., Wheeler, M. T., Cappola, T., Ashley, E. A. 2019; 10 (1): 2760

    Abstract

    Heart failure is a leading cause of mortality, yet our understanding of the genetic interactions underlying this disease remains incomplete. Here, we harvest 1352 healthy and failing human hearts directly from transplant center operating rooms, and obtain genome-wide genotyping and gene expression measurements for a subset of 313. We build failing and non-failing cardiac regulatory gene networks, revealing important regulators and cardiac expression quantitative trait loci (eQTLs). PPP1R3A emerges as a regulator whose network connectivity changes significantly between health and disease. RNA sequencing after PPP1R3A knockdown validates network-based predictions, and highlights metabolic pathway regulation associated with increased cardiomyocyte size and perturbed respiratory metabolism. Mice lacking PPP1R3A are protected against pressure-overload heart failure. We present a global gene interaction map of the human heart failure transition, identify previously unreported cardiac eQTLs, and demonstrate the discovery potential of disease-specific networks through the description of PPP1R3A as a central regulator in heart failure.

    View details for DOI 10.1038/s41467-019-10591-5

    View details for PubMedID 31235787

  • Genotype and Lifetime Burden of Disease in Hypertrophic Cardiomyopathy: Insights From the Sarcomeric Human Cardiomyopathy Registry (SHaRe) CIRCULATION Ho, C. Y., Day, S. M., Ashley, E. A., Michels, M., Pereira, A. C., Jacoby, D., Cirino, A. L., Fox, J. C., Lakdawala, N. K., Ware, J. S., Caleshu, C. A., Helms, A. S., Colan, S. D., Girolami, F., Cecchi, F., Seidman, C. E., Sajeev, G., Signorovitch, J., Green, E. M., Olivotto, I., SHaRe Investigators 2018; 138 (14): 1387–98

    Abstract

    A better understanding of the factors that contribute to heterogeneous outcomes and lifetime disease burden in hypertrophic cardiomyopathy (HCM) is critically needed to improve patient management and outcomes. The Sarcomeric Human Cardiomyopathy Registry (SHaRe) was established to provide the scale of data required to address these issues, aggregating longitudinal datasets curated by eight international HCM specialty centers.Data on 4591 HCM patients (2763 genotyped), followed for a mean of 5.4±6.9 years (24,791 patient-years; median [interquartile range] 2.9 [0.3-7.9] years) were analyzed regarding cardiac arrest, cardiac transplantation, appropriate implantable cardioverter-defibrillator (ICD) therapy, all-cause death, atrial fibrillation, stroke, New York Heart Association Functional Class III/IV symptoms (all comprising the overall composite endpoint), and left ventricular ejection fraction (LVEF)<35%. Outcomes were analyzed individually and as composite endpoints.Median age of diagnosis was 45.8 [30.9-58.1] years and 37% of patients were female. Age of diagnosis and sarcomere mutation status were predictive of outcomes. Patients <40 years old at diagnosis had a 77% [95% confidence interval: 72%, 80%] cumulative incidence of the overall composite outcome by age 60, compared to 32% [29%, 36%] by age 70 for patients diagnosed >60 years. Young HCM patients (20-29 years) had 4-fold higher mortality than the general United States population at a similar age. Patients with pathogenic/likely pathogenic sarcomere mutations had two-fold greater risk for adverse outcomes compared to patients without mutations; sarcomere variants of uncertain significance were associated with intermediate risk. Heart failure and atrial fibrillation were the most prevalent adverse events, although typically not emerging for several years after diagnosis. Ventricular arrhythmias occurred in 32% [23%, 40%] of patients <40 years at diagnosis, but in 1% [1%, 2%] >60 years.The cumulative burden of HCM is substantial and dominated by heart failure and atrial fibrillation occurring many years following diagnosis. Young age of diagnosis and the presence of a sarcomere mutation are powerful predictors of adverse outcomes. These findings highlight the need for close surveillance throughout life, and the need to develop disease-modifying therapies.

    View details for PubMedID 30297972

    View details for PubMedCentralID PMC6170149

  • Artificial Intelligence in Cardiology JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Johnson, K. W., Soto, J., Glicksberg, B. S., Shameer, K., Miotto, R., Ali, M., Ashley, E., Dudley, J. T. 2018; 71 (23): 2668–79

    Abstract

    Artificial intelligence and machine learning are poised to influence nearly every aspect of the human condition, and cardiology is not an exception to this trend. This paper provides a guide for clinicians on relevant aspects of artificial intelligence and machine learning, reviews selected applications of these methods in cardiology to date, and identifies how cardiovascular medicine could incorporate artificial intelligence in the future. In particular, the paper first reviews predictive modeling concepts relevant to cardiology such as feature selection and frequent pitfalls such as improper dichotomization. Second, it discusses common algorithms used in supervised learning and reviews selected applications in cardiology and related disciplines. Third, it describes the advent of deep learning and related methods collectively called unsupervised learning, provides contextual examples both in general medicine and in cardiovascular medicine, and then explains how these methods could be applied to enable precision cardiology and improve patient outcomes.

    View details for PubMedID 29880128

  • Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. The New England journal of medicine Splinter, K. n., Adams, D. R., Bacino, C. A., Bellen, H. J., Bernstein, J. A., Cheatle-Jarvela, A. M., Eng, C. M., Esteves, C. n., Gahl, W. A., Hamid, R. n., Jacob, H. J., Kikani, B. n., Koeller, D. M., Kohane, I. S., Lee, B. H., Loscalzo, J. n., Luo, X. n., McCray, A. T., Metz, T. O., Mulvihill, J. J., Nelson, S. F., Palmer, C. G., Phillips, J. A., Pick, L. n., Postlethwait, J. H., Reuter, C. n., Shashi, V. n., Sweetser, D. A., Tifft, C. J., Walley, N. M., Wangler, M. F., Westerfield, M. n., Wheeler, M. T., Wise, A. L., Worthey, E. A., Yamamoto, S. n., Ashley, E. A. 2018

    Abstract

    Many patients remain without a diagnosis despite extensive medical evaluation. The Undiagnosed Diseases Network (UDN) was established to apply a multidisciplinary model in the evaluation of the most challenging cases and to identify the biologic characteristics of newly discovered diseases. The UDN, which is funded by the National Institutes of Health, was formed in 2014 as a network of seven clinical sites, two sequencing cores, and a coordinating center. Later, a central biorepository, a metabolomics core, and a model organisms screening center were added.We evaluated patients who were referred to the UDN over a period of 20 months. The patients were required to have an undiagnosed condition despite thorough evaluation by a health care provider. We determined the rate of diagnosis among patients who subsequently had a complete evaluation, and we observed the effect of diagnosis on medical care.A total of 1519 patients (53% female) were referred to the UDN, of whom 601 (40%) were accepted for evaluation. Of the accepted patients, 192 (32%) had previously undergone exome sequencing. Symptoms were neurologic in 40% of the applicants, musculoskeletal in 10%, immunologic in 7%, gastrointestinal in 7%, and rheumatologic in 6%. Of the 382 patients who had a complete evaluation, 132 received a diagnosis, yielding a rate of diagnosis of 35%. A total of 15 diagnoses (11%) were made by clinical review alone, and 98 (74%) were made by exome or genome sequencing. Of the diagnoses, 21% led to recommendations regarding changes in therapy, 37% led to changes in diagnostic testing, and 36% led to variant-specific genetic counseling. We defined 31 new syndromes.The UDN established a diagnosis in 132 of the 382 patients who had a complete evaluation, yielding a rate of diagnosis of 35%. (Funded by the National Institutes of Health Common Fund.).

    View details for PubMedID 30304647

  • Accuracy in Wrist-Worn, Sensor-Based Measurements of Heart Rate and Energy Expenditure in a Diverse Cohort. Journal of personalized medicine Shcherbina, A., Mattsson, C. M., Waggott, D., Salisbury, H., Christle, J. W., Hastie, T., Wheeler, M. T., Ashley, E. A. 2017; 7 (2)

    Abstract

    The ability to measure physical activity through wrist-worn devices provides an opportunity for cardiovascular medicine. However, the accuracy of commercial devices is largely unknown. The aim of this work is to assess the accuracy of seven commercially available wrist-worn devices in estimating heart rate (HR) and energy expenditure (EE) and to propose a wearable sensor evaluation framework. We evaluated the Apple Watch, Basis Peak, Fitbit Surge, Microsoft Band, Mio Alpha 2, PulseOn, and Samsung Gear S2. Participants wore devices while being simultaneously assessed with continuous telemetry and indirect calorimetry while sitting, walking, running, and cycling. Sixty volunteers (29 male, 31 female, age 38 ± 11 years) of diverse age, height, weight, skin tone, and fitness level were selected. Error in HR and EE was computed for each subject/device/activity combination. Devices reported the lowest error for cycling and the highest for walking. Device error was higher for males, greater body mass index, darker skin tone, and walking. Six of the devices achieved a median error for HR below 5% during cycling. No device achieved an error in EE below 20 percent. The Apple Watch achieved the lowest overall error in both HR and EE, while the Samsung Gear S2 reported the highest. In conclusion, most wrist-worn devices adequately measure HR in laboratory-based activities, but poorly estimate EE, suggesting caution in the use of EE measurements as part of health improvement programs. We propose reference standards for the validation of consumer health devices (http://precision.stanford.edu/).

    View details for DOI 10.3390/jpm7020003

    View details for PubMedID 28538708

  • Effect of Moderate-Intensity Exercise Training on Peak Oxygen Consumption in Patients With Hypertrophic Cardiomyopathy A Randomized Clinical Trial JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Saberi, S., Wheeler, M., Bragg-Gresham, J., Hornsby, W., Agarwal, P. P., Attili, A., Concannon, M., Dries, A. M., Shmargad, Y., Salisbury, H., Kumar, S., Herrera, J., Myers, J., Helms, A. S., Ashley, E. A., Day, S. M. 2017; 317 (13): 1349-1357

    Abstract

    Formulating exercise recommendations for patients with hypertrophic cardiomyopathy is challenging because of concern about triggering ventricular arrhythmias and because a clinical benefit has not been previously established in this population.To determine whether moderate-intensity exercise training improves exercise capacity in adults with hypertrophic cardiomyopathy.A randomized clinical trial involving 136 patients with hypertrophic cardiomyopathy was conducted between April 2010 and October 2015 at 2 academic medical centers in the United States (University of Michigan Health System and Stanford University Medical Center). Date of last follow-up was November 2016.Participants were randomly assigned to 16 weeks of moderate-intensity exercise training (n = 67) or usual activity (n = 69).The primary outcome measure was change in peak oxygen consumption from baseline to 16 weeks.Among the 136 randomized participants (mean age, 50.4 [SD, 13.3] years; 42% women), 113 (83%) completed the study. At 16 weeks, the change in mean peak oxygen consumption was +1.35 (95% CI, 0.50 to 2.21) mL/kg/min among participants in the exercise training group and +0.08 (95% CI, -0.62 to 0.79) mL/kg/min among participants in the usual-activity group (between-group difference, 1.27 [95% CI, 0.17 to 2.37]; P = .02). There were no occurrences of sustained ventricular arrhythmia, sudden cardiac arrest, appropriate defibrillator shock, or death in either group.In this preliminary study involving patients with hypertrophic cardiomyopathy, moderate-intensity exercise compared with usual activity resulted in a statistically significant but small increase in exercise capacity at 16 weeks. Further research is needed to understand the clinical importance of this finding in patients with hypertrophic cardiomyopathy, as well as the long-term safety of exercise at moderate and higher levels of intensity.clinicaltrials.gov Identifier: NCT01127061.

    View details for DOI 10.1001/jama.2017.2503

    View details for Web of Science ID 000398434200019

    View details for PubMedID 28306757

  • The Changing Face of Informed Consent NEW ENGLAND JOURNAL OF MEDICINE Grady, C., Cummings, S. R., Rowbotham, M. C., McConnell, M. V., Ashley, E. A., Kang, G. 2017; 376 (9): 856-867
  • Feasibility of Obtaining Measures of Lifestyle From a Smartphone App: The MyHeart Counts Cardiovascular Health Study. JAMA cardiology McConnell, M. V., Shcherbina, A., Pavlovic, A., Homburger, J. R., Goldfeder, R. L., Waggot, D., Cho, M. K., Rosenberger, M. E., Haskell, W. L., Myers, J., Champagne, M. A., Mignot, E., Landray, M., Tarassenko, L., Harrington, R. A., Yeung, A. C., Ashley, E. A. 2017; 2 (1): 67-76

    Abstract

    Studies have established the importance of physical activity and fitness, yet limited data exist on the associations between objective, real-world physical activity patterns, fitness, sleep, and cardiovascular health.To assess the feasibility of obtaining measures of physical activity, fitness, and sleep from smartphones and to gain insights into activity patterns associated with life satisfaction and self-reported disease.The MyHeart Counts smartphone app was made available in March 2015, and prospective participants downloaded the free app between March and October 2015. In this smartphone-based study of cardiovascular health, participants recorded physical activity, filled out health questionnaires, and completed a 6-minute walk test. The app was available to download within the United States.The feasibility of consent and data collection entirely on a smartphone, the use of machine learning to cluster participants, and the associations between activity patterns, life satisfaction, and self-reported disease.From the launch to the time of the data freeze for this study (March to October 2015), the number of individuals (self-selected) who consented to participate was 48 968, representing all 50 states and the District of Columbia. Their median age was 36 years (interquartile range, 27-50 years), and 82.2% (30 338 male, 6556 female, 10 other, and 3115 unknown) were male. In total, 40 017 (81.7% of those who consented) uploaded data. Among those who consented, 20 345 individuals (41.5%) completed 4 of the 7 days of motion data collection, and 4552 individuals (9.3%) completed all 7 days. Among those who consented, 40 017 (81.7%) filled out some portion of the questionnaires, and 4990 (10.2%) completed the 6-minute walk test, made available only at the end of 7 days. The Heart Age Questionnaire, also available after 7 days, required entering lipid values and age 40 to 79 years (among 17 245 individuals, 43.1% of participants). Consequently, 1334 (2.7%) of those who consented completed all fields needed to compute heart age and a 10-year risk score. Physical activity was detected for a mean (SD) of 14.5% (8.0%) of individuals' total recorded time. Physical activity patterns were identified by cluster analysis. A pattern of lower overall activity but more frequent transitions between active and inactive states was associated with equivalent self-reported cardiovascular disease as a pattern of higher overall activity with fewer transitions. Individuals' perception of their activity and risk bore little relation to sensor-estimated activity or calculated cardiovascular risk.A smartphone-based study of cardiovascular health is feasible, and improvements in participant diversity and engagement will maximize yield from consented participants. Large-scale, real-world assessment of physical activity, fitness, and sleep using mobile devices may be a useful addition to future population health studies.

    View details for DOI 10.1001/jamacardio.2016.4395

    View details for PubMedID 27973671

  • Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in medicine : official journal of the American College of Medical Genetics Merker, J. D., Wenger, A. M., Sneddon, T. n., Grove, M. n., Zappala, Z. n., Fresard, L. n., Waggott, D. n., Utiramerur, S. n., Hou, Y. n., Smith, K. S., Montgomery, S. B., Wheeler, M. n., Buchan, J. G., Lambert, C. C., Eng, K. S., Hickey, L. n., Korlach, J. n., Ford, J. n., Ashley, E. A. 2017

    Abstract

    PurposeCurrent clinical genomics assays primarily utilize short-read sequencing (SRS), but SRS has limited ability to evaluate repetitive regions and structural variants. Long-read sequencing (LRS) has complementary strengths, and we aimed to determine whether LRS could offer a means to identify overlooked genetic variation in patients undiagnosed by SRS.MethodsWe performed low-coverage genome LRS to identify structural variants in a patient who presented with multiple neoplasia and cardiac myxomata, in whom the results of targeted clinical testing and genome SRS were negative.ResultsThis LRS approach yielded 6,971 deletions and 6,821 insertions > 50 bp. Filtering for variants that are absent in an unrelated control and overlap a disease gene coding exon identified three deletions and three insertions. One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon of PRKAR1A, which is implicated in autosomal dominant Carney complex. RNA sequencing demonstrated decreased PRKAR1A expression. The deletion was classified as pathogenic based on guidelines for interpretation of sequence variants.ConclusionThis first successful application of genome LRS to identify a pathogenic variant in a patient suggests that LRS has significant potential for the identification of disease-causing structural variation. Larger studies will ultimately be required to evaluate the potential clinical utility of LRS.GENETICS in MEDICINE advance online publication, 22 June 2017; doi:10.1038/gim.2017.86.

    View details for PubMedID 28640241

  • Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. PLoS computational biology Van Valen, D. A., Kudo, T., Lane, K. M., Macklin, D. N., Quach, N. T., DeFelice, M. M., Maayan, I., Tanouchi, Y., Ashley, E. A., Covert, M. W. 2016; 12 (11)

    Abstract

    Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life. We demonstrate that this approach can robustly segment fluorescent images of cell nuclei as well as phase images of the cytoplasms of individual bacterial and mammalian cells from phase contrast images without the need for a fluorescent cytoplasmic marker. These networks also enable the simultaneous segmentation and identification of different mammalian cell types grown in co-culture. A quantitative comparison with prior methods demonstrates that convolutional neural networks have improved accuracy and lead to a significant reduction in curation time. We relay our experience in designing and optimizing deep convolutional neural networks for this task and outline several design rules that we found led to robust performance. We conclude that deep convolutional neural networks are an accurate method that require less curation time, are generalizable to a multiplicity of cell types, from bacteria to mammalian cells, and expand live-cell imaging capabilities to include multi-cell type systems.

    View details for DOI 10.1371/journal.pcbi.1005177

    View details for PubMedID 27814364

    View details for PubMedCentralID PMC5096676

  • Early somatic mosaicism is a rare cause of long-QT syndrome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Priest, J. R., Gawad, C., Kahlig, K. M., Yu, J. K., O'Hara, T., Boyle, P. M., Rajamani, S., Clark, M. J., Garcia, S. T., Ceresnak, S., Harris, J., Boyle, S., Dewey, F. E., Malloy-Walton, L., Dunn, K., Grove, M., Perez, M. V., Neff, N. F., Chen, R., Maeda, K., Dubin, A., Belardinelli, L., West, J., Antolik, C., Macaya, D., Quertermous, T., Trayanova, N. A., Quake, S. R., Ashley, E. A. 2016; 113 (41): 11555-11560

    Abstract

    Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel NaV1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband. Genotyping of single circulating leukocytes demonstrated the mutation in the genomes of 8% of patient cells, and RNA sequencing of cardiac tissue from the infant confirmed the expression of the mutant allele at mosaic ratios. Heterologous expression of the mutant channel revealed significantly delayed sodium current with a dominant negative effect. To investigate the mechanism by which mosaicism might cause arrhythmia, we built a finite element simulation model incorporating Purkinje fiber activation. This model confirmed the pathogenic consequences of cardiac cellular mosaicism and, under the presenting conditions of this case, recapitulated 2:1 AV block and arrhythmia. To investigate the extent to which mosaicism might explain undiagnosed arrhythmia, we studied 7,500 affected probands undergoing commercial gene-panel testing. Four individuals with pathogenic variants arising from early somatic mutation events were found. Here we establish cardiac mosaicism as a causal mechanism for LQTS and present methods by which the general phenomenon, likely to be relevant for all genetic diseases, can be detected through single-cell analysis and next-generation sequencing.

    View details for DOI 10.1073/pnas.1607187113

    View details for PubMedID 27681629

  • In Vivo Post-Cardiac Arrest Myocardial Dysfunction Is Supported by Ca2+/Calmodulin-Dependent Protein Kinase II-Mediated Calcium Long-Term Potentiation and Mitigated by Alda-1, an Agonist of Aldehyde Dehydrogenase Type 2. Circulation Woods, C. E., Shang, C., Taghavi, F., Downey, P., Zalewski, A., Rubio, G. R., Liu, J., Homburger, J. R., Grunwald, Z., Qi, W., Bollensdorff, C., Thanaporn, P., Ali, A., Riemer, R. K., Kohl, P., Mochly-Rosen, D., Gerstenfeld, E., Large, S., Ali, Z. A., Ashley, E. A. 2016; 134 (13): 961-977

    Abstract

    Survival after sudden cardiac arrest is limited by postarrest myocardial dysfunction, but understanding of this phenomenon is constrained by a lack of data from a physiological model of disease. In this study, we established an in vivo model of cardiac arrest and resuscitation, characterized the biology of the associated myocardial dysfunction, and tested novel therapeutic strategies.We developed rodent models of in vivo postarrest myocardial dysfunction using extracorporeal membrane oxygenation resuscitation followed by invasive hemodynamics measurement. In postarrest isolated cardiomyocytes, we assessed mechanical load and Ca(2) (+)-induced Ca(2+) release (CICR) simultaneously using the microcarbon fiber technique and observed reduced function and myofilament calcium sensitivity. We used a novel fiberoptic catheter imaging system and a genetically encoded calcium sensor, GCaMP6f, to image CICR in vivo.We found potentiation of CICR in isolated cells from this extracorporeal membrane oxygenation model and in cells isolated from an ischemia/reperfusion Langendorff model perfused with oxygenated blood from an arrested animal but not when reperfused in saline. We established that CICR potentiation begins in vivo. The augmented CICR observed after arrest was mediated by the activation of Ca(2+)/calmodulin-dependent protein kinase II (CaMKII). Increased phosphorylation of CaMKII, phospholamban, and ryanodine receptor 2 was detected in the postarrest period. Exogenous adrenergic activation in vivo recapitulated Ca(2+) potentiation but was associated with lesser CaMKII activation. Because oxidative stress and aldehydic adduct formation were high after arrest, we tested a small-molecule activator of aldehyde dehydrogenase type 2, Alda-1, which reduced oxidative stress, restored calcium and CaMKII homeostasis, and improved cardiac function and postarrest outcome in vivo.Cardiac arrest and reperfusion lead to CaMKII activation and calcium long-term potentiation, which support cardiomyocyte contractility in the face of impaired postarrest myofilament calcium sensitivity. Alda-1 mitigates these effects, normalizes calcium cycling, and improves outcome.

    View details for DOI 10.1161/CIRCULATIONAHA.116.021618

    View details for PubMedID 27582424

  • Towards precision medicine. Nature reviews. Genetics Ashley, E. A. 2016; 17 (9): 507-522

    Abstract

    There is great potential for genome sequencing to enhance patient care through improved diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential, genomics strategies that have been developed for genetic discovery - including DNA-sequencing technologies and analysis algorithms - need to be adapted to fit clinical needs. This will require the optimization of alignment algorithms, attention to quality-coverage metrics, tailored solutions for paralogous or low-complexity areas of the genome, and the adoption of consensus standards for variant calling and interpretation. Global sharing of this more accurate genotypic and phenotypic data will accelerate the determination of causality for novel genes or variants. Thus, a deeper understanding of disease will be realized that will allow its targeting with much greater therapeutic precision.

    View details for DOI 10.1038/nrg.2016.86

    View details for PubMedID 27528417

  • Multidimensional structure-function relationships in human beta-cardiac myosin from population-scale genetic variation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Homburger, J. R., Green, E. M., Caleshu, C., Sunitha, M. S., Taylor, R. E., Ruppel, K. M., Metpally, R. P., Colan, S. D., Michels, M., Day, S. M., Olivotto, I., Bustamante, C. D., Dewey, F. E., Ho, C. Y., Spudich, J. A., Ashley, E. A. 2016; 113 (24): 6701-6706

    Abstract

    Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin. We first developed computational models of the human β-cardiac myosin protein before and after the myosin power stroke. Then, using a spatial scan statistic modified to analyze genetic variation in protein 3D space, we found significant enrichment of disease-associated variants in the converter, a kinetic domain that transduces force from the catalytic domain to the lever arm to accomplish the power stroke. Focusing our analysis on surface-exposed residues, we identified a larger region significantly enriched for disease-associated variants that contains both the converter domain and residues on a single flat surface on the myosin head described as the myosin mesa. Notably, patients with HCM with variants in the enriched regions have earlier disease onset than patients who have HCM with variants elsewhere. Our study provides a model for integrating protein structure, large-scale genetic sequencing, and detailed phenotypic data to reveal insight into time-shifted protein structures and genetic disease.

    View details for DOI 10.1073/pnas.1606950113

    View details for Web of Science ID 000377948800046

    View details for PubMedID 27247418

    View details for PubMedCentralID PMC4914177

  • Systems Genomics Identifies a Key Role for Hypocretin/Orexin Receptor-2 in Human Heart Failure JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Perez, M. V., Pavlovic, A., Shang, C., Wheeler, M. T., Miller, C. L., Liu, J., Dewey, F. E., Pan, S., Thanaporn, P. K., Absher, D., Brandimarto, J., Salisbury, H., Chan, K., Mukherjee, R., Konadhode, R. P., Myers, R. M., Sedehi, D., Scammell, T. E., Quertermous, T., Cappola, T., Ashley, E. A. 2015; 66 (22): 2522-2533

    Abstract

    The genetic determinants of heart failure (HF) and response to medical therapy remain unknown. We hypothesized that identifying genetic variants of HF that associate with response to medical therapy would elucidate the genetic basis of cardiac function.This study sought to identify genetic variations associated with response to HF therapy.This study compared extremes of response to medical therapy in 866 HF patients using a genome-wide approach that informed the systems-based design of a customized single nucleotide variant array. The effect of genotype on gene expression was measured using allele-specific luciferase reporter assays. Candidate gene transcription-deficient mice underwent echocardiography and treadmill exercise. The ability of the target gene agonist to rescue mice from chemically-induced HF was assessed with echocardiography.Of 866 HF patients, 136 had an ejection fraction improvement of 20% attributed to resynchronization (n = 83), revascularization (n = 7), tachycardia resolution (n = 2), alcohol cessation (n = 1), or medications (n = 43). Those with the minor allele for rs7767652, upstream of hypocretin (orexin) receptor-2 (HCRTR2), were less likely to have improved left ventricular function (odds ratio: 0.40 per minor allele; p = 3.29 × 10(-5)). In a replication cohort of 798 patients, those with a minor allele for rs7767652 had a lower prevalence of ejection fraction >35% (odds ratio: 0.769 per minor allele; p = 0.021). In an HF model, HCRTR2-deficient mice exhibited poorer cardiac function, worse treadmill exercise capacity, and greater myocardial scarring. Orexin, an HCRTR2 agonist, rescued function in this HF mouse model.A systems approach identified a novel genetic contribution to human HF and a promising therapeutic agent efficacious in an HF model.

    View details for DOI 10.1016/j.jacc.2015.09.061

    View details for Web of Science ID 000366094500009

    View details for PubMedID 26653627

  • The Undiagnosed Diseases Network of the National Institutes of Health A National Extension JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Gahl, W. A., Wise, A. L., Ashley, E. A. 2015; 314 (17): 1797-1798

    View details for DOI 10.1001/jama.2015.12249

    View details for Web of Science ID 000363960200008

    View details for PubMedID 26375289

  • ClinGen - The Clinical Genome Resource NEW ENGLAND JOURNAL OF MEDICINE Rehm, H. L., Berg, J. S., Brooks, L. D., Bustamante, C. D., Evans, J. P., Landrum, M. J., Ledbetter, D. H., Maglott, D. R., Martin, C. L., Nussbaum, R. L., Plon, S. E., Ramos, E. M., Sherry, S. T., Watson, M. S. 2015; 372 (23): 2235-2242

    View details for DOI 10.1056/NEJMsr1406261

    View details for PubMedID 26014595

  • The precision medicine initiative: a new national effort. JAMA Ashley, E. A. 2015; 313 (21): 2119–20

    View details for PubMedID 25928209

  • Clinical Phenotype and Outcome of Hypertrophic Cardiomyopathy Associated With Thin-Filament Gene Mutations JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Coppini, R., Ho, C. Y., Ashley, E., Day, S., Ferrantini, C., Girolami, F., Tomberli, B., Bardi, S., Torricelli, F., Cecchi, F., Mugelli, A., Poggesi, C., Tardiff, J., Olivotto, I. 2014; 64 (24): 2589-2600

    Abstract

    Mild hypertrophy but increased arrhythmic risk characterizes the stereotypic phenotype proposed for hypertrophic cardiomyopathy (HCM) caused by thin-filament mutations. However, whether such clinical profile is different from more prevalent thick-filament-associated disease is unresolved.This study aimed to assess clinical features and outcomes in a large cohort of patients with HCM associated with thin-filament mutations compared with thick-filament HCM.Adult HCM patients (age >18 years), 80 with thin-filament and 150 with thick-filament mutations, were followed for an average of 4.5 years.Compared with thick-filament HCM, patients with thin-filament mutations showed: 1) milder and atypically distributed left ventricular (LV) hypertrophy (maximal wall thickness 18 ± 5 mm vs. 24 ± 6 mm; p < 0.001) and less prevalent outflow tract obstruction (19% vs. 34%; p = 0.015); 2) higher rate of progression to New York Heart Association functional class III or IV (15% vs. 5%; p = 0.013); 3) higher prevalence of systolic dysfunction or restrictive LV filling at last evaluation (20% vs. 9%; p = 0.038); 4) 2.4-fold increase in prevalence of triphasic LV filling pattern (26% vs. 11%; p = 0.002); and 5) similar rates of malignant ventricular arrhythmias and sudden cardiac death (p = 0.593).In adult HCM patients, thin-filament mutations are associated with increased likelihood of advanced LV dysfunction and heart failure compared with thick-filament disease, whereas arrhythmic risk in both subsets is comparable. Triphasic LV filling is particularly common in thin-filament HCM, reflecting profound diastolic dysfunction.

    View details for DOI 10.1016/j.jacc.2014.09.059

    View details for Web of Science ID 000346349300006

    View details for PubMedID 25524337

    View details for PubMedCentralID PMC4270453

  • Oxido-reductive regulation of vascular remodeling by receptor tyrosine kinase ROS1 JOURNAL OF CLINICAL INVESTIGATION Ali, Z. A., Perez, V. D., Yuan, K., Orcholski, M., Pan, S., Qi, W., Chopra, G., Adams, C., Kojima, Y., Leeper, N. J., Qu, X., Zaleta-Rivera, K., Kato, K., Yamada, Y., Oguri, M., Kuchinsky, A., Hazen, S. L., Jukema, J. W., Ganesh, S. K., Nabe, E. G., Channon, K., Leon, M. B., Charest, A., Quertermous, T., Ashley, E. A. 2014; 124 (12): 5159-5174

    Abstract

    Angioplasty and stenting is the primary treatment for flow-limiting atherosclerosis; however, this strategy is limited by pathological vascular remodeling. Using a systems approach, we identified a role for the network hub gene glutathione peroxidase-1 (GPX1) in pathological remodeling following human blood vessel stenting. Constitutive deletion of Gpx1 in atherosclerotic mice recapitulated this phenotype of increased vascular smooth muscle cell (VSMC) proliferation and plaque formation. In an independent patient cohort, gene variant pair analysis identified an interaction of GPX1 with the orphan protooncogene receptor tyrosine kinase ROS1. A meta-analysis of the only genome-wide association studies of human neointima-induced in-stent stenosis confirmed the association of the ROS1 variant with pathological remodeling. Decreased GPX1 expression in atherosclerotic mice led to reductive stress via a time-dependent increase in glutathione, corresponding to phosphorylation of the ROS1 kinase activation site Y2274. Loss of GPX1 function was associated with both oxidative and reductive stress, the latter driving ROS1 activity via s-glutathiolation of critical residues of the ROS1 tyrosine phosphatase SHP-2. ROS1 inhibition with crizotinib and deglutathiolation of SHP-2 abolished GPX1-mediated increases in VSMC proliferation while leaving endothelialization intact. Our results indicate that GPX1-dependent alterations in oxido-reductive stress promote ROS1 activation and mediate vascular remodeling.

    View details for DOI 10.1172/JCI77484

    View details for Web of Science ID 000345677200011

    View details for PubMedID 25401476

  • A long noncoding RNA protects the heart from pathological hypertrophy. Nature Han, P., Li, W., Lin, C., Yang, J., Shang, C., Nurnberg, S. T., Jin, K. K., Xu, W., Lin, C., Lin, C., Xiong, Y., Chien, H., Zhou, B., Ashley, E., Bernstein, D., Chen, P., Chen, H. V., Quertermous, T., Chang, C. 2014; 514 (7520): 102-106

    Abstract

    The role of long noncoding RNA (lncRNA) in adult hearts is unknown; also unclear is how lncRNA modulates nucleosome remodelling. An estimated 70% of mouse genes undergo antisense transcription, including myosin heavy chain 7 (Myh7), which encodes molecular motor proteins for heart contraction. Here we identify a cluster of lncRNA transcripts from Myh7 loci and demonstrate a new lncRNA-chromatin mechanism for heart failure. In mice, these transcripts, which we named myosin heavy-chain-associated RNA transcripts (Myheart, or Mhrt), are cardiac-specific and abundant in adult hearts. Pathological stress activates the Brg1-Hdac-Parp chromatin repressor complex to inhibit Mhrt transcription in the heart. Such stress-induced Mhrt repression is essential for cardiomyopathy to develop: restoring Mhrt to the pre-stress level protects the heart from hypertrophy and failure. Mhrt antagonizes the function of Brg1, a chromatin-remodelling factor that is activated by stress to trigger aberrant gene expression and cardiac myopathy. Mhrt prevents Brg1 from recognizing its genomic DNA targets, thus inhibiting chromatin targeting and gene regulation by Brg1. It does so by binding to the helicase domain of Brg1, a domain that is crucial for tethering Brg1 to chromatinized DNA targets. Brg1 helicase has dual nucleic-acid-binding specificities: it is capable of binding lncRNA (Mhrt) and chromatinized--but not naked--DNA. This dual-binding feature of helicase enables a competitive inhibition mechanism by which Mhrt sequesters Brg1 from its genomic DNA targets to prevent chromatin remodelling. A Mhrt-Brg1 feedback circuit is thus crucial for heart function. Human MHRT also originates from MYH7 loci and is repressed in various types of myopathic hearts, suggesting a conserved lncRNA mechanism in human cardiomyopathy. Our studies identify a cardioprotective lncRNA, define a new targeting mechanism for ATP-dependent chromatin-remodelling factors, and establish a new paradigm for lncRNA-chromatin interaction.

    View details for DOI 10.1038/nature13596

    View details for PubMedID 25119045

  • Molecular diagnosis of long QT syndrome at 10 days of life by rapid whole genome sequencing. Heart rhythm Priest, J. R., Ceresnak, S. R., Dewey, F. E., Malloy-Walton, L. E., Dunn, K., Grove, M. E., Perez, M. V., Maeda, K., Dubin, A. M., Ashley, E. A. 2014; 11 (10): 1707-1713

    Abstract

    The advent of clinical next generation sequencing is rapidly changing the landscape of rare disease medicine. Molecular diagnosis of long QT syndrome (LQTS) can impact clinical management, including risk stratification and selection of pharmacotherapy based on the type of ion channel affected, but results from current gene panel testing requires 4 to 16 weeks before return to clinicians.A term female infant presented with 2:1 atrioventricular block and ventricular arrhythmias consistent with perinatal LQTS, requiring aggressive treatment including epicardial pacemaker, and cardioverter-defibrillator implantation and sympathectomy on day of life two. We sought to provide a rapid molecular diagnosis for optimization of treatment strategies.We performed CLIA-certified rapid whole genome sequencing (WGS) with a speed-optimized bioinformatics platform to achieve molecular diagnosis at 10 days of life.We detected a known pathogenic variant in KCNH2 that was demonstrated to be paternally inherited by followup genotyping. The unbiased assessment of the entire catalog of human genes provided by whole genome sequencing revealed a maternally inherited variant of unknown significance in a novel gene.Rapid clinical WGS provides faster and more comprehensive diagnostic information by 10 days of life than standard gene-panel testing. In selected clinical scenarios such as perinatal LQTS, rapid WGS may be able to provide more timely and clinically actionable information than a standard commercial test.

    View details for DOI 10.1016/j.hrthm.2014.06.030

    View details for PubMedID 24973560

  • Guidelines for investigating causality of sequence variants in human disease NATURE MacArthur, D. G., Manolio, T. A., Dimmock, D. P., Rehm, H. L., Shendure, J., Abecasis, G. R., Adams, D. R., Altman, R. B., Antonarakis, S. E., Ashley, E. A., Barrett, J. C., Biesecker, L. G., Conrad, D. F., Cooper, G. M., Cox, N. J., Daly, M. J., Gerstein, M. B., Goldstein, D. B., Hirschhorn, J. N., Leal, S. M., Pennacchio, L. A., Stamatoyannopoulos, J. A., Sunyaev, S. R., Valle, D., Voight, B. F., Winckler, W., Gunter, C. 2014; 508 (7497): 469-476

    Abstract

    The discovery of rare genetic variants is accelerating, and clear guidelines for distinguishing disease-causing sequence variants from the many potentially functional variants present in any human genome are urgently needed. Without rigorous standards we risk an acceleration of false-positive reports of causality, which would impede the translation of genomic research findings into the clinical diagnostic setting and hinder biological understanding of disease. Here we discuss the key challenges of assessing sequence variants in human disease, integrating both gene-level and variant-level support for causality. We propose guidelines for summarizing confidence in variant pathogenicity and highlight several areas that require further resource development.

    View details for DOI 10.1038/nature13127

    View details for Web of Science ID 000334741600026

    View details for PubMedID 24759409

  • Clinical interpretation and implications of whole-genome sequencing. JAMA Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

    Abstract

    Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

    View details for DOI 10.1001/jama.2014.1717

    View details for PubMedID 24618965

  • Clinical interpretation and implications of whole-genome sequencing. JAMA : the journal of the American Medical Association Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

    Abstract

    Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

    View details for DOI 10.1001/jama.2014.1717

    View details for PubMedID 24618965

    View details for PubMedCentralID PMC4119063

  • APJ acts as a dual receptor in cardiac hypertrophy NATURE Scimia, M. C., Hurtado, C., Ray, S., Metzler, S., Wei, K., Wang, J., Woods, C. E., Purcell, N. H., Catalucci, D., Akasaka, T., Bueno, O. F., Vlasuk, G. P., Kaliman, P., Bodmer, R., Smith, L. H., Ashley, E., Mercola, M., Brown, J. H., Ruiz-Lozano, P. 2012; 488 (7411): 394-398

    Abstract

    Cardiac hypertrophy is initiated as an adaptive response to sustained overload but progresses pathologically as heart failure ensues. Here we report that genetic loss of APJ, a G-protein-coupled receptor, confers resistance to chronic pressure overload by markedly reducing myocardial hypertrophy and heart failure. In contrast, mice lacking apelin (the endogenous APJ ligand) remain sensitive, suggesting an apelin-independent function of APJ. Freshly isolated APJ-null cardiomyocytes exhibit an attenuated response to stretch, indicating that APJ is a mechanosensor. Activation of APJ by stretch increases cardiomyocyte cell size and induces molecular markers of hypertrophy. Whereas apelin stimulates APJ to activate Gαi and elicits a protective response, stretch signals in an APJ-dependent, G-protein-independent fashion to induce hypertrophy. Stretch-mediated hypertrophy is prevented by knockdown of β-arrestins or by pharmacological doses of apelin acting through Gαi. Taken together, our data indicate that APJ is a bifunctional receptor for both mechanical stretch and the endogenous peptide apelin. By sensing the balance between these stimuli, APJ occupies a pivotal point linking sustained overload to cardiomyocyte hypertrophy.

    View details for DOI 10.1038/nature11263

    View details for Web of Science ID 000307501000045

    View details for PubMedID 22810587

    View details for PubMedCentralID PMC3422434

  • Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes CELL Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L., Lam, H. Y., Chen, R., Miriami, E., Karczewski, K. J., Hariharan, M., Dewey, F. E., Cheng, Y., Clark, M. J., Im, H., Habegger, L., Balasubramanian, S., O'Huallachain, M., Dudley, J. T., Hillenmeyer, S., Haraksingh, R., Sharon, D., Euskirchen, G., Lacroute, P., Bettinger, K., Boyle, A. P., Kasowski, M., Grubert, F., Seki, S., Garcia, M., Whirl-Carrillo, M., Gallardo, M., Blasco, M. A., Greenberg, P. L., Snyder, P., Klein, T. E., Altman, R. B., Butte, A. J., Ashley, E. A., Gerstein, M., Nadeau, K. C., Tang, H., Snyder, M. 2012; 148 (6): 1293-1307

    Abstract

    Personalized medicine is expected to benefit from combining genomic information with regular monitoring of physiological states by multiple high-throughput methods. Here, we present an integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism. This study demonstrates that longitudinal iPOP can be used to interpret healthy and diseased states by connecting genomic information with additional dynamic omics activity.

    View details for DOI 10.1016/j.cell.2012.02.009

    View details for PubMedID 22424236

  • Performance comparison of whole-genome sequencing platforms NATURE BIOTECHNOLOGY Lam, H. Y., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O'Huallachain, M., Dewey, F. E., Habegger, L., Ashley, E. A., Gerstein, M. B., Butte, A. J., Ji, H. P., Snyder, M. 2012; 30 (1): 78-U118

    Abstract

    Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies to a high average coverage of ∼76×, and compared their performance with respect to sequence coverage and calling of single-nucleotide variants (SNVs), insertions and deletions (indels). Although 88.1% of the ∼3.7 million unique SNVs were concordant between platforms, there were tens of thousands of platform-specific calls located in genes and other genomic regions. In contrast, 26.5% of indels were concordant between platforms. Target enrichment validated 92.7% of the concordant SNVs, whereas validation by genotyping array revealed a sensitivity of 99.3%. The validation experiments also suggested that >60% of the platform-specific variants were indeed present in the genome. Our results have important implications for understanding the accuracy and completeness of the genome sequencing platforms.

    View details for DOI 10.1038/nbt.2065

    View details for Web of Science ID 000299110600023

  • Chromatin regulation by Brg1 underlies heart muscle development and disease NATURE Hang, C. T., Yang, J., Han, P., Cheng, H., Shang, C., Ashley, E., Zhou, B., Chang, C. 2010; 466 (7302): 62-U74

    Abstract

    Cardiac hypertrophy and failure are characterized by transcriptional reprogramming of gene expression. Adult cardiomyocytes in mice primarily express alpha-myosin heavy chain (alpha-MHC, also known as Myh6), whereas embryonic cardiomyocytes express beta-MHC (also known as Myh7). Cardiac stress triggers adult hearts to undergo hypertrophy and a shift from alpha-MHC to fetal beta-MHC expression. Here we show that Brg1, a chromatin-remodelling protein, has a critical role in regulating cardiac growth, differentiation and gene expression. In embryos, Brg1 promotes myocyte proliferation by maintaining Bmp10 and suppressing p57(kip2) expression. It preserves fetal cardiac differentiation by interacting with histone deacetylase (HDAC) and poly (ADP ribose) polymerase (PARP) to repress alpha-MHC and activate beta-MHC. In adults, Brg1 (also known as Smarca4) is turned off in cardiomyocytes. It is reactivated by cardiac stresses and forms a complex with its embryonic partners, HDAC and PARP, to induce a pathological alpha-MHC to beta-MHC shift. Preventing Brg1 re-expression decreases hypertrophy and reverses this MHC switch. BRG1 is activated in certain patients with hypertrophic cardiomyopathy, its level correlating with disease severity and MHC changes. Our studies show that Brg1 maintains cardiomyocytes in an embryonic state, and demonstrate an epigenetic mechanism by which three classes of chromatin-modifying factors-Brg1, HDAC and PARP-cooperate to control developmental and pathological gene expression.

    View details for DOI 10.1038/nature09130

    View details for Web of Science ID 000279343800035

    View details for PubMedID 20596014

    View details for PubMedCentralID PMC2898892

  • Clinical assessment incorporating a personal genome LANCET Ashley, E. A., Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., Dudley, J. T., Ormond, K. E., Pavlovic, A., Morgan, A. A., Pushkarev, D., Neff, N. F., Hudgins, L., Gong, L., Hodges, L. M., Berlin, D. S., Thorn, C. F., Sangkuhl, K., Hebert, J. M., Woon, M., Sagreiya, H., Whaley, R., Knowles, J. W., Chou, M. F., Thakuria, J. V., Rosenbaum, A. M., Zaranek, A. W., Church, G. M., Greely, H. T., Quake, S. R., Altman, R. B. 2010; 375 (9725): 1525-1535

    Abstract

    The cost of genomic information has fallen steeply, but the clinical translation of genetic risk estimates remains unclear. We aimed to undertake an integrated analysis of a complete human genome in a clinical context.We assessed a patient with a family history of vascular disease and early sudden death. Clinical assessment included analysis of this patient's full genome sequence, risk prediction for coronary artery disease, screening for causes of sudden cardiac death, and genetic counselling. Genetic analysis included the development of novel methods for the integration of whole genome and clinical risk. Disease and risk analysis focused on prediction of genetic risk of variants associated with mendelian disease, recognised drug responses, and pathogenicity for novel variants. We queried disease-specific mutation databases and pharmacogenomics databases to identify genes and mutations with known associations with disease and drug response. We estimated post-test probabilities of disease by applying likelihood ratios derived from integration of multiple common variants to age-appropriate and sex-appropriate pre-test probabilities. We also accounted for gene-environment interactions and conditionally dependent risks.Analysis of 2.6 million single nucleotide polymorphisms and 752 copy number variations showed increased genetic risk for myocardial infarction, type 2 diabetes, and some cancers. We discovered rare variants in three genes that are clinically associated with sudden cardiac death-TMEM43, DSP, and MYBPC3. A variant in LPA was consistent with a family history of coronary artery disease. The patient had a heterozygous null mutation in CYP2C19 suggesting probable clopidogrel resistance, several variants associated with a positive response to lipid-lowering therapy, and variants in CYP4F2 and VKORC1 that suggest he might have a low initial dosing requirement for warfarin. Many variants of uncertain importance were reported.Although challenges remain, our results suggest that whole-genome sequencing can yield useful and clinically relevant information for individual patients.National Institute of General Medical Sciences; National Heart, Lung And Blood Institute; National Human Genome Research Institute; Howard Hughes Medical Institute; National Library of Medicine, Lucile Packard Foundation for Children's Health; Hewlett Packard Foundation; Breetwor Family Foundation.

    View details for Web of Science ID 000277655100025

    View details for PubMedID 20435227

  • Large-scale mutational analysis identifies UNC93B1 variants that drive TLR-mediated autoimmunity in mice and humans. The Journal of experimental medicine Rael, V. E., Yano, J. A., Huizar, J. P., Slayden, L. C., Weiss, M. A., Turcotte, E. A., Terry, J. M., Zuo, W., Thiffault, I., Pastinen, T., Farrow, E. G., Jenkins, J. L., Becker, M. L., Wong, S. C., Stevens, A. M., Otten, C., Allenspach, E. J., Bonner, D. E., Bernstein, J. A., Wheeler, M. T., Saxton, R. A., Undiagnosed Diseases Network, Liu, B., Majer, O., Barton, G. M., Acosta, M. T., Adams, D. R., Alvarez, R. L., Alvey, J., Allworth, A., Andrews, A., Ashley, E. A., Afzali, B., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Briere, L. C., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Cassini, T., Chanprasert, S., Chao, H., Chinn, I., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Delgado, M., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Fu, J., Gahl, W. A., Glass, I., Goddard, P. C., Godfrey, R. A., Gropman, A., Halley, M. C., Hamid, R., Hanchard, N., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Hutchison, S., Introne, W., Izumi, K., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Kaitryn, E., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, C., Lanpher, B. C., Lanza, I. R., LeBlanc, K., Lee, B. H., Lewis, R. A., Liu, P., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Maghiro, A., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McConkie-Rosell, A., McCray, A. T., McGee, E., Might, M., Mikati, M., Miller, D., Mirzaa, G., Morava, E., Moretti, P., Morimoto, M., Mulvihill, J. J., Nakano-Okuno, M., Nelson, S. F., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Papp, J. C., Parker, N. H., Petcharet, L., Phillips, J. A., Posey, J. E., Potocki, L., Pusey Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenthal, E., Rossignol, F., Ruzhnikov, M., Sabaii, M., Sampson, J. B., Schedl, T., Schoch, K., Scott, D. A., Seto, E., Sharma, P., Shashi, V., Shelkowitz, E., Sheppeard, S., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, K. S., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stergachis, A., Stoler, J. M., Sullivan, K., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tarakad, A., Taylor, H., Tekin, M., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Yamamoto, S., Zhang, Z., Zuchner, S. 2024; 221 (8)

    Abstract

    Nucleic acid-sensing Toll-like receptors (TLR) 3, 7/8, and 9 are key innate immune sensors whose activities must be tightly regulated to prevent systemic autoimmune or autoinflammatory disease or virus-associated immunopathology. Here, we report a systematic scanning-alanine mutagenesis screen of all cytosolic and luminal residues of the TLR chaperone protein UNC93B1, which identified both negative and positive regulatory regions affecting TLR3, TLR7, and TLR9 responses. We subsequently identified two families harboring heterozygous coding mutations in UNC93B1, UNC93B1+/T93I and UNC93B1+/R336C, both in key negative regulatory regions identified in our screen. These patients presented with cutaneous tumid lupus and juvenile idiopathic arthritis plus neuroinflammatory disease, respectively. Disruption of UNC93B1-mediated regulation by these mutations led to enhanced TLR7/8 responses, and both variants resulted in systemic autoimmune or inflammatory disease when introduced into mice via genome editing. Altogether, our results implicate the UNC93B1-TLR7/8 axis in human monogenic autoimmune diseases and provide a functional resource to assess the impact of yet-to-be-reported UNC93B1 mutations.

    View details for DOI 10.1084/jem.20232005

    View details for PubMedID 38780621

  • Prediction of diagnosis and diastolic filling pressure by AI-enhanced cardiac MRI: a modelling study of hospital data. The Lancet. Digital health Lehmann, D. H., Gomes, B., Vetter, N., Braun, O., Amr, A., Hilbel, T., Müller, J., Köthe, U., Reich, C., Kayvanpour, E., Sedaghat-Hamedani, F., Meder, M., Haas, J., Ashley, E., Rottbauer, W., Felbel, D., Bekeredjian, R., Mahrholdt, H., Keller, A., Ong, P., Seitz, A., Hund, H., Geis, N., André, F., Engelhardt, S., Katus, H. A., Frey, N., Heuveline, V., Meder, B. 2024; 6 (6): e407-e417

    Abstract

    With increasing numbers of patients and novel drugs for distinct causes of systolic and diastolic heart failure, automated assessment of cardiac function is important. We aimed to provide a non-invasive method to predict diagnosis of patients undergoing cardiac MRI (cMRI) and to obtain left ventricular end-diastolic pressure (LVEDP).For this modelling study, patients who had undergone cardiac catheterisation at University Hospital Heidelberg (Heidelberg, Germany) between July 15, 2004 and March 16, 2023, were identified, as were individual left ventricular pressure measurements. We used existing patient data from routine cardiac diagnostics. From this initial group, we extracted patients who had been diagnosed with ischaemic cardiomyopathy, dilated cardiomyopathy, hypertrophic cardiomyopathy, or amyloidosis, as well as control individuals with no structural phenotype. Data were pseudonymised and only processed within the university hospital's AI infrastructure. We used the data to build different models to predict either demographic (ie, AI-age and AI-sex), diagnostic (ie, AI-coronary artery disease and AI-cardiomyopathy [AI-CMP]), or functional parameters (ie, AI-LVEDP). We randomly divided our datasets via computer into training, validation, and test datasets. AI-CMP was not compared with other models, but was validated in a prospective setting. Benchmarking was also done.66 936 patients who had undergone cardiac catheterisation at University Hospital Heidelberg were identified, with more than 183 772 individual left ventricular pressure measurements. We extracted 4390 patients from this initial group, of whom 1131 (25·8%) had been diagnosed with ischaemic cardiomyopathy, 1064 (24·2%) had been diagnosed with dilated cardiomyopathy, 816 (18·6%) had been diagnosed with hypertrophic cardiomyopathy, 202 (4·6%) had been diagnosed with amyloidosis, and 1177 (26·7%) were control individuals with no structural phenotype. The core cohort only included patients with cardiac catherisation and cMRI within 30 days, and emergency cases were excluded. AI-sex was able to predict patient sex with areas under the receiver operating characteristic curves (AUCs) of 0·78 (95% CI 0·77-0·78) and AI-age was able to predict patient age with a mean absolute error of 7·86 years (7·77-7·95), with a Pearson correlation of 0·57 (95% CI 0·56-0·57). The AUCs for the classification tasks ranged between 0·82 (95% CI 0·79-0·84) for ischaemic cardiomyopathy and 0·92 (0·91-0·94) for hypertrophic cardiomyopathy.Our AI models could be easily integrated into clinical practice and provide added value to the information content of cMRI, allowing for disease classification and prediction of diastolic function.Informatics for Life initiative of the Klaus-Tschira Foundation, German Center for Cardiovascular Research, eCardiology section of the German Cardiac Society, and AI Health Innovation Cluster Heidelberg.

    View details for DOI 10.1016/S2589-7500(24)00063-3

    View details for PubMedID 38789141

  • Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Genetics in medicine : official journal of the American College of Medical Genetics Kohler, J. N., Legro, N. R., Baldridge, D., Shin, J., Bowman, A., Ugur, B., Jackstadt, M. M., Shriver, L. P., Patti, G. J., Zhang, B., Feng, W., McAdow, A. R., Goddard, P., Ungar, R. A., Jensen, T., Smith, K. S., Fresard, L., Alvarez, R., Bonner, D., Reuter, C. M., McCormack, C., Kravets, E., Marwaha, S., Holt, J. M., Worthey, E., Ashley, E. A., Montgomery, S. B., Fisher, P., Postlethwait, J., De Camilli, P., Solnica-Krezel, L., Bernstein, J. A., Wheeler, M. T. 2024: 101166

    Abstract

    The function of FAM177A1 and its relationship to human disease is largely unknown. Recent studies have demonstrated FAM177A1 to be a critical immune-associated gene. One previous case study has linked FAM177A1 to a neurodevelopmental disorder in four siblings.We identified five individuals from three unrelated families with biallelic variants in FAM177A1. The physiological function of FAM177A1 was studied in a zebrafish model organism and human cell lines with loss-of-function variants similar to the affected cohort.These individuals share a characteristic phenotype defined by macrocephaly, global developmental delay, intellectual disability, seizures, behavioral abnormalities, hypotonia, and gait disturbance. We show that FAM177A1 localizes to the Golgi complex in mammalian and zebrafish cells. Intersection of the RNA-seq and metabolomic datasets from FAM177A1-deficient human fibroblasts and whole zebrafish larvae demonstrated dysregulation of pathways associated with apoptosis, inflammation, and negative regulation of cell proliferation.Our data sheds light on the emerging function of FAM177A1 and defines FAM177A1-related neurodevelopmental disorder as a new clinical entity.

    View details for DOI 10.1016/j.gim.2024.101166

    View details for PubMedID 38767059

  • The impact of exercise on gene regulation in association with complex trait genetics. Nature communications Vetr, N. G., Gay, N. R., MoTrPAC Study Group, Montgomery, S. B., Adkins, J. N., Albertson, B. G., Amar, D., Amper, M. A., Armenteros, J. J., Ashley, E., Avila-Pacheco, J., Bae, D., Balci, A. T., Bamman, M., Bararpour, N., Barton, E. R., Jean Beltran, P. M., Bergman, B. C., Bessesen, D. H., Bodine, S. C., Booth, F. W., Bouverat, B., Buford, T. W., Burant, C. F., Caputo, T., Carr, S., Chambers, T. L., Chavez, C., Chikina, M., Chiu, R., Cicha, M., Clish, C. B., Coen, P. M., Cooper, D., Cornell, E., Cutter, G., Dalton, K. P., Dasari, S., Dennis, C., Esser, K., Evans, C. R., Farrar, R., Fernadez, F. M., Gadde, K., Gagne, N., Gaul, D. A., Ge, Y., Gerszten, R. E., Goodpaster, B. H., Goodyear, L. J., Gritsenko, M. A., Guevara, K., Haddad, F., Hansen, J. R., Harris, M., Hastie, T., Hennig, K. M., Hershman, S. G., Hevener, A., Hirshman, M. F., Hou, Z., Hsu, F., Huffman, K. M., Hung, C., Hutchinson-Bunch, C., Ivanova, A. A., Jackson, B. E., Jankowski, C. M., Jimenez-Morales, D., Jin, C. A., Johannsen, N. M., Newton, R. L., Kachman, M. T., Ke, B. G., Keshishian, H., Kohrt, W. M., Kramer, K. S., Kraus, W. E., Lanza, I., Leeuwenburgh, C., Lessard, S. J., Lester, B., Li, J. Z., Lindholm, M. E., Lira, A. K., Liu, X., Lu, C., Makarewicz, N. S., Maner-Smith, K. M., Mani, D. R., Many, G. M., Marjanovic, N., Marshall, A., Marwaha, S., May, S., Melanson, E. L., Miller, M. E., Monroe, M. E., Moore, S. G., Moore, R. J., Moreau, K. L., Mundorff, C. C., Musi, N., Nachun, D., Nair, V. D., Nair, K. S., Nestor, M. D., Nicklas, B., Nigro, P., Nudelman, G., Ortlund, E. A., Pahor, M., Pearce, C., Petyuk, V. A., Piehowski, P. D., Pincas, H., Powers, S., Presby, D. M., Qian, W., Radom-Aizik, S., Raja, A. N., Ramachandran, K., Ramaker, M. E., Ramos, I., Rankinen, T., Raskind, A. S., Rasmussen, B. B., Ravussin, E., Rector, R. S., Rejeski, W. J., Richards, C. Z., Rirak, S., Robbins, J. M., Rooney, J. L., Rubenstein, A. B., Ruf-Zamojski, F., Rushing, S., Sagendorf, T. J., Samdarshi, M., Sanford, J. A., Savage, E. M., Schauer, I. E., Schenk, S., Schwartz, R. S., Sealfon, S. C., Seenarine, N., Smith, K. S., Smith, G. R., Snyder, M. P., Soni, T., Oliveira De Sousa, L. G., Sparks, L. M., Steep, A., Stowe, C. L., Sun, Y., Teng, C., Thalacker-Mercer, A., Thyfault, J., Tibshirani, R., Tracy, R., Trappe, S., Trappe, T. A., Uppal, K., Vangeti, S., Vasoya, M., Volpi, E., Vornholt, A., Walkup, M. P., Walsh, M. J., Wheeler, M. T., Williams, J. P., Wu, S., Xia, A., Yan, Z., Yu, X., Zang, C., Zaslavsky, E., Zebarjadi, N., Zhang, T., Zhao, B., Zhen, J. 2024; 15 (1): 3346

    Abstract

    Endurance exercise training is known to reduce risk for a range of complex diseases. However, the molecular basis of this effect has been challenging to study and largely restricted to analyses of either few or easily biopsied tissues. Extensive transcriptome data collected across 15 tissues during exercise training in rats as part of the Molecular Transducers of Physical Activity Consortium has provided a unique opportunity to clarify how exercise can affect tissue-specific gene expression and further suggest how exercise adaptation may impact complex disease-associated genes. To build this map, we integrate this multi-tissue atlas of gene expression changes with gene-disease targets, genetic regulation of expression, and trait relationship data in humans. Consensus from multiple approaches prioritizes specific tissues and genes where endurance exercise impacts disease-relevant gene expression. Specifically, we identify a total of 5523 trait-tissue-gene triplets to serve as a valuable starting point for future investigations [Exercise; Transcription; Human Phenotypic Variation].

    View details for DOI 10.1038/s41467-024-45966-w

    View details for PubMedID 38693125

  • Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue. Nature metabolism Many, G. M., Sanford, J. A., Sagendorf, T. J., Hou, Z., Nigro, P., Whytock, K. L., Amar, D., Caputo, T., Gay, N. R., Gaul, D. A., Hirshman, M. F., Jimenez-Morales, D., Lindholm, M. E., Muehlbauer, M. J., Vamvini, M., Bergman, B. C., Fernandez, F. M., Goodyear, L. J., Hevener, A. L., Ortlund, E. A., Sparks, L. M., Xia, A., Adkins, J. N., Bodine, S. C., Newgard, C. B., Schenk, S., MoTrPAC Study Group, Armenteros, J. J., Amper, M. A., Ashley, E., Asokan, A. K., Avila-Pacheco, J., Bae, D., Bamman, M. M., Bararpour, N., Barnes, J., Buford, T. W., Burant, C. F., Carbone, N. P., Carr, S. A., Chambers, T. L., Chavez, C., Chiu, R., Clish, C. B., Cutter, G. R., Dasari, S., Dennis, C., Evans, C. R., Fernandez, F. M., Gagne, N., Ge, Y., Goodpaster, B. H., Gritsenko, M. A., Hansen, J. R., Hennig, K. M., Huffman, K. M., Hung, C., Hutchinson-Bunch, C., Ilkayeva, O., Ivanova, A. A., Beltran, P. M., Jin, C. A., Kachman, M. T., Keshishian, H., Kraus, W. E., Lanza, I., Lester, B., Li, J. Z., Lira, A. K., Liu, X., Maner-Smith, K. M., May, S., Monroe, M. R., Montgomery, S., Moore, R. J., Moore, S. G., Nachun, D., Nair, K. S., Nair, V., Raja, A. N., Nestor, M. D., Nudelman, G., Petyuk, V. A., Piehowski, P. D., Pincas, H., Qian, W., Raskind, A., Rasmussen, B. B., Rooney, J. L., Rushing, S., Samdarshi, M., Sealfon, S. C., Smith, K. S., Smith, G. R., Snyder, M., Stowe, C. L., Talton, J. W., Teng, C., Thalacker-Mercer, A., Tracy, R., Trappe, T. A., Vasoya, M., Vetr, N. G., Volpi, E., Walkup, M. P., Walsh, M. J., Wheeler, M. T., Wu, S., Zaslavsky, E., Zebarjadi, N., Zhang, T., Zhao, B., Zhen, J. 2024

    Abstract

    Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT.

    View details for DOI 10.1038/s42255-023-00959-9

    View details for PubMedID 38693320

  • Simple models vs. deep learning in detecting low ejection fraction from the electrocardiogram EUROPEAN HEART JOURNAL - DIGITAL HEALTH Hughes, J., Somani, S., Elias, P., Tooley, J., Rogers, A. J., Poterucha, T., Haggerty, C. M., Salerno, M., Ouyang, D., Ashley, E., Zou, J., Perez, M. 2024
  • The mitochondrial multi-omic response to exercise training across rat tissues. Cell metabolism Amar, D., Gay, N. R., Jimenez-Morales, D., Jean Beltran, P. M., Ramaker, M. E., Raja, A. N., Zhao, B., Sun, Y., Marwaha, S., Gaul, D. A., Hershman, S. G., Ferrasse, A., Xia, A., Lanza, I., Fernández, F. M., Montgomery, S. B., Hevener, A. L., Ashley, E. A., Walsh, M. J., Sparks, L. M., Burant, C. F., Rector, R. S., Thyfault, J., Wheeler, M. T., Goodpaster, B. H., Coen, P. M., Schenk, S., Bodine, S. C., Lindholm, M. E. 2024

    Abstract

    Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.

    View details for DOI 10.1016/j.cmet.2023.12.021

    View details for PubMedID 38701776

  • Advancing access to genome sequencing for rare genetic disorders: recent progress and call to action. NPJ genomic medicine Jobanputra, V., Schroeder, B., Rehm, H. L., Shen, W., Spiteri, E., Nakouzi, G., Taylor, S., Marshall, C. R., Meng, L., Kingsmore, S. F., Ellsworth, K., Ashley, E., Taft, R. J. 2024; 9 (1): 23

    View details for DOI 10.1038/s41525-024-00410-2

    View details for PubMedID 38538605

    View details for PubMedCentralID 8322922

  • Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. medRxiv : the preprint server for health sciences Jensen, T. D., Ni, B., Reuter, C. M., Gorzynski, J. E., Fazal, S., Bonner, D., Ungar, R. A., Goddard, P. C., Raja, A., Ashley, E. A., Bernstein, J. A., Zuchner, S., Greicius, M. D., Montgomery, S. B., Schatz, M. C., Wheeler, M. T., Battle, A. 2024

    Abstract

    Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.

    View details for DOI 10.1101/2024.03.22.24304565

    View details for PubMedID 38585781

    View details for PubMedCentralID PMC10996727

  • Regional Variation in Cardiovascular Genes Enables a Tractable Genome Editing Strategy. Circulation. Genomic and precision medicine Krysov, V. A., Wilson, R. H., Ten, N. S., Youlton, N., De Jong, H. N., Sutton, S., Huang, Y., Reuter, C. M., Grove, M. E., Wheeler, M. T., Ashley, E. A., Parikh, V. N. 2024: e004370

    Abstract

    To realize the potential of genome engineering therapeutics, tractable strategies must be identified that balance personalized therapy with the need for off-the-shelf availability. We hypothesized that regional clustering of pathogenic variants can inform the design of rational prime editing therapeutics to treat the majority of genetic cardiovascular diseases with a limited number of reagents.We collated 2435 high-confidence pathogenic/likely pathogenic (P/LP) variants in 82 cardiovascular disease genes from ClinVar. We assessed the regional density of these variants by defining a regional clustering index. We then combined a highly active base editor with prime editing to demonstrate the feasibility of a P/LP hotspot-directed genome engineering therapeutic strategy in vitro.P/LP variants in cardiovascular disease genes display higher regional density than rare variants found in the general population. P/LP missense variants displayed higher average regional density than P/LP truncating variants. Following hypermutagenesis at a pathogenic hotspot, mean prime editing efficiency across introduced variants was 57±27%.Designing therapeutics that target pathogenic hotspots will not only address known missense P/LP variants but also novel P/LP variants identified in these hotspots as well. Moreover, the clustering of P/LP missense rather than truncating variants in these hotspots suggests that prime editing technology is particularly valuable for dominant negative disease. Although prime editing technology in relation to cardiac health continues to improve, this study presents an approach to targeting the most impactful regions of the genome for inherited cardiovascular disease.

    View details for DOI 10.1161/CIRCGEN.123.004370

    View details for PubMedID 38506054

  • Deep learning to detect left ventricular structural abnormalities in chest X-rays. European heart journal Bhave, S., Rodriguez, V., Poterucha, T., Mutasa, S., Aberle, D., Capaccione, K. M., Chen, Y., Dsouza, B., Dumeer, S., Goldstein, J., Hodes, A., Leb, J., Lungren, M., Miller, M., Monoky, D., Navot, B., Wattamwar, K., Wattamwar, A., Clerkin, K., Ouyang, D., Ashley, E., Topkara, V. K., Maurer, M., Einstein, A. J., Uriel, N., Homma, S., Schwartz, A., Jaramillo, D., Perotte, A. J., Elias, P. 2024

    Abstract

    Early identification of cardiac structural abnormalities indicative of heart failure is crucial to improving patient outcomes. Chest X-rays (CXRs) are routinely conducted on a broad population of patients, presenting an opportunity to build scalable screening tools for structural abnormalities indicative of Stage B or worse heart failure with deep learning methods. In this study, a model was developed to identify severe left ventricular hypertrophy (SLVH) and dilated left ventricle (DLV) using CXRs.A total of 71 589 unique CXRs from 24 689 different patients completed within 1 year of echocardiograms were identified. Labels for SLVH, DLV, and a composite label indicating the presence of either were extracted from echocardiograms. A deep learning model was developed and evaluated using area under the receiver operating characteristic curve (AUROC). Performance was additionally validated on 8003 CXRs from an external site and compared against visual assessment by 15 board-certified radiologists.The model yielded an AUROC of 0.79 (0.76-0.81) for SLVH, 0.80 (0.77-0.84) for DLV, and 0.80 (0.78-0.83) for the composite label, with similar performance on an external data set. The model outperformed all 15 individual radiologists for predicting the composite label and achieved a sensitivity of 71% vs. 66% against the consensus vote across all radiologists at a fixed specificity of 73%.Deep learning analysis of CXRs can accurately detect the presence of certain structural abnormalities and may be useful in early identification of patients with LV hypertrophy and dilation. As a resource to promote further innovation, 71 589 CXRs with adjoining echocardiographic labels have been made publicly available.

    View details for DOI 10.1093/eurheartj/ehad782

    View details for PubMedID 38503537

  • Quantifying assumptions underlying peak oxygen consumption equations across the body mass spectrum. Clinical obesity Busque, V., Christle, J. W., Moneghetti, K. J., Cauwenberghs, N., Kouznetsova, T., Blumberg, Y., Wheeler, M. T., Ashley, E., Haddad, F., Myers, J. 2024: e12653

    Abstract

    The goal of this study is to quantify the assumptions associated with the Wasserman-Hansen (WH) and Fitness Registry and the Importance of Exercise: A National Database (FRIEND) predictive peak oxygen consumption (pVO2 ) equations across body mass index (BMI). Assumptions in pVO2 for both equations were first determined using a simulation and then evaluated using exercise data from the Stanford Exercise Testing registry. We calculated percent-predicted VO2 (ppVO2 ) values for both equations and compared them using the Bland-Altman method. Assumptions associated with pVO2 across BMI categories were quantified by comparing the slopes of age-adjusted VO2 ratios (pVO2 /pre-exercise VO2 ) and ppVO2 values for different BMI categories. The simulation revealed lower predicted fitness among adults with obesity using the FRIEND equation compared to the WH equations. In the clinical cohort, we evaluated 2471 patients (56.9% male, 22% with BMI >30 kg/m2 , pVO2 26.8 mlO2 /kg/min). The Bland-Altman plot revealed an average relative difference of -1.7% (95% CI: -2.1 to -1.2%) between WH and FRIEND ppVO2 values with greater differences among those with obesity. Analysis of the VO2 ratio to ppVO2 slopes across the BMI spectrum confirmed the assumption of lower fitness in those with obesity, and this trend was more pronounced using the FRIEND equation. Peak VO2 estimations between the WH and FRIEND equations differed significantly among individuals with obesity. The FRIEND equation resulted in a greater attributable reduction in pVO2 associated with obesity relative to the WH equations. The outlined relationships between BMI and predicted VO2 may better inform the clinical interpretation of ppVO2 values during cardiopulmonary exercise test evaluations.

    View details for DOI 10.1111/cob.12653

    View details for PubMedID 38475989

  • Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genetics in medicine : official journal of the American College of Medical Genetics Pucel, J., Briere, L. C., Reuter, C., Gochyyev, P., LeBlanc, K. 2024: 101115

    Abstract

    Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases.In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network (UDN), all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS.Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS prior to acceptance to the UDN (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively).We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.

    View details for DOI 10.1016/j.gim.2024.101115

    View details for PubMedID 38436216

  • Knowledge and attitudes on implementing cardiovascular pharmacogenomic testing. Clinical and translational science Russell, C., Campion, M., Grove, M. E., Matsuda, K., Klein, T. E., Ashley, E., Naik, H., Wheeler, M. T., Scott, S. A. 2024; 17 (3): e13737

    Abstract

    Pharmacogenomics has the potential to inform drug dosing and selection, reduce adverse events, and improve medication efficacy; however, provider knowledge of pharmacogenomic testing varies across provider types and specialties. Given that many actionable pharmacogenomic genes are implicated in cardiovascular medication response variability, this study aimed to evaluate cardiology providers' knowledge and attitudes on implementing clinical pharmacogenomic testing. Sixty-one providers responded to an online survey, including pharmacists (46%), physicians (31%), genetic counselors (15%), and nurses (8%). Most respondents (94%) reported previous genetics education; however, only 52% felt their genetics education prepared them to order a clinical pharmacogenomic test. In addition, most respondents (66%) were familiar with pharmacogenomics, with genetic counselors being most likely to be familiar (p < 0.001). Only 15% of respondents had previously ordered a clinical pharmacogenomic test and a total of 36% indicated they are likely to order a pharmacogenomic test in the future; however, the vast majority of respondents (89%) were interested in pharmacogenomic testing being incorporated into diagnostic cardiovascular genetic tests. Moreover, 84% of providers preferred pharmacogenomic panel testing compared to 16% who preferred single gene testing. Half of the providers reported being comfortable discussing pharmacogenomic results with their patients, but the majority (60%) expressed discomfort with the logistics of test ordering. Reported barriers to implementation included uncertainty about the clinical utility and difficulty choosing an appropriate test. Taken together, cardiology providers have moderate familiarity with pharmacogenomics and limited experience with test ordering; however, they are interested in incorporating pharmacogenomics into diagnostic genetic tests and ordering pharmacogenomic panels.

    View details for DOI 10.1111/cts.13737

    View details for PubMedID 38421234

  • Recurring homozygous ACTN2 variant (p.Arg506Gly) causes a recessive myopathy. Annals of clinical and translational neurology Donkervoort, S., Mohassel, P., O'Leary, M., Bonner, D. E., Hartley, T., Acquaye, N., Brull, A., Mozaffar, T., Saporta, M. A., Dyment, D. A., Sampson, J. B., Pajusalu, S., Austin-Tse, C., Hurth, K., Cohen, J. S., McWalter, K., Warman-Chardon, J., Crunk, A., Foley, A. R., Mammen, A. L., Wheeler, M. T., O'Donnell-Luria, A., Bönnemann, C. G. 2024

    Abstract

    ACTN2, encoding alpha-actinin-2, is essential for cardiac and skeletal muscle sarcomeric function. ACTN2 variants are a known cause of cardiomyopathy without skeletal muscle involvement. Recently, specific dominant monoallelic variants were reported as a rare cause of core myopathy of variable clinical onset, although the pathomechanism remains to be elucidated. The possibility of a recessively inherited ACTN2-myopathy has also been proposed in a single series.We provide clinical, imaging, and histological characterization of a series of patients with a novel biallelic ACTN2 variant.We report seven patients from five families with a recurring biallelic variant in ACTN2: c.1516A>G (p.Arg506Gly), all manifesting with a consistent phenotype of asymmetric, progressive, proximal, and distal lower extremity predominant muscle weakness. None of the patients have cardiomyopathy or respiratory insufficiency. Notably, all patients report Palestinian ethnicity, suggesting a possible founder ACTN2 variant, which was confirmed through haplotype analysis in two families. Muscle biopsies reveal an underlying myopathic process with disruption of the intermyofibrillar architecture, Type I fiber predominance and atrophy. MRI of the lower extremities demonstrate a distinct pattern of asymmetric muscle involvement with selective involvement of the hamstrings and adductors in the thigh, and anterior tibial group and soleus in the lower leg. Using an in vitro splicing assay, we show that c.1516A>G ACTN2 does not impair normal splicing.This series further establishes ACTN2 as a muscle disease gene, now also including variants with a recessive inheritance mode, and expands the clinical spectrum of actinopathies to adult-onset progressive muscle disease.

    View details for DOI 10.1002/acn3.51983

    View details for PubMedID 38311799

  • Improving Reporting of Exercise Capacity Across Age Ranges Using Novel Workload Reference Equations. The American journal of cardiology Santana, E. J., Christle, J. W., Cauwenberghs, N., Peterman, J. E., Busque, V., Gomes, B., Bagherzadeh, S. P., Moneghetti, K., Kuznetsova, T., Wheeler, M., Ashley, E., Harber, M. P., Arena, R., Kaminsky, L. A., Myers, J., Haddad, F. 2024

    Abstract

    Exercise capacity (EC) is an important predictor of survival in the general population as well as in individuals with cardiopulmonary disease. Despite its relevance, considering percent-predicted workload (%pWL) given by current equations may overestimate EC in older adults. Therefore, to improve the reporting of EC in clinical practice, our main objective was to develop workload reference equations (pWL) that better reflect the relation between workload and age. Using the Fitness Registry and the Importance of Exercise National Database (FRIEND), we analyzed a reference group of 6,966 apparently healthy participants and 1,060 participants with HF who underwent graded treadmill cardiopulmonary exercise testing. For the first group, the mean age was 44 years [18-79]; 56.5% of individuals were male and 15.4% had obesity. Peak VO2 was 11.6 ± 3.0 METs in males and 8.5±2.4 METs in females. After partition analysis, we first developed sex-specific pWL equations to allow comparisons to a healthy weight reference. For males, pWL (METs) = 14.1 - 0.9 × 10-3 × age2 and for female 11.5 - 0.87 × 10-3 × age2. We used those equations as denominators of %pWL and, based on their distribution, we determined thresholds for EC classification, with average EC defined by the range corresponding to 85-115%pWL. Compared to %pWL using current equations, the new equations yielded better-calibrated %pWL across different age ranges. We also derived body mass index-adjusted pWL equations that better assessed EC in individuals with HF. In conclusion, the novel pWL equations have the potential to impact the report of EC in practice.

    View details for DOI 10.1016/j.amjcard.2024.01.022

    View details for PubMedID 38301753

  • APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology. Neuron Chemparathy, A., Le Guen, Y., Chen, S., Lee, E. G., Leong, L., Gorzynski, J. E., Jensen, T. D., Ferrasse, A., Xu, G., Xiang, H., Belloy, M. E., Kasireddy, N., Peña-Tauber, A., Williams, K., Stewart, I., Talozzi, L., Wingo, T. S., Lah, J. J., Jayadev, S., Hales, C. M., Peskind, E., Child, D. D., Roeber, S., Keene, C. D., Cong, L., Ashley, E. A., Yu, C. E., Greicius, M. D. 2024

    Abstract

    The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years. Two APOE ε3/ε4 controls carried a stop-gain affecting ε4: one was cognitively normal at 90 years and had no neuritic plaques at autopsy; the other was cognitively healthy at 79 years, and lumbar puncture at 76 years showed normal levels of amyloid. These results suggest that ε4 drives AD risk through the gain of abnormal function and support ε4 knockdown as a viable therapeutic option.

    View details for DOI 10.1016/j.neuron.2024.01.008

    View details for PubMedID 38301647

  • Learning epistatic polygenic phenotypes with Boolean interactions. PloS one Behr, M., Kumbier, K., Cordova-Palomera, A., Aguirre, M., Ronen, O., Ye, C., Ashley, E., Butte, A. J., Arnaout, R., Brown, B., Priest, J., Yu, B. 2024; 19 (4): e0298906

    Abstract

    Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1, a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

    View details for DOI 10.1371/journal.pone.0298906

    View details for PubMedID 38625909

  • Unsupervised machine learning to investigate trajectory patterns of COVID-19 symptoms and physical activity measured via the MyHeart Counts App and smart devices. NPJ digital medicine Gupta, V., Kariotis, S., Rajab, M. D., Errington, N., Alhathli, E., Jammeh, E., Brook, M., Meardon, N., Collini, P., Cole, J., Wild, J. M., Hershman, S., Javed, A., Thompson, A. A., de Silva, T., Ashley, E. A., Wang, D., Lawrie, A. 2023; 6 (1): 239

    Abstract

    Previous studies have associated COVID-19 symptoms severity with levels of physical activity. We therefore investigated longitudinal trajectories of COVID-19 symptoms in a cohort of healthcare workers (HCWs) with non-hospitalised COVID-19 and their real-world physical activity. 121 HCWs with a history of COVID-19 infection who had symptoms monitored through at least two research clinic visits, and via smartphone were examined. HCWs with a compatible smartphone were provided with an Apple Watch Series 4 and were asked to install the MyHeart Counts Study App to collect COVID-19 symptom data and multiple physical activity parameters. Unsupervised classification analysis of symptoms identified two trajectory patterns of long and short symptom duration. The prevalence for longitudinal persistence of any COVID-19 symptom was 36% with fatigue and loss of smell being the two most prevalent individual symptom trajectories (24.8% and 21.5%, respectively). 8 physical activity features obtained via the MyHeart Counts App identified two groups of trajectories for high and low activity. Of these 8 parameters only 'distance moved walking or running' was associated with COVID-19 symptom trajectories. We report a high prevalence of long-term symptoms of COVID-19 in a non-hospitalised cohort of HCWs, a method to identify physical activity trends, and investigate their association. These data highlight the importance of tracking symptoms from onset to recovery even in non-hospitalised COVID-19 individuals. The increasing ease in collecting real-world physical activity data non-invasively from wearable devices provides opportunity to investigate the association of physical activity to symptoms of COVID-19 and other cardio-respiratory diseases.

    View details for DOI 10.1038/s41746-023-00974-w

    View details for PubMedID 38135699

    View details for PubMedCentralID PMC10746711

  • Race, Sex, and Age Disparities in the Performance of ECG Deep Learning Models Predicting Heart Failure. Circulation. Heart failure Kaur, D., Hughes, J. W., Rogers, A. J., Kang, G., Narayan, S. M., Ashley, E. A., Perez, M. V. 2023: e010879

    Abstract

    Deep learning models may combat widening racial disparities in heart failure outcomes through early identification of individuals at high risk. However, demographic biases in the performance of these models have not been well-studied.This retrospective analysis used 12-lead ECGs taken between 2008 and 2018 from 326 518 patient encounters referred for standard clinical indications to Stanford Hospital. The primary model was a convolutional neural network model trained to predict incident heart failure within 5 years. Biases were evaluated on the testing set (160 312 ECGs) using the area under the receiver operating characteristic curve, stratified across the protected attributes of race, ethnicity, age, and sex.There were 59 817 cases of incident heart failure observed within 5 years of ECG collection. The performance of the primary model declined with age. There were no significant differences observed between racial groups overall. However, the primary model performed significantly worse in Black patients aged 0 to 40 years compared with all other racial groups in this age group, with differences most pronounced among young Black women. Disparities in model performance did not improve with the integration of race, ethnicity, sex, and age into model architecture, by training separate models for each racial group, or by providing the model with a data set of equal racial representation. Using probability thresholds individualized for race, age, and sex offered substantial improvements in F1 scores.The biases found in this study warrant caution against perpetuating disparities through the development of machine learning tools for the prognosis and management of heart failure. Customizing the application of these models by using probability thresholds individualized by race, ethnicity, age, and sex may offer an avenue to mitigate existing algorithmic disparities.

    View details for DOI 10.1161/CIRCHEARTFAILURE.123.010879

    View details for PubMedID 38126168

  • Epistasis regulates genetic control of cardiac hypertrophy. Research square Wang, Q., Tang, T. M., Youlton, N., Weldy, C. S., Kenney, A. M., Ronen, O., Hughes, J. W., Chin, E. T., Sutton, S. C., Agarwal, A., Li, X., Behr, M., Kumbier, K., Moravec, C. S., Tang, W. H., Margulies, K. B., Cappola, T. P., Butte, A. J., Arnaout, R., Brown, J. B., Priest, J. R., Parikh, V. N., Yu, B., Ashley, E. A. 2023

    Abstract

    The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141, IGF1R, TTN, and TNKS. Several loci not prioritized by univariate genome-wide association analysis are identified. Functional genomic and integrative enrichment analyses reveal a complex gene regulatory network in which genes mapped from these loci share biological processes and myogenic regulatory factors. Through a network analysis of transcriptomic data from 313 explanted human hearts, we show that these interactions are preserved at the level of the cardiac transcriptome. We assess causality of epistatic effects via RNA silencing of gene-gene interactions in human induced pluripotent stem cell-derived cardiomyocytes. Finally, single-cell morphology analysis using a novel high-throughput microfluidic system shows that cardiomyocyte hypertrophy is non-additively modifiable by specific pairwise interactions between CCDC141 and both TTN and IGF1R. Our results expand the scope of genetic regulation of cardiac structure to epistasis.

    View details for DOI 10.21203/rs.3.rs-3509208/v1

    View details for PubMedID 38045390

    View details for PubMedCentralID PMC10690313

  • Epistasis regulates genetic control of cardiac hypertrophy. medRxiv : the preprint server for health sciences Wang, Q., Tang, T. M., Youlton, N., Weldy, C. S., Kenney, A. M., Ronen, O., Hughes, J. W., Chin, E. T., Sutton, S. C., Agarwal, A., Li, X., Behr, M., Kumbier, K., Moravec, C. S., Tang, W. H., Margulies, K. B., Cappola, T. P., Butte, A. J., Arnaout, R., Brown, J. B., Priest, J. R., Parikh, V. N., Yu, B., Ashley, E. A. 2023

    Abstract

    The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141, IGF1R, TTN, and TNKS. Several loci not prioritized by univariate genome-wide association analysis are identified. Functional genomic and integrative enrichment analyses reveal a complex gene regulatory network in which genes mapped from these loci share biological processes and myogenic regulatory factors. Through a network analysis of transcriptomic data from 313 explanted human hearts, we show that these interactions are preserved at the level of the cardiac transcriptome. We assess causality of epistatic effects via RNA silencing of gene-gene interactions in human induced pluripotent stem cell-derived cardiomyocytes. Finally, single-cell morphology analysis using a novel high-throughput microfluidic system shows that cardiomyocyte hypertrophy is non-additively modifiable by specific pairwise interactions between CCDC141 and both TTN and IGF1R. Our results expand the scope of genetic regulation of cardiac structure to epistasis.

    View details for DOI 10.1101/2023.11.06.23297858

    View details for PubMedID 37987017

    View details for PubMedCentralID PMC10659487

  • Long term outcome after septal reduction therapies in patients with hypertrophic cardiomyopathy: insights from the SHaRe registry Maurizi, N., Day, S., Ashley, E., Michels, M., Pereira, A. C., Helms, A., Saberi, S., Jacoby, D., Ware, J., Colan, S., Semsarian, C., Ingles, J., Ho, C., Olivotto, I. OXFORD UNIV PRESS. 2023
  • A fast, novel technique for detection of left ventricular hypertrophy by electrocardiography Somani, S., Hughes, J. W., Ashley, E. A., Witteles, R. M., Perez, M. V. OXFORD UNIV PRESS. 2023
  • Two epilepsy-associated variants in KCNA2 (KV1.2) at position H310 oppositely affect channel functional expression. The Journal of physiology Minguez-Vinas, T., Prakash, V., Wang, K., Lindstrom, S. H., Pozzi, S., Scott, S. A., Spiteri, E., Stevenson, D. A., Ashley, E. A., Gunnarsson, C., Pantazis, A. 2023

    Abstract

    Two KCNA2 variants (p.H310Y and p.H310R) were discovered in paediatric patients with epilepsy and developmental delay. KCNA2 encodes KV 1.2-channel subunits, which regulate neuronal excitability. Both gain and loss of KV 1.2 function cause epilepsy, precluding the prediction of variant effects; and while H310 is conserved throughout the KV -channel superfamily, it is largely understudied. We investigated both variants in heterologously expressed, human KV 1.2 channels by immunocytochemistry, electrophysiology and voltage-clamp fluorometry. Despite affecting the same channel, at the same position, and being associated with severe neurological disease, the two variants had diametrically opposite effects on KV 1.2 functional expression. The p.H310Y variant produced 'dual gain of function', increasing both cell-surface trafficking and activity, delaying channel closure. We found that the latter is due to the formation of a hydrogen bond that stabilizes the active state of the voltage-sensor domain. Additionally, H310Y abolished 'ball and chain' inactivation of KV 1.2 by KV beta1 subunits, enhancing gain of function. In contrast, p.H310R caused 'dual loss of function', diminishing surface levels by multiple impediments to trafficking and inhibiting voltage-dependent channel opening. We discuss the implications for KV -channel biogenesis and function, an emergent hotspot for disease-associated variants, and mechanisms of epileptogenesis. KEY POINTS: KCNA2 encodes the subunits of KV 1.2 voltage-activated, K+ -selective ion channels, which regulate electrical signalling in neurons. We characterize two KCNA2 variants from patients with developmental delay and epilepsy. Both variants affect position H310, highly conserved in KV channels. The p.H310Y variant caused 'dual gain of function', increasing both KV 1.2-channel activity and the number of KV 1.2 subunits on the cell surface. H310Y abolished 'ball and chain' (N-type) inactivation of KV 1.2 by KV beta1 subunits, enhancing the gain-of-function phenotype. The p.H310R variant caused 'dual loss of function', diminishing the presence of KV 1.2 subunits on the cell surface and inhibiting voltage-dependent channel opening. As H310Y stabilizes the voltage-sensor active conformation and abolishes N-type inactivation, it can serve as an investigative tool for functional and pharmacological studies.

    View details for DOI 10.1113/JP285052

    View details for PubMedID 37883018

  • Author Correction: COSMOS: a platform for real-time morphology-based, label-free cell sorting using deep learning. Communications biology Salek, M., Li, N., Chou, H. P., Saini, K., Jovic, A., Jacobs, K. B., Johnson, C., Lu, V., Lee, E. J., Chang, C., Nguyen, P., Mei, J., Pant, K. P., Wong-Thai, A. Y., Smith, Q. F., Huang, S., Chow, R., Cruz, J., Walker, J., Chan, B., Musci, T. J., Ashley, E. A., Masaeli, M. M. 2023; 6 (1): 1023

    View details for DOI 10.1038/s42003-023-05415-8

    View details for PubMedID 37813962

  • Rare variant associations with plasma protein levels in the UK Biobank NATURE Dhindsa, R. S., Burren, O. S., Sun, B. B., Prins, B. P., Matelska, D., Wheeler, E., Mitchell, J., Oerton, E., Hristova, V. A., Smith, K. R., Carss, K., Wasilewski, S., Harper, A. R., Paul, D. S., Fabre, M. A., Runz, H., Viollet, C., Challis, B., Platt, A., AstraZeneca Genomics Initiative, D., Vitsios, D., Ashley, E. A., Whelan, C. D., Pangalos, M. N., Wang, Q., Petrovski, S. 2023
  • Assessment of maximal effort for weaker individuals with NMD during the assisted six-minute cycling test Blumberg, Y., De Monts, C., Tang, W., Montalvo, S., Ataide, P., Young, S., Wheeler, M., Ashley, E., Myers, J., Day, J., Christle, J., Duong, T. PERGAMON-ELSEVIER SCIENCE LTD. 2023: S187
  • Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care JOURNAL OF PEDIATRICS Halley, M. C., Young, J. L., Tang, C., Mintz, K. T., Lucas-Griffin, S., Maghiro, A., Ashley, E. A., Tabor, H. K., Undiagnosed Diseases Network 2023; 261
  • The Stanford Medicine data science ecosystem for clinical and translational research. JAMIA open Callahan, A., Ashley, E., Datta, S., Desai, P., Ferris, T. A., Fries, J. A., Halaas, M., Langlotz, C. P., Mackey, S., Posada, J. D., Pfeffer, M. A., Shah, N. H. 2023; 6 (3): ooad054

    Abstract

    To describe the infrastructure, tools, and services developed at Stanford Medicine to maintain its data science ecosystem and research patient data repository for clinical and translational research.The data science ecosystem, dubbed the Stanford Data Science Resources (SDSR), includes infrastructure and tools to create, search, retrieve, and analyze patient data, as well as services for data deidentification, linkage, and processing to extract high-value information from healthcare IT systems. Data are made available via self-service and concierge access, on HIPAA compliant secure computing infrastructure supported by in-depth user training.The Stanford Medicine Research Data Repository (STARR) functions as the SDSR data integration point, and includes electronic medical records, clinical images, text, bedside monitoring data and HL7 messages. SDSR tools include tools for electronic phenotyping, cohort building, and a search engine for patient timelines. The SDSR supports patient data collection, reproducible research, and teaching using healthcare data, and facilitates industry collaborations and large-scale observational studies.Research patient data repositories and their underlying data science infrastructure are essential to realizing a learning health system and advancing the mission of academic medical centers. Challenges to maintaining the SDSR include ensuring sufficient financial support while providing researchers and clinicians with maximal access to data and digital infrastructure, balancing tool development with user training, and supporting the diverse needs of users.Our experience maintaining the SDSR offers a case study for academic medical centers developing data science and research informatics infrastructure.

    View details for DOI 10.1093/jamiaopen/ooad054

    View details for PubMedID 37545984

    View details for PubMedCentralID PMC10397535

  • Personalized digital behaviour interventions increase short-term physical activity: a randomized control crossover trial substudy of the MyHeart Counts Cardiovascular Health Study. European heart journal. Digital health Javed, A., Kim, D. S., Hershman, S. G., Shcherbina, A., Johnson, A., Tolas, A., O'Sullivan, J. W., McConnell, M. V., Lazzeroni, L., King, A. C., Christle, J. W., Oppezzo, M., Mattsson, C. M., Harrington, R. A., Wheeler, M. T., Ashley, E. A. 2023; 4 (5): 411-419

    Abstract

    Physical activity is associated with decreased incidence of the chronic diseases associated with aging. We previously demonstrated that digital interventions delivered through a smartphone app can increase short-term physical activity.We offered enrolment to community-living iPhone-using adults aged ≥18 years in the USA, UK, and Hong Kong who downloaded the MyHeart Counts app. After completion of a 1-week baseline period, e-consented participants were randomized to four 7-day interventions. Interventions consisted of: (i) daily personalized e-coaching based on the individual's baseline activity patterns, (ii) daily prompts to complete 10 000 steps, (iii) hourly prompts to stand following inactivity, and (iv) daily instructions to read guidelines from the American Heart Association (AHA) website. After completion of one 7-day intervention, participants subsequently randomized to the next intervention of the crossover trial. The trial was completed in a free-living setting, where neither the participants nor investigators were blinded to the intervention. The primary outcome was change in mean daily step count from baseline for each of the four interventions, assessed in a modified intention-to-treat analysis (modified in that participants had to complete 7 days of baseline monitoring and at least 1 day of an intervention to be included in analyses). This trial is registered with ClinicalTrials.gov, NCT03090321.Between 1 January 2017 and 1 April 2022, 4500 participants consented to enrol in the trial (a subset of the approximately 50 000 participants in the larger MyHeart Counts study), of whom 2458 completed 7 days of baseline monitoring (mean daily steps 4232 ± 73) and at least 1 day of one of the four interventions. Personalized e-coaching prompts, tailored to an individual based on their baseline activity, increased step count significantly (+402 ± 71 steps from baseline, P = 7.1⨯10-8). Hourly stand prompts (+292 steps from baseline, P = 0.00029) and a daily prompt to read AHA guidelines (+215 steps from baseline, P = 0.021) were significantly associated with increased mean daily step count, while a daily reminder to complete 10 000 steps was not (+170 steps from baseline, P = 0.11). Digital studies have a significant advantage over traditional clinical trials in that they can continuously recruit participants in a cost-effective manner, allowing for new insights provided by increased statistical power and refinement of prior signals. Here, we present a novel finding that digital interventions tailored to an individual are effective in increasing short-term physical activity in a free-living cohort. These data suggest that participants are more likely to react positively and increase their physical activity when prompts are personalized. Further studies are needed to determine the effects of digital interventions on long-term outcomes.

    View details for DOI 10.1093/ehjdh/ztad047

    View details for PubMedID 37794870

    View details for PubMedCentralID PMC10545510

  • Artificial Intelligence in Molecular Medicine. Reply. The New England journal of medicine Gomes, B., Ashley, E. A. 2023; 389 (13): 1252

    View details for DOI 10.1056/NEJMc2308776

    View details for PubMedID 37754302

  • Local read haplotagging enables accurate long-read small variant calling. bioRxiv : the preprint server for biology Kolesnikov, A., Cook, D., Nattestad, M., McNulty, B., Gorzynski, J., Goenka, S., Ashley, E. A., Jain, M., Miga, K. H., Paten, B., Chang, P. C., Carroll, A., Shafin, K. 2023

    Abstract

    Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation makes DeepVariant a universal variant calling solution for long-read sequencing platforms.

    View details for DOI 10.1101/2023.09.07.556731

    View details for PubMedID 37745389

    View details for PubMedCentralID PMC10515762

  • A deep learning-based electrocardiogram risk score for long term cardiovascular death and disease. NPJ digital medicine Hughes, J. W., Tooley, J., Torres Soto, J., Ostropolets, A., Poterucha, T., Christensen, M. K., Yuan, N., Ehlert, B., Kaur, D., Kang, G., Rogers, A., Narayan, S., Elias, P., Ouyang, D., Ashley, E., Zou, J., Perez, M. V. 2023; 6 (1): 169

    Abstract

    The electrocardiogram (ECG) is the most frequently performed cardiovascular diagnostic test, but it is unclear how much information resting ECGs contain about long term cardiovascular risk. Here we report that a deep convolutional neural network can accurately predict the long-term risk of cardiovascular mortality and disease based on a resting ECG alone. Using a large dataset of resting 12-lead ECGs collected at Stanford University Medical Center, we developed SEER, the Stanford Estimator of Electrocardiogram Risk. SEER predicts 5-year cardiovascular mortality with an area under the receiver operator characteristic curve (AUC) of 0.83 in a held-out test set at Stanford, and with AUCs of 0.78 and 0.83 respectively when independently evaluated at Cedars-Sinai Medical Center and Columbia University Irving Medical Center. SEER predicts 5-year atherosclerotic disease (ASCVD) with an AUC of 0.67, similar to the Pooled Cohort Equations for ASCVD Risk, while being only modestly correlated. When used in conjunction with the Pooled Cohort Equations, SEER accurately reclassified 16% of patients from low to moderate risk, uncovering a group with an actual average 9.9% 10-year ASCVD risk who would not have otherwise been indicated for statin therapy. SEER can also predict several other cardiovascular conditions such as heart failure and atrial fibrillation. Using only lead I of the ECG it predicts 5-year cardiovascular mortality with an AUC of 0.80. SEER, used alongside the Pooled Cohort Equations and other risk tools, can substantially improve cardiovascular risk stratification and aid in medical decision making.

    View details for DOI 10.1038/s41746-023-00916-6

    View details for PubMedID 37700032

    View details for PubMedCentralID 8145781

  • Cardiac Remodeling in Subclinical Hypertrophic Cardiomyopathy: The VANISH Randomized Clinical Trial. JAMA cardiology Vissing, C. R., Axelsson Raja, A., Day, S. M., Russell, M. W., Zahka, K., Lever, H. M., Pereira, A. C., Colan, S. D., Margossian, R., Murphy, A. M., Canter, C., Bach, R. G., Wheeler, M. T., Rossano, J. W., Owens, A. T., Benson, L., Mestroni, L., Taylor, M. R., Patel, A. R., Wilmot, I., Thrush, P., Soslow, J. H., Becker, J. R., Seidman, C. E., Lakdawala, N. K., Cirino, A. L., McMurray, J. J., MacRae, C. A., Solomon, S. D., Bundgaard, H., Orav, E. J., Ho, C. Y., Valsartan for Attenuating Disease Evolution in Early Sarcomeric Hypertrophic Cardiomyopathy (VANISH) Investigators, Krieger, J. E., Sacilotto, L., Arteaga, E., Antunes, M. O., Ashley, E., Lin, K. Y., Hall, E. K., Choudhury, L., Pahl, E., Vargas, J. D., Lewis, G. D., Desai, A. S. 2023

    Abstract

    Importance: Valsartan has shown promise in attenuating cardiac remodeling in patients with early-stage sarcomeric hypertrophic cardiomyopathy (HCM). Genetic testing can identify individuals at risk of HCM in a subclinical stage who could benefit from therapies that prevent disease progression.Objective: To explore the potential for valsartan to modify disease development, and to characterize short-term phenotypic progression in subclinical HCM.Design, Setting, and Participants: The multicenter, double-blind, placebo-controlled Valsartan for Attenuating Disease Evolution in Early Sarcomeric Hypertrophic Cardiomyopathy (VANISH) randomized clinical trial was conducted from April 2014 to July 2019 at 17 sites in 4 countries (Brazil, Canada, Denmark, and the US), with 2 years of follow-up. The prespecified exploratory VANISH cohort studied here included sarcomere variant carriers with subclinical HCM and early phenotypic manifestations (reduced E' velocity, electrocardiographic abnormalities, or an increased left ventricular [LV] wall thickness [LVWT] to cavity diameter ratio) but no LV hypertrophy (LVH). Data were analyzed between March and December 2022.Interventions: Treatment with placebo or valsartan (80 mg/d for children weighing <35 kg, 160 mg/d for children weighing ≥35 kg, or 320 mg/d for adults aged ≥18 years).Main Outcomes and Measures: The primary outcome was a composite z score incorporating changes in 9 parameters of cardiac remodeling (LV cavity volume, LVWT, and LV mass; left atrial [LA] volume; E' velocity and S' velocity; and serum troponin and N-terminal prohormone of brain natriuretic peptide levels).Results: This study included 34 participants, with a mean (SD) age of 16(5) years (all were White). A total of 18 participants (8 female [44%] and 10 male [56%]) were randomized to valsartan and 16 (9 female [56%] and 7 male [44%]) were randomized to placebo. No statistically significant effects of valsartan on cardiac remodeling were detected (mean change in composite z score compared with placebo: -0.01 [95% CI, -0.29 to 0.26]; P=.92). Overall, 2-year phenotypic progression was modest, with only a mild increase in LA volume detected (increased by 3.5 mL/m2 [95% CI, 1.4-6.0 mL/m2]; P=.002). Nine participants (26%) had increased LVWT, including 6 (18%) who developed clinically overt HCM. Baseline LA volume index (LAVI; 35 vs 28 mL/m2; P=.01) and average interventricular septum thickness (8.5 vs 7.0 mm; P=.009) were higher in participants who developed HCM.Conclusions and Relevance: In this exploratory cohort, valsartan was not proven to slow progression of subclinical HCM. Minimal changes in markers of cardiac remodeling were observed, although nearly one-fifth of patients developed clinically overt HCM. Transition to disease was associated with greater baseline interventricular septum thickness and LAVI. These findings highlight the importance of following sarcomere variant carriers longitudinally and the critical need to improve understanding of factors that drive disease penetrance and progression.Trial Registration: ClinicalTrials.gov Identifier: NCT01912534.

    View details for DOI 10.1001/jamacardio.2023.2808

    View details for PubMedID 37672268

  • Emery-Dreifuss Muscular Dystrophy 1 is associated with high risk of malignant ventricular arrhythmias and end-stage heart failure. European heart journal Cannie, D. E., Syrris, P., Protonotarios, A., Bakalakos, A., Pruny, J. F., Ditaranto, R., Martinez-Veira, C., Larrañaga-Moreira, J. M., Medo, K., Bermúdez-Jiménez, F. J., Ben Yaou, R., Leturq, F., Mezcua, A. R., Marini-Bettolo, C., Cabrera, E., Reuter, C., Limeres Freire, J., Rodríguez-Palomares, J. F., Mestroni, L., Taylor, M. R., Parikh, V. N., Ashley, E. A., Barriales-Villa, R., Jiménez-Jáimez, J., Garcia-Pavia, P., Charron, P., Biagini, E., García Pinilla, J. M., Bourke, J., Savvatis, K., Wahbi, K., Elliott, P. M. 2023

    Abstract

    Emery-Dreifuss muscular dystrophy (EDMD) is caused by variants in EMD (EDMD1) and LMNA (EDMD2). Cardiac conduction defects and atrial arrhythmia are common to both, but LMNA variants also cause end-stage heart failure (ESHF) and malignant ventricular arrhythmia (MVA). This study aimed to better characterise the cardiac complications of EMD variants.Consecutively referred EMD variant-carriers were retrospectively recruited from 12 international cardiomyopathy units. MVA and ESHF incidence in male and female variant-carriers was determined. Male EMD variant-carriers with a cardiac phenotype at baseline (EMDCARDIAC) were compared to consecutively recruited male LMNA variant-carriers with a cardiac phenotype at baseline (LMNACARDIAC).Longitudinal follow-up data were available for 38 male and 21 female EMD variant-carriers (mean [SD] ages 33.4 [13.3] and 43.3 [16.8] years, respectively). Nine (23.6%) males developed MVA and five (13.2%) developed ESHF during a median [IQR] follow-up of 65.0 [24.3, 109.5] months. No female EMD variant-carrier had MVA or ESHF, but nine (42.8%) developed a cardiac phenotype at a median [IQR] age of 58.6 [53.2, 60.4] years. Incidence rates for MVA were similar for EMDCARDIAC and LMNACARDIAC (4.8 and 6.6 per 100 person-years, respectively; log-rank p = 0.49). Incidence rates for ESHF were 2.4 and 5.9 per 100 person-years for EMDCARDIAC and LMNACARDIAC, respectively (log-rank p = 0.09).Male EMD variant-carriers have a risk of progressive heart failure and ventricular arrhythmias similar to that of male LMNA variant-carriers. Early implantable cardioverter defibrillator implantation and heart failure drug therapy should be considered in male EMD variant-carriers with cardiac disease.

    View details for DOI 10.1093/eurheartj/ehad561

    View details for PubMedID 37639473

  • The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change. Genetics in medicine : official journal of the American College of Medical Genetics Rehm, H. L., Alaimo, J. T., Aradhya, S., Bayrak-Toydemir, P., Best, H., Brandon, R., Buchan, J. G., Chao, E. C., Chen, E., Clifford, J., Cohen, A. S., Conlin, L. K., Das, S., Davis, K. W., Gaudio, D. D., Del Viso, F., DiVincenzo, C., Eisenberg, M., Guidugli, L., Hammer, M. B., Harrison, S. M., Hatchell, K. E., Dyer, L. H., Hoang, L. U., Holt, J. M., Jobanputra, V., Karbassi, I. D., Kearney, H. M., Kelly, M. A., Kelly, J. M., Kluge, M. L., Komala, T., Kruszka, P., Lau, L., Lebo, M. S., Marshall, C. R., McKnight, D., McWalter, K., Meng, Y., Nagan, N., Neckelmann, C. S., Neerman, N., Niu, Z., Paolillo, V. K., Paolucci, S. A., Perry, D., Pesaran, T., Radtke, K., Rasmussen, K. J., Retterer, K., Saunders, C. J., Spiteri, E., Stanley, C., Szuto, A., Taft, R. J., Thiffault, I., Thomas, B. C., Thomas-Wilson, A., Thorpe, E., Tidwell, T. J., Towne, M. C., Zouk, H. 2023: 100947

    Abstract

    Variants of uncertain significance (VUS) are a common result of diagnostic genetic testing and can be difficult to manage with potential misinterpretation and downstream costs, including time investment by clinicians. We investigated the rate of VUS reported on diagnostic testing via multi-gene panels (MGPs) and exome and genome sequencing (ES/GS) to measure the magnitude of uncertain results and explore ways to reduce their potentially detrimental impact.Rates of inconclusive results due to VUS were collected from over 1.5 million sequencing test results from 19 clinical laboratories in North America from 2020 - 2021.We found a lower rate of inconclusive test results due to VUSs from ES/GS (22.5%) compared to MGPs (32.6%; p<0.0001). For MGPs, the rate of inconclusive results correlated with panel size. The use of trios reduced inconclusive rates (18.9% vs 27.6%; p<0.001) whereas the use of GS compared to ES had no impact (22.2% vs 22.6%; p=ns).The high rate of VUS observed in diagnostic MGP testing warrants examining current variant reporting practices. We propose several approaches to reduce reported VUS rates, while directing clinician resources towards important VUS follow-up.

    View details for DOI 10.1016/j.gim.2023.100947

    View details for PubMedID 37534744

  • APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's Disease pathology. medRxiv : the preprint server for health sciences Chemparathy, A., Guen, Y. L., Chen, S., Lee, E. G., Leong, L., Gorzynski, J., Xu, G., Belloy, M., Kasireddy, N., Tauber, A. P., Williams, K., Stewart, I., Wingo, T., Lah, J., Jayadev, S., Hales, C., Peskind, E., Child, D. D., Keene, C. D., Cong, L., Ashley, E., Yu, C. E., Greicius, M. D. 2023

    Abstract

    The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's Disease (AD). Knockdown of this allele may provide a therapeutic strategy for AD, but the effect of APOE loss-of-function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of older controls and patients with AD and identified six heterozygote carriers of APOE LoF variants. Five carriers were controls (ages 71-90) and one was an AD case with an unremarkable age-at-onset between 75-79. Two APOE ε3/ε4 controls (Subjects 1 and 2) carried a stop-gain affecting the ε4 allele. Subject 1 was cognitively normal at 90+ and had no neuritic plaques at autopsy. Subject 2 was cognitively healthy within the age range 75-79 and underwent lumbar puncture at between ages 75-79 with normal levels of amyloid. The results provide the strongest human genetics evidence yet available suggesting that ε4 drives AD risk through a gain of abnormal function and support knockdown of APOE ε4 or its protein product as a viable therapeutic option.

    View details for DOI 10.1101/2023.07.20.23292771

    View details for PubMedID 37547016

    View details for PubMedCentralID PMC10402217

  • Right Ventricular Dysfunction Patterns Among Patients with COVID-19 in the Intensive Care Unit - a Retrospective Cohort Analysis. Annals of the American Thoracic Society Sanchez, P. A., O'Donnell, C. T., Francisco, N., Santana, E. J., Moore, A. R., Pacheco-Navarro, A., Roque, J., Lebold, K. M., Parmer, C. M., Pienkos, S. M., Celestin, B. E., Levitt, J. E., Collins, W. J., Lanspa, M. J., Ashley, E. A., Wilson, J. G., Haddad, F., Rogers, A. J. 2023

    Abstract

    Right ventricular (RV) dysfunction is common among patients hospitalized with COVID-19; however, its epidemiology may depend on the echocardiographic parameters used to define it.To evaluate the prevalence of abnormalities in three common echocardiographic parameters of RV function among COVID-19 patients admitted to the intensive care unit, as well as the effect of RV dilatation on differential parameter abnormality and the association of RV dysfunction with 60-day mortality.Retrospective cohort study of COVID-19 ICU patients between March 4th,2020 to March 4th, 2021, who received a transthoracic echocardiogram within 48 hours before to at most 7 days after ICU admission. RV dysfunction and dilatation respectively defined by guideline thresholds for tricuspid annular plane systolic excursion (TAPSE), RV fractional area change (RVFAC), RV free wall longitudinal strain (RVFWS), and RV basal dimension or RV end-diastolic area. Association of RV dysfunction with 60-day mortality assessed through logistic regression adjusting for age, prior history of congestive heart failure, invasive ventilation at time of TTE and APACHE II score.116 patients were included, of which 69% had RV dysfunction by > 1 parameter and 36.3% of these had RV dilatation. The three most common patterns of RV dysfunction included: Presence of 3 abnormalities, the combination of abnormal RVFWS and TAPSE, and isolated TAPSE abnormality. Patients with RV dilatation had worse RVFAC (24% vs 36%, p = 0.001), worse RVFWS (16.3% vs 19.1%, p = 0.005), higher RVSP (45mmHg vs 31mmHg, p = 0.001) but similar TAPSE (13mm vs 13mm, p = 0.30) compared to those with normal RV size. After multivariable adjustment, 60-day mortality was significantly associated with RV dysfunction (OR 2.91, 95% CI 1.01 - 9.44), as was the presence of at least 2 parameter abnormalities.ICU patients with COVID-19 had significant heterogeneity in RV function abnormalities present with different patterns associated with RV dilatation. RV dysfunction by any parameter was associated with increased mortality. Therefore, a multiparameter evaluation may be critical in recognizing RV dysfunction in COVID-19.

    View details for DOI 10.1513/AnnalsATS.202303-235OC

    View details for PubMedID 37478340

  • A 3' UTR Deletion Is a Leading Candidate Causal Variant at the TMEM106B Locus Reducing Risk for FTLD-TDP. medRxiv : the preprint server for health sciences Chemparathy, A., Le Guen, Y., Zeng, Y., Gorzynski, J., Jensen, T., Kasireddy, N., Talozzi, L., Belloy, M. E., Stewart, I., Gitler, A. D., Wagner, A. D., Mormino, E., Henderson, V. W., Wyss-Coray, T., Ashley, E., Greicius, M. D. 2023

    Abstract

    Single nucleotide variants (SNVs) near TMEM106B have been associated with risk of frontotemporal lobar dementia with TDP pathology (FTLD-TDP) but the causal variant at this locus has not yet been isolated. The initial leading FTLD-TDP genome-wide association study (GWAS) hit at this locus, rs1990622, is intergenic and is in linkage disequilibrium (LD) with a TMEM106B coding SNV, rs3173615. We developed a long-read sequencing (LRS) dataset of 407 individuals in order to identify structural variants associated with neurodegenerative disorders. We identified a prevalent 322 base pair deletion on the TMEM106B 3' untranslated region (UTR) that was in perfect linkage with rs1990622 and near-perfect linkage with rs3173615 (genotype discordance in two of 274 individuals who had LRS and short-read next-generation sequencing). In Alzheimer's Disease Sequencing Project (ADSP) participants, this deletion was in greater LD with rs1990622 (R2=0.920916, D'=0.963472) than with rs3173615 (R2=0.883776, D'=0.963575). rs1990622 and rs3173615 are less closely linked (R2=0.7403, D'=0.9915) in African populations. Among African ancestry individuals in the ADSP, the deletion is in even greater LD with rs1990622 (R2=0.936841, D'=0.976782) than with rs3173615 (R2=0.764242, D'=0.974406). Querying publicly available genetic datasets with associated mRNA expression and protein levels, we confirmed that rs1990622 is consistently a protein quantitative trait locus but not an expression quantitative trait locus, consistent with a causal variant present on the TMEM106B 3'UTR. In summary, the TMEM106B 3' UTR deletion is a large genetic variant on the TMEM106B transcript that is in higher LD with the leading GWAS hit rs1990622 than rs3173615 and may mediate the protective effect of this locus in neurodegenerative disease.

    View details for DOI 10.1101/2023.07.06.23292312

    View details for PubMedID 37461476

    View details for PubMedCentralID PMC10350161

  • Wearable technology and the cardiovascular system: the future of patient assessment. The Lancet. Digital health Williams, G. J., Al-Baraikan, A., Rademakers, F. E., Ciravegna, F., van de Vosse, F. N., Lawrie, A., Rothman, A., Ashley, E. A., Wilkins, M. R., Lawford, P. V., Omholt, S. W., Wisløff, U., Hose, D. R., Chico, T. J., Gunn, J. P., Morris, P. D. 2023; 5 (7): e467-e476

    Abstract

    The past decade has seen a dramatic rise in consumer technologies able to monitor a variety of cardiovascular parameters. Such devices initially recorded markers of exercise, but now include physiological and health-care focused measurements. The public are keen to adopt these devices in the belief that they are useful to identify and monitor cardiovascular disease. Clinicians are therefore often presented with health app data accompanied by a diverse range of concerns and queries. Herein, we assess whether these devices are accurate, their outputs validated, and whether they are suitable for professionals to make management decisions. We review underpinning methods and technologies and explore the evidence supporting the use of these devices as diagnostic and monitoring tools in hypertension, arrhythmia, heart failure, coronary artery disease, pulmonary hypertension, and valvular heart disease. Used correctly, they might improve health care and support research.

    View details for DOI 10.1016/S2589-7500(23)00087-0

    View details for PubMedID 37391266

  • Respiratory gas kinetics in patients with congestive heart failure during recovery from peak exercise. Clinics (Sao Paulo, Brazil) Patti, A., Blumberg, Y., Hedman, K., Neunhäuserer, D., Haddad, F., Wheeler, M., Ashley, E., Moneghetti, K. J., Myers, J., Christle, J. W. 2023; 78: 100225

    Abstract

    Cardiopulmonary Exercise Testing (CPX) is essential for the assessment of exercise capacity for patients with Chronic Heart Failure (CHF). Respiratory gas and hemodynamic parameters such as Ventilatory Efficiency (VE/VCO2 slope), peak oxygen uptake (peak VO2), and heart rate recovery are established diagnostic and prognostic markers for clinical populations. Previous studies have suggested the clinical value of metrics related to respiratory gas collected during recovery from peak exercise, particularly recovery time to 50% (T1/2) of peak VO2. The current study explores these metrics in detail during recovery from peak exercise in CHF.Patients with CHF who were referred for CPX and healthy individuals without formal diagnoses were assessed for inclusion. All subjects performed CPX on cycle ergometers to volitional exhaustion and were monitored for at least five minutes of recovery. CPX data were analyzed for overshoot of respiratory exchange ratio (RER=VCO2/VO2), ventilatory equivalent for oxygen (VE/VO2), end-tidal partial pressure of oxygen (PETO2), and T1/2 of peak VO2 and VCO2.Thirty-two patients with CHF and 30 controls were included. Peak VO2 differed significantly between patients and controls (13.5 ± 3.8 vs. 32.5 ± 9.8 mL/Kg*min-1, p < 0.001). Mean Left Ventricular Ejection Fraction (LVEF) was 35.9 ± 9.8% for patients with CHF compared to 61.1 ± 8.2% in the control group. The T1/2 of VO2, VCO2 and VE was significantly higher in patients (111.3 ± 51.0, 132.0 ± 38.8 and 155.6 ± 45.5s) than in controls (58.08 ± 13.2, 74.3 ± 21.1, 96.7 ± 36.8s; p < 0.001) while the overshoot of PETO2, VE/VO2 and RER was significantly lower in patients (7.2 ± 3.3, 41.9 ± 29.1 and 25.0 ± 13.6%) than in controls (10.1 ± 4.6, 62.1 ± 17.7 and 38.7 ± 15.1%; all p < 0.01). Most of the recovery metrics were significantly correlated with peak VO2 in CHF patients, but not with LVEF.Patients with CHF have a significantly blunted recovery from peak exercise. This is reflected in delays of VO2, VCO2, VE, PETO2, RER and VE/VO2, reflecting a greater energy required to return to baseline. Abnormal respiratory gas kinetics in CHF was negatively correlated with peak VO2 but not baseline LVEF.

    View details for DOI 10.1016/j.clinsp.2023.100225

    View details for PubMedID 37356413

  • Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care. The Journal of pediatrics Halley, M. C., Young, J. L., Tang, C., Mintz, K. T., Lucas-Griffin, S., Maghiro, A. S., Ashley, E. A., Tabor, H. K. 2023: 113537

    Abstract

    To explore the perspectives of parents of undiagnosed children enrolled in genomic diagnosis research regarding their motivations for enrolling their children, their understanding of the potential burdens and benefits, and the extent to which their experiences ultimately aligned with or diverged from their original expectations.In-depth interviews were conducted with parents, audio-recorded and transcribed. A structured codebook was applied to each transcript, after which iterative memoing was used to identify themes.Fifty-four parents participated, including 17 (31.5%) whose child received a diagnosis through research. Themes describing parents' expectations and experiences of genomic diagnosis research included: 1) the extent to which parents' motivations for participation focused on their hope that it would directly benefit their child; 2) the ways in which parents' frustrations regarding the research process confused the dual clinical and research goals of their participation; and 3) the limited clinical benefits parents ultimately experienced for their children.Our results suggest that parents of undiagnosed children seeking enrollment in genomic diagnosis research are at risk of a form of therapeutic misconception - in this case, diagnostic misconception. These findings indicate the need to examine the processes and procedures associated with this research in order to appropriately communicate and balance the potential burdens and benefits of study participation.

    View details for DOI 10.1016/j.jpeds.2023.113537

    View details for PubMedID 37271495

  • Left Ventricular Systolic Dysfunction in Patients Diagnosed With Hypertrophic Cardiomyopathy During Childhood: Insights From the SHaRe Registry (Sarcomeric Human Cardiomyopathy). Circulation Alaiwi, S. A., Roston, T. M., Marstrand, P., Claggett, B. L., Parikh, V. N., Helms, A. S., Ingles, J., Lampert, R., Lakdawala, N. K., Michels, M., Owens, A. T., Rossano, J. W., Saberi, S., Abrams, D. J., Ashley, E. A., Semsarian, C., Stendahl, J. C., Ware, J. S., Miller, E., Ryan, T. D., Russell, M. W., Day, S. M., Olivotto, I., Vissing, C. R., Ho, C. Y. 2023

    Abstract

    The development of left ventricular systolic dysfunction (LVSD) in hypertrophic cardiomyopathy (HCM) is rare but serious and associated with poor outcomes in adults. Little is known about the prevalence, predictors, and prognosis of LVSD in patients diagnosed with HCM as children.Data from patients with HCM in the international, multicenter SHaRe Registry (Sarcomeric Human Cardiomyopathy) were analyzed. LVSD was defined as left ventricular ejection fraction <50% on echocardiographic reports. Prognosis was assessed by a composite of death, cardiac transplantation, and left ventricular assist device implantation. Predictors of developing incident LVSD and subsequent prognosis with LVSD were assessed using Cox proportional hazards models.We studied 1010 patients diagnosed with HCM during childhood (<18 years of age) and compared them with 6741 patients with HCM diagnosed as adults. In the pediatric HCM cohort, median age at HCM diagnosis was 12.7 years (interquartile range, 8.0-15.3), and 393 (36%) patients were female. At initial SHaRe Registry site evaluation, 56 (5.5%) patients with childhood-diagnosed HCM had prevalent LVSD, and 92 (9.1%) developed incident LVSD during a median follow-up of 5.5 years. Overall LVSD prevalence was 14.7% compared with 8.7% in patients with adult-diagnosed HCM. Median age at incident LVSD was 32.6 years (interquartile range, 21.3-41.6) for the pediatric cohort and 57.2 years (interquartile range, 47.3-66.5) for the adult cohort. Predictors of developing incident LVSD in childhood-diagnosed HCM included age <12 years at HCM diagnosis (hazard ratio [HR], 1.72 [CI, 1.13-2.62), male sex (HR, 3.1 [CI, 1.88-5.2), carrying a pathogenic sarcomere variant (HR, 2.19 [CI, 1.08-4.4]), previous septal reduction therapy (HR, 2.34 [CI, 1.42-3.9]), and lower initial left ventricular ejection fraction (HR, 1.53 [CI, 1.38-1.69] per 5% decrease). Forty percent of patients with LVSD and HCM diagnosed during childhood met the composite outcome, with higher rates in female participants (HR, 2.60 [CI, 1.41-4.78]) and patients with a left ventricular ejection fraction <35% (HR, 3.76 [2.16-6.52]).Patients with childhood-diagnosed HCM have a significantly higher lifetime risk of developing LVSD, and LVSD emerges earlier than for patients with adult-diagnosed HCM. Regardless of age at diagnosis with HCM or LVSD, the prognosis with LVSD is poor, warranting careful surveillance for LVSD, especially as children with HCM transition to adult care.

    View details for DOI 10.1161/CIRCULATIONAHA.122.062517

    View details for PubMedID 37226762

  • Vigorous Exercise in Patients With Hypertrophic Cardiomyopathy. JAMA cardiology Lampert, R., Ackerman, M. J., Marino, B. S., Burg, M., Ainsworth, B., Salberg, L., Tome Esteban, M. T., Ho, C. Y., Abraham, R., Balaji, S., Barth, C., Berul, C. I., Bos, M., Cannom, D., Choudhury, L., Concannon, M., Cooper, R., Czosek, R. J., Dubin, A. M., Dziura, J., Eidem, B., Emery, M. S., Estes, N. A., Etheridge, S. P., Geske, J. B., Gray, B., Hall, K., Harmon, K. G., James, C. A., Lal, A. K., Law, I. H., Li, F., Link, M. S., McKenna, W. J., Molossi, S., Olshansky, B., Ommen, S. R., Saarel, E. V., Saberi, S., Simone, L., Tomaselli, G., Ware, J. S., Zipes, D. P., Day, S. M., LIVE Consortium, Abrahms, D., Ashley, E., Aziz, P., Batra, A., Cerrone, M., Colan, S., Erickson, C., Ferhaan, A., Gollob, M. J., Johnsrude, C., Kannankeril, P., Kanter, R., Li, W., Masri, A., Murphy, A., Nandi, D., Perez, M., Perry, J., Popjes, E., Rao, R., Rosenthal, D., Sanatani, S., Semsarian, C., Shah, M., Skinner, J., Tardif, J., Towbin, J., Turer, A., Webster, G., Wever-Pinzon, O., Wong, T. 2023

    Abstract

    Importance: Whether vigorous intensity exercise is associated with an increase in risk of ventricular arrhythmias in individuals with hypertrophic cardiomyopathy (HCM) is unknown.Objective: To determine whether engagement in vigorous exercise is associated with increased risk for ventricular arrhythmias and/or mortality in individuals with HCM. The a priori hypothesis was that participants engaging in vigorous activity were not more likely to have an arrhythmic event or die than those who reported nonvigorous activity.Design, Setting, and Participants: This was an investigator-initiated, prospective cohort study. Participants were enrolled from May 18, 2015, to April 25, 2019, with completion in February 28, 2022. Participants were categorized according to self-reported levels of physical activity: sedentary, moderate, or vigorous-intensity exercise. This was a multicenter, observational registry with recruitment at 42 high-volume HCM centers in the US and internationally; patients could also self-enroll through the central site. Individuals aged 8 to 60 years diagnosed with HCM or genotype positive without left ventricular hypertrophy (phenotype negative) without conditions precluding exercise were enrolled.Exposures: Amount and intensity of physical activity.Main Outcomes and Measures: The primary prespecified composite end point included death, resuscitated sudden cardiac arrest, arrhythmic syncope, and appropriate shock from an implantable cardioverter defibrillator. All outcome events were adjudicated by an events committee blinded to the patient's exercise category.Results: Among the 1660 total participants (mean [SD] age, 39 [15] years; 996 male [60%]), 252 (15%) were classified as sedentary, and 709 (43%) participated in moderate exercise. Among the 699 individuals (42%) who participated in vigorous-intensity exercise, 259 (37%) participated competitively. A total of 77 individuals (4.6%) reached the composite end point. These individuals included 44 (4.6%) of those classified as nonvigorous and 33 (4.7%) of those classified as vigorous, with corresponding rates of 15.3 and 15.9 per 1000 person-years, respectively. In multivariate Cox regression analysis of the primary composite end point, individuals engaging in vigorous exercise did not experience a higher rate of events compared with the nonvigorous group with an adjusted hazard ratio of 1.01. The upper 95% 1-sided confidence level was 1.48, which was below the prespecified boundary of 1.5 for noninferiority.Conclusions and Relevance: Results of this cohort study suggest that among individuals with HCM or those who are genotype positive/phenotype negative and are treated in experienced centers, those exercising vigorously did not experience a higher rate of death or life-threatening arrhythmias than those exercising moderately or those who were sedentary. These data may inform discussion between the patient and their expert clinician around exercise participation.

    View details for DOI 10.1001/jamacardio.2023.1042

    View details for PubMedID 37195701

  • Almanac: Retrieval-Augmented Language Models for Clinical Medicine. Research square Zakka, C., Chaurasia, A., Shad, R., Dalal, A. R., Kim, J. L., Moor, M., Alexander, K., Ashley, E., Boyd, J., Boyd, K., Hirsch, K., Langlotz, C., Nelson, J., Hiesinger, W. 2023

    Abstract

    Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n= 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

    View details for DOI 10.21203/rs.3.rs-2883198/v1

    View details for PubMedID 37205549

    View details for PubMedCentralID PMC10187428

  • Participation in a national diagnostic research study: assessing the patient experience. Orphanet journal of rare diseases Rosenfeld, L. E., LeBlanc, K., Nagy, A., Ego, B. K., Undiagnosed Diseases Network, McCray, A. T., Acosta, M. T., Adam, M., Adams, D. R., Alvarez, R. L., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Bacino, C. A., Bademci, G., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bellen, H. J., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Cassini, T., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Corona, R., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Dell'Angelica, E. C., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Falk, M., Fieg, E. L., Fisher, P. G., Fogel, B. L., Forghani, I., Gahl, W. A., Glass, I., Gochuico, B., Goddard, P. C., Godfrey, R. A., Golden-Grant, K., Grajewski, A., Hadley, D., Hahn, S., Halley, M. C., Hamid, R., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Hutchison, S., Introne, W., Isasi, R., Izumi, K., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Jean-Marie, O., Jobanputra, V., Karaviti, L., Kennedy, J., Ketkar, S., Kiley, D., Kilich, G., Kobren, S. N., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Lee, B. H., Levitt, R., Lewis, R. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Mahoney, R., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P., Mulvihill, J., Nakano-Okuno, M., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Swerdzewski, B. N., Quinlan, A., Rao, D. A., Raper, A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Scott, C. R., Shashi, V., Shin, J., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stoler, J. M., Sullivan, K., Sullivan, J. A., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, Q. K., Tan, A. L., Tekin, M., Telischi, F., Thorson, W., Tifft, C. J., Toro, C., Tran, A. A., Ungar, R. A., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Hubshman, M. W., Wener, M., Wenger, T., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Worley, K., Xiao, C., Yamamoto, S., Yang, J., Zhang, Z., Zuchner, S. 2023; 18 (1): 73

    Abstract

    INTRODUCTION: The Undiagnosed Diseases Network (UDN), a clinical research study funded by the National Institutes of Health, aims to provide answers for patients with undiagnosed conditions and generate knowledge about underlying disease mechanisms. UDN evaluations involve collaboration between clinicians and researchers and go beyond what is possible in clinical settings. While medical and research outcomes of UDN evaluations have been explored, this is the first formal assessment of the patient and caregiver experience.METHODS: We invited UDN participants and caregivers to participate in focus groups via email, newsletter, and a private participant Facebook group. We developed focus group questions based on research team expertise, literature focused on patients with rare and undiagnosed conditions, and UDN participant and family member feedback. In March 2021, we conducted, recorded, and transcribed four 60-min focus groups via Zoom. Transcripts were evaluated using a thematic analysis approach.RESULTS: The adult undiagnosed focus group described the UDN evaluation as validating and an avenue for access to medical providers. They also noted that the experience impacted professional choices and helped them rely on others for support. The adult diagnosed focus group described the healthcare system as not set up for rare disease. In the pediatric undiagnosed focus group, caregivers discussed a continued desire for information and gratitude for the UDN evaluation. They also described an ability to rule out information and coming to terms with not having answers. The pediatric diagnosed focus group discussed how the experience helped them focus on management and improved communication. Across focus groups, adults (undiagnosed/diagnosed) noted the comprehensiveness of the evaluation. Undiagnosed focus groups (adult/pediatric) discussed a desire for ongoing communication and care with the UDN. Diagnosed focus groups (adult/pediatric) highlighted the importance of the diagnosis they received in the UDN. The majority of the focus groups noted a positive future orientation after participation.CONCLUSION: Our findings are consistent with prior literature focused on the patient experience of rare and undiagnosed conditions and highlight benefits from comprehensive evaluations, regardless of whether a diagnosis is obtained. Focus group themes also suggest areas for improvement and future research related to the diagnostic odyssey.

    View details for DOI 10.1186/s13023-023-02695-5

    View details for PubMedID 37032333

  • Proactive Variant Effect Mapping Aids Diagnosis in Pediatric Cardiac Arrest. Circulation. Genomic and precision medicine Floyd, B. J., Weile, J., Kannankeril, P. J., Glazer, A. M., Reuter, C. M., MacRae, C. A., Ashley, E. A., Roden, D. M., Roth, F. P., Parikh, V. N. 2023

    View details for DOI 10.1161/CIRCGEN.122.003792

    View details for PubMedID 36716194

  • Cardiac splicing as a diagnostic and therapeutic target. Nature reviews. Cardiology Gotthardt, M., Badillo-Lisakowski, V., Parikh, V. N., Ashley, E., Furtado, M., Carmo-Fonseca, M., Schudy, S., Meder, B., Grosch, M., Steinmetz, L., Crocini, C., Leinwand, L. 2023

    Abstract

    Despite advances in therapeutics for heart failure and arrhythmias, a substantial proportion of patients with cardiomyopathy do not respond to interventions, indicating a need to identify novel modifiable myocardial pathobiology. Human genetic variation associated with severe forms of cardiomyopathy and arrhythmias has highlighted the crucial role of alternative splicing in myocardial health and disease, given that it determines which mature RNA transcripts drive the mechanical, structural, signalling and metabolic properties of the heart. In this Review, we discuss how the analysis of cardiac isoform expression has been facilitated by technical advances in multiomics and long-read and single-cell sequencing technologies. The resulting insights into the regulation of alternative splicing - including theidentification of cardiac splice regulators as therapeutic targets and the development of a translational pipeline to evaluate splice modulators in human engineered heart tissue, animal models and clinical trials - provide a basis for improved diagnosis and therapy. Finally, we consider how the medical and scientific communities can benefit from facilitated acquisition and interpretation of splicing data towards improved clinical decision-making and patient care.

    View details for DOI 10.1038/s41569-022-00828-0

    View details for PubMedID 36653465

  • The mitochondrial multi-omic response to exercise training across tissues. bioRxiv : the preprint server for biology Amar, D., Gay, N. R., Jimenez-Morales, D., Beltran, P. M., Ramaker, M. E., Raja, A. N., Zhao, B., Sun, Y., Marwaha, S., Gaul, D., Hershman, S. G., Xia, A., Lanza, I., Fernandez, F. M., Montgomery, S. B., Hevener, A. L., Ashley, E. A., Walsh, M. J., Sparks, L. M., Burant, C. F., Rector, R. S., Thyfault, J., Wheeler, M. T., Goodpaster, B. H., Coen, P. M., Schenk, S., Bodine, S. C., Lindholm, M. E. 2023

    Abstract

    Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.

    View details for DOI 10.1101/2023.01.13.523698

    View details for PubMedID 36711881

    View details for PubMedCentralID PMC9882193

  • Defining left ventricular remodeling using lean body mass allometry: a UK Biobank study. European journal of applied physiology Gomes, B., Hedman, K., Kuznetsova, T., Cauwenberghs, N., Hsu, D., Kobayashi, Y., Ingelsson, E., Oxborough, D., George, K., Salerno, M., Ashley, E., Haddad, F. 2023

    Abstract

    PURPOSE: The geometric patterns of ventricular remodeling are determined using indexed left ventricular mass (LVM), end-diastolic volume (LVEDV) and concentricity, most often measured using the mass-to-volume ratio (MVR). The aims of this study were to validate lean body mass (LBM)-based allometric coefficients for scaling and to determine an index of concentricity that is independent of both volume and LBM.METHODS: Participants from the UK Biobank who underwent both CMR and dual-energy X-ray absorptiometry (DXA) during 2014-2015 were considered (n=5064). We excluded participants aged≥70years or those with cardiometabolic risk factors. We determined allometric coefficients for scaling using linear regression of the logarithmically transformed ventricular remodeling parameters. We further defined a multiplicative allometric relationship for LV concentricity (LVC) adjusting for both LVEDV and LBM.RESULTS: A total of 1638 individuals (1057 female) were included. In subjects with lower body fat percentage (<25% in males,<35% in females, n=644), the LBM allometric coefficients for scaling LVM and LVEDV were 0.85±0.06 and 0.85±0.03 respectively (R2=0.61 and 0.57, P<0.001), with no evidence of sex-allometry interaction. While the MVR was independent of LBM, it demonstrated a negative association with LVEDV in (females: r=-0.44, P<0.001; males: -0.38, P<0.001). In contrast, LVC was independent of both LVEDV and LBM [LVC=LVM/(LVEDV0.40*LBM0.50)] leading to increased overlap between LV hypertrophy and higher concentricity.CONCLUSIONS: We validated allometric coefficients for LBM-based scaling for CMR indexed parameters relevant for classifying geometric patterns of ventricular remodeling.

    View details for DOI 10.1007/s00421-022-05125-9

    View details for PubMedID 36617359

  • Generation of two human iPSC lines with Exon 3 mutations in BCL2-Associated Athanogene 3 (BAG3) from dilated cardiomyopathy patients. Stem cell research Zushin, P. H., Zhou, Y., Li, A., Ashley, E. A., Wheeler, M. T., Wu, J. C. 2023; 67: 103019

    Abstract

    Dilated cardiomyopathies (DCM) are one of the main causes of heart failure as one ages. BAG3 is a chaperone protein that is heavily implicated in the development of DCM and speed of progression toward heart failure. Here we generate two human iPSC lines from individuals with mutations in exon 3 of BAG3 and provide validation of their pluripotency and ability to differentiate toward the three primary germ layers. These two cell lines can help our understanding of BAG3 and its role in DCM by providing a good model for BAG3 inactivation and insufficiency.

    View details for DOI 10.1016/j.scr.2023.103019

    View details for PubMedID 36642055

  • Plain Language Summary of Publication of the safety and efficacy of ARRY-371797 in people with dilated cardiomyopathy and a faulty LMNA gene. Future cardiology MacRae, C. A., Taylor, M. R., Mestroni, L., Moses, J., Ashley, E. A., Wheeler, M. T., Lakdawala, N. K., Hershberger, R. E., Sandor, V., Saunders, M. E., Oliver, C., Lee, P. A., Judge, D. P. 2023

    Abstract

    WHAT IS THIS PLAIN LANGUAGE SUMMARY ABOUT?: This plain language summary describes the results of a study looking at the effects of a medicine called ARRY-371797 (also known as PF-07265803) in people with dilated cardiomyopathy (DCM for short) caused by a faulty LMNA gene. This condition is called LMNA-related DCM. DCM happens when the heart becomes bigger and weaker than normal, impacting functional capacity and leading to symptoms of heart failure. This means the heart is not able to pump blood around the body as easily, and people are unable to do as much in their daily lives (like getting dressed and going shopping). People may inherit a faulty LMNA gene from one of their parents, or a faulty LMNA gene may develop when mistakes happen during cell growth and replication. ARRY-371797 targets a specific mechanism in the body that can lead to heart problems in people with a faulty LMNA gene. As ARRY-371797 is not currently approved for use outside of clinical trials, it doesn't currently have an easily recognizable trade name.WHAT WERE THE RESULTS?: 12 American people (average age 50years) with LMNA-related DCM took part in the study and received 400mg or 100mg of ARRY-371797 twice daily for 48weeks. People knew which dose of ARRY-371797 they were taking. People were checked after 4, 12, 24, 36 and 48weeks of taking ARRY-371797 to see how far they could walk in the 6-minute walk test (6MWT for short). The level of NT-proBNP in their blood was also measured. NT-proBNP is a biomarker used to measure the severity of heart failure. A biomarker is something found in the body that can be measured to indicate the extent of a disease. -After taking ARRY-371797 for 12weeks, people were able to walk further in the 6MWT and had lower levels of NT-proBNP in their blood. This suggests improvement in functional capacity (exercise tolerance) and heart function. Researchers also asked people about their quality of life using the Kansas City Cardiomyopathy Questionnaire (KCCQ for short), and looked for any side effects. -Researchers saw some improvement in KCCQ scores. -Researchers saw no major side effects that they considered to be related to ARRY-371797 treatment. A side effect is something that people feel was caused by a medicine or treatment. Overall, this study showed that people with LMNA-related DCM who took ARRY-371797 had improved functional capacity (exercise tolerance), improved heart function, and improved quality of life. Phase 2 study (NCT02057341) Phase 2 long-term extension study (NCT02351856) Phase 3 REALM-DCM study (NCT03439514).

    View details for DOI 10.2217/fca-2022-0099

    View details for PubMedID 36718638

  • Development and validation of a rapid visual technique for left ventricular hypertrophy detection from the electrocardiogram. Frontiers in cardiovascular medicine Somani, S., Hughes, J. W., Ashley, E. A., Witteles, R. M., Perez, M. V. 2023; 10: 1251511

    Abstract

    Introduction: Left ventricular hypertrophy (LVH) detection techniques on by electrocardiogram (ECG) are cumbersome to remember with modest performance. This study validated a rapid technique for LVH detection and measured its performance against other techniques.Methods: This was a retrospective cohort study of patients at Stanford Health Care who received ECGs and resting transthoracic echocardiograms (TTE) from 2006 through 2018. The novel technique, Witteles-Somani (WS), assesses for S- and R-wave overlap on adjacent precordial leads. The WS, Sokolow-Lyon, Cornell, and Peguero-Lo Presti techniques were algorithmically implemented on ECGs. Classification metrics, receiver-operator curves, and Pearson correlations measured performance. Age- and sex-adjusted Cox proportional hazard models evaluated associations between incident cardiovascular outcomes and each technique.Results: A total of 53,333 ECG-TTE pairs from 18,873 patients were identified. Of all ECG-TTE pairs, 21,638 (40.6%) had TTE-diagnosed LVH. The WS technique had a sensitivity of 0.46, specificity of 0.66, and AUROC of 0.56, compared to Sokolow-Lyon (AUROC 0.55), Cornell (AUROC 0.63), and Peguero-Lo Presti (AUROC 0.63). Patients meeting LVH by WS technique had a higher risk of cardiovascular mortality [HR 1.18, 95% CI (1.12, 1.24), P<0.001] and a higher risk of developing any cardiovascular disease [HR 1.29, 95% CI (1.22, 1.36), P<0.001], myocardial infarction [HR 1.60, 95% CI (1.44, 1.78), P<0.005], and heart failure [HR 1.24, 95% CI (1.17, 1.32), P<0.001].Conclusions: The WS criteria is a rapid visual technique for LVH detection with performance like other LVH detection techniques and is associated with incident cardiovascular outcomes.

    View details for DOI 10.3389/fcvm.2023.1251511

    View details for PubMedID 37711561

  • HOMOZYGOUS FRAMESHIFT VARIANT IN LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3 IN A PATIENT WITH INTERSTITIAL LUNG DISEASE DUE TO POSSIBLE SURFACTANT PROTEIN DYSFUNCTION Keehan, L., Bonner, D., Kravets, E., Kohler, J., Reuter, C., Marwaha, S., Network, U., Fisher, P., Ashley, E., Wheeler, M., Bernstein, J. A. SAGE PUBLICATIONS LTD. 2023: NP389
  • CHARACTERIZATION OF TWO NOVEL DNASE1L3 VARIANTS IN A PATIENT WITH A MONOGENIC FORM OF SYSTEMIC LUPUS ERYTHEMATOSUS Leon, A., Vera, P. L., Bonner, D., Kohler, J., Reuter, C., Zastrow, D., Majcherska, M., Fernandez, L., McCormack, C., Marwaha, S., Fisher, P., Ashley, E., Maller, J., Hsu, J., Balboni, Bernstein, J., Wheeler, M., Gomez-Ospina, N. SAGE PUBLICATIONS LTD. 2023: NP391-NP392
  • Variant Location Is a Novel Risk Factor for Individuals With Arrhythmogenic Cardiomyopathy Due to a Desmoplakin (DSP) Truncating Variant. Circulation. Genomic and precision medicine Hoorntje, E. T., Burns, C., Marsili, L., Corden, B., Parikh, V. N., Te Meerman, G. J., Gray, B., Adiyaman, A., Bagnall, R. D., Barge-Schaapveld, D. Q., van den Berg, M. P., Bootsma, M., Bosman, L. P., Correnti, G., Duflou, J., Eppinga, R. N., Fatkin, D., Fietz, M., Haan, E., Jongbloed, J. D., Hauer, A. D., Lam, L., van Lint, F. H., Lota, A., Marcelis, C., McCarthy, H. J., van Mil, A. M., Oldenburg, R. A., Pachter, N., Planken, R. N., Reuter, C., Semsarian, C., van der Smagt, J. J., Thompson, T., Vohra, J., Volders, P. G., van Waning, J. I., Whiffin, N., van den Wijngaard, A., Amin, A. S., Wilde, A. A., van Woerden, G., Yeates, L., Zentner, D., Ashley, E. A., Wheeler, M. T., Ware, J. S., van Tintelen, J. P., Ingles, J. 2022: e003672

    Abstract

    Truncating variants in desmoplakin (DSPtv) are an important cause of arrhythmogenic cardiomyopathy; however the genetic architecture and genotype-specific risk factors are incompletely understood. We evaluated phenotype, risk factors for ventricular arrhythmias, and underlying genetics of DSPtv cardiomyopathy.Individuals with DSPtv and any cardiac phenotype, and their gene-positive family members were included from multiple international centers. Clinical data and family history information were collected. Event-free survival from ventricular arrhythmia was assessed. Variant location was compared between cases and controls, and literature review of reported DSPtv performed.There were 98 probands and 72 family members (mean age at diagnosis 43±8 years, 59% women) with a DSPtv, of which 146 were considered clinically affected. Ventricular arrhythmia (sudden cardiac arrest, sustained ventricular tachycardia, appropriate implantable cardioverter defibrillator therapy) occurred in 56 (33%) individuals. DSPtv location and proband status were independent risk factors for ventricular arrhythmia. Further, gene region was important with variants in cases (cohort n=98; Clinvar n=167) more likely to occur in the regions, resulting in nonsense mediated decay of both major DSP isoforms, compared with n=124 gnomAD control variants (148 [83.6%] versus 29 [16.4%]; P<0.0001).In the largest series of individuals with DSPtv, we demonstrate that variant location is a novel risk factor for ventricular arrhythmia, can inform variant interpretation, and provide critical insights to allow for precision-based clinical management.

    View details for DOI 10.1161/CIRCGEN.121.003672

    View details for PubMedID 36580316

  • Efficacy and Safety of ARRY-371797 in LMNA-Related Dilated Cardiomyopathy: A Phase 2 Study. Circulation. Genomic and precision medicine MacRae, C. A., Taylor, M. R., Mestroni, L., Moses, J., Ashley, E. A., Wheeler, M. T., Lakdawala, N. K., Hershberger, R. E., Sandor, V., Saunders, M. E., Oliver, C., Lee, P. A., Judge, D. P. 2022: e003730

    Abstract

    BACKGROUND: Lamin A/C gene (LMNA)-related dilated cardiomyopathy is a serious and life-threatening condition with a high unmet medical need. This phase 2 study assessed the effects of the oral selective p38 mitogen-activated protein kinase inhibitor ARRY-371797 on functional capacity and cardiac function in patients with LMNA-related dilated cardiomyopathy.METHODS: Patients with LMNA-related dilated cardiomyopathy in New York Heart Association class II-IIIA, on background heart failure treatment, received ARRY-371797 100 or 400 mg twice daily for 48 weeks. The primary end point was change from baseline in the 6-minute walk test distance at 12 weeks. Secondary end points included changes over time in 6-minute walk test distance, NT-proBNP (N-terminal pro-B-type natriuretic peptide) concentration, left ventricular ejection fraction, and quality-of-life scores on the Kansas City Cardiomyopathy Questionnaire. Data from the 2 dose groups were combined.RESULTS: Twelve patients were enrolled; median (minimum, maximum) 6-minute walk test distance at baseline was 314 (246, 412) m. At week 12, the mean (80% CI) increase from baseline in 6-minute walk test distance was 69 (39, 100) m (median, 47 m). Median NT-proBNP concentration declined from 1409 pg/mL at baseline to 848 pg/mL at week 12. Mean left ventricular ejection fraction was stable at week 12. There was a trend toward improvement in Kansas City Cardiomyopathy Questionnaire Overall and Clinical Summary scores at week 12. No clinically significant drug-related safety concerns were identified.CONCLUSIONS: ARRY-371797 was well tolerated and resulted in increases in functional capacity and lower concentrations of cardiac biomarker NT-proBNP in patients with LMNA-related dilated cardiomyopathy.REGISTRATION: URL: https://clinicaltrials.gov; Unique identifier: NCT02057341.

    View details for DOI 10.1161/CIRCGEN.122.003730

    View details for PubMedID 36515663

  • Polygenic risk scores for the prediction of cardiometabolic disease. European heart journal O'Sullivan, J. W., Ashley, E. A., Elliott, P. M. 2022

    Abstract

    Cardiometabolic diseases contribute more to global morbidity and mortality than any other group of disorders. Polygenic risk scores (PRSs), the weighted summation of individually small-effect genetic variants, represent an advance in our ability to predict the development and complications of cardiometabolic diseases. This article reviews the evidence supporting the use of PRS in seven common cardiometabolic diseases: coronary artery disease (CAD), stroke, hypertension, heart failure and cardiomyopathies, obesity, atrial fibrillation (AF), and type 2 diabetes mellitus (T2DM). Data suggest that PRS for CAD, AF, and T2DM consistently improves prediction when incorporated into existing clinical risk tools. In other areas such as ischaemic stroke and hypertension, clinical application appears premature but emerging evidence suggests that the study of larger and more diverse populations coupled with more granular phenotyping will propel the translation of PRS into practical clinical prediction tools.

    View details for DOI 10.1093/eurheartj/ehac648

    View details for PubMedID 36478054

  • Case-Control cardiopulmonary exercise testing for patients with neuromuscular disease Duong, T., Parker, D., Stevens, V., Young, S., Tang, W., Myers, J., Ashley, E., Wheeler, M., Christle, J. PERGAMON-ELSEVIER SCIENCE LTD. 2022: S75
  • Mobile Health Study Incorporating Novel Fitness Test. Journal of cardiovascular translational research Johnson, A., Hershman, S. G., Javed, A., Mattsson, C. M., Christle, J., Oppezzo, M., Ashley, E. A. 2022

    Abstract

    Mobile health (mHealth) is a rapidly expanding field within precision medicine and precision health that provides healthcare support and interventions using mobile technologies, such as smartphones and smartwatches. The growing ubiquity of commercial wireless signals and smartphones allows mHealth technologies to have a substantially broader reach than traditional healthcare networks. My Fitness Counts, a cross-platform My Heart Counts spinout study, is a pioneer cross-platform mHealth study for measuring cardiovascular fitness levels. The study uses Real-World Insights, a platform designed to host mHealth studies. In this paper, we present insights gained through the quality control process undertaken prior to the release of the cross-platform mHealth study My Fitness Counts. Through extensive testing of the 21 iOS and 11 Android builds of the application, over 70 bugs were identified and corrected during the 5-month development process of My Fitness Counts.

    View details for DOI 10.1007/s12265-022-10317-x

    View details for PubMedID 36136239

  • Mind the Gap: The Complete Human Genome Unlocks Benefits for Clinical Genomics. Clinical chemistry Kim, D. S., Wiel, L., Ashley, E. A. 2022

    View details for DOI 10.1093/clinchem/hvac133

    View details for PubMedID 36112529

  • Multimodal deep learning enhances diagnostic precision in left ventricular hypertrophy. European heart journal. Digital health Soto, J. T., Weston Hughes, J., Sanchez, P. A., Perez, M., Ouyang, D., Ashley, E. A. 2022; 3 (3): 380-389

    Abstract

    Aims: Determining the aetiology of left ventricular hypertrophy (LVH) can be challenging due to the similarity in clinical presentation and cardiac morphological features of diverse causes of disease. In particular, distinguishing individuals with hypertrophic cardiomyopathy (HCM) from the much larger set of individuals with manifest or occult hypertension (HTN) is of major importance for family screening and the prevention of sudden death. We hypothesized that an artificial intelligence method based joint interpretation of 12-lead electrocardiograms and echocardiogram videos could augment physician interpretation.Methods and results: We chose not to train on proximate data labels such as physician over-reads of ECGs or echocardiograms but instead took advantage of electronic health record derived clinical blood pressure measurements and diagnostic consensus (often including molecular testing) among physicians in an HCM centre of excellence. Using more than 18000 combined instances of electrocardiograms and echocardiograms from 2728 patients, we developed LVH-fusion. On held-out test data, LVH-fusion achieved an F1-score of 0.71 in predicting HCM, and 0.96 in predicting HTN. In head-to-head comparison with human readers LVH-fusion had higher sensitivity and specificity rates than its human counterparts. Finally, we use explainability techniques to investigate local and global features that positively and negatively impact LVH-fusion prediction estimates providing confirmation from unsupervised analysis the diagnostic power of lateral T-wave inversion on the ECG and proximal septal hypertrophy on the echocardiogram for HCM.Conclusion: These results show that deep learning can provide effective physician augmentation in the face of a common diagnostic dilemma with far reaching implications for the prevention of sudden cardiac death.

    View details for DOI 10.1093/ehjdh/ztac033

    View details for PubMedID 36712167

  • Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nature communications Parikh, V. N., Ioannidis, A. G., Jimenez-Morales, D., Gorzynski, J. E., De Jong, H. N., Liu, X., Roque, J., Cepeda-Espinoza, V. P., Osoegawa, K., Hughes, C., Sutton, S. C., Youlton, N., Joshi, R., Amar, D., Tanigawa, Y., Russo, D., Wong, J., Lauzon, J. T., Edelson, J., Mas Montserrat, D., Kwon, Y., Rubinacci, S., Delaneau, O., Cappello, L., Kim, J., Shoura, M. J., Raja, A. N., Watson, N., Hammond, N., Spiteri, E., Mallempati, K. C., Montero-Martín, G., Christle, J., Kim, J., Kirillova, A., Seo, K., Huang, Y., Zhao, C., Moreno-Grau, S., Hershman, S. G., Dalton, K. P., Zhen, J., Kamm, J., Bhatt, K. D., Isakova, A., Morri, M., Ranganath, T., Blish, C. A., Rogers, A. J., Nadeau, K., Yang, S., Blomkalns, A., O'Hara, R., Neff, N. F., DeBoever, C., Szalma, S., Wheeler, M. T., Gates, C. M., Farh, K., Schroth, G. P., Febbo, P., deSouza, F., Cornejo, O. E., Fernandez-Vina, M., Kistler, A., Palacios, J. A., Pinsky, B. A., Bustamante, C. D., Rivas, M. A., Ashley, E. A. 2022; 13 (1): 5107

    Abstract

    The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.

    View details for DOI 10.1038/s41467-022-32397-8

    View details for PubMedID 36042219

  • Polygenic Risk Scores for Cardiovascular Disease: A Scientific Statement From the American Heart Association CIRCULATION O'Sullivan, J. W., Raghavan, S., Marquez-Luna, C., Luzum, J. A., Damrauer, S. M., Ashley, E. A., O'Donnell, C. J., Willer, C. J., Natarajan, P., Amer Heart Assoc Council Genomic, Council Clinical Cardiology, Council Arteriosclerosis Thrombosi, Council Cardiovasc Radiology Inter, Council Lifestyle Cardiometab Hlth, Council Peripheral Vasc Dis 2022; 146 (8): E93-E118

    Abstract

    Cardiovascular disease is the leading contributor to years lost due to disability or premature death among adults. Current efforts focus on risk prediction and risk factor mitigation' which have been recognized for the past half-century. However, despite advances, risk prediction remains imprecise with persistently high rates of incident cardiovascular disease. Genetic characterization has been proposed as an approach to enable earlier and potentially tailored prevention. Rare mendelian pathogenic variants predisposing to cardiometabolic conditions have long been known to contribute to disease risk in some families. However, twin and familial aggregation studies imply that diverse cardiovascular conditions are heritable in the general population. Significant technological and methodological advances since the Human Genome Project are facilitating population-based comprehensive genetic profiling at decreasing costs. Genome-wide association studies from such endeavors continue to elucidate causal mechanisms for cardiovascular diseases. Systematic cataloging for cardiovascular risk alleles also enabled the development of polygenic risk scores. Genetic profiling is becoming widespread in large-scale research, including in health care-associated biobanks, randomized controlled trials, and direct-to-consumer profiling in tens of millions of people. Thus, individuals and their physicians are increasingly presented with polygenic risk scores for cardiovascular conditions in clinical encounters. In this scientific statement, we review the contemporary science, clinical considerations, and future challenges for polygenic risk scores for cardiovascular diseases. We selected 5 cardiometabolic diseases (coronary artery disease, hypercholesterolemia, type 2 diabetes, atrial fibrillation, and venous thromboembolic disease) and response to drug therapy and offer provisional guidance to health care professionals, researchers, policymakers, and patients.

    View details for DOI 10.1161/CIR.0000000000001077

    View details for Web of Science ID 000841526000003

    View details for PubMedID 35862132

  • Impact of SARS-Cov-2 infection in patients with hypertrophic cardiomyopathy: results of an international multicentre registry. ESC heart failure Gimeno, J. R., Olivotto, I., Rodríguez, A. I., Ho, C. Y., Fernández, A., Quiroga, A., Espinosa, M. A., Gómez-González, C., Robledo, M., Tojal-Sierra, L., Day, S. M., Owens, A., Barriales-Villa, R., Larrañaga, J. M., Rodríguez-Palomares, J., González-Del-Hoyo, M., Piqueras-Flores, J., Reza, N., Chumakova, O., Ashley, E. A., Parikh, V., Wheeler, M., Jacoby, D., Pereira, A. C., Saberi, S., Helms, A. S., Villacorta, E., Gallego-Delgado, M., de Castro, D., Domínguez, F., Ripoll-Vera, T., Zorio-Grima, E., Sánchez-Martínez, J. C., García-Álvarez, A., Arbelo, E., Mogollón, M. V., Fuentes-Cañamero, M. E., Grande, E., Peña, C., Monserrat, L., Lakdawala, N. K. 2022; 9 (4): 2189-2198

    Abstract

    To describe the natural history of SARS-CoV-2 infection in patients with hypertrophic cardiomyopathy (HCM) compared with a control group and to identify predictors of adverse events.Three hundred and five patients [age 56.6 ± 16.9 years old, 191 (62.6%) male patients] with HCM and SARS-Cov-2 infection were enrolled. The control group consisted of 91 131 infected individuals. Endpoints were (i) SARS-CoV-2 related mortality and (ii) severe clinical course [death or intensive care unit (ICU) admission]. New onset of atrial fibrillation, ventricular arrhythmias, shock, stroke, and cardiac arrest were also recorded. Sixty-nine (22.9%) HCM patients were hospitalized for non-ICU level care, and 21 (7.0%) required ICU care. Seventeen (5.6%) died: eight (2.6%) of respiratory failure, four (1.3%) of heart failure, two (0.7%) suddenly, and three (1.0%) due to other SARS-CoV-2-related complications. Covariates associated with mortality in the multivariable were age {odds ratio (OR) per 10 year increase 2.25 [95% confidence interval (CI): 1.12-4.51], P = 0.0229}, baseline New York Heart Association class [OR per one-unit increase 4.01 (95%CI: 1.75-9.20), P = 0.0011], presence of left ventricular outflow tract obstruction [OR 5.59 (95%CI: 1.16-26.92), P = 0.0317], and left ventricular systolic impairment [OR 7.72 (95%CI: 1.20-49.79), P = 0.0316]. Controlling for age and sex and comparing HCM patients with a community-based SARS-CoV-2 cohort, the presence of HCM was associated with a borderline significant increased risk of mortality OR 1.70 (95%CI: 0.98-2.91, P = 0.0600).Over one-fourth of HCM patients infected with SARS-Cov-2 required hospitalization, including 6% in an ICU setting. Age and cardiac features related to HCM, including baseline functional class, left ventricular outflow tract obstruction, and systolic impairment, conveyed increased risk of mortality.

    View details for DOI 10.1002/ehf2.13964

    View details for PubMedID 36255281

  • Temporal dynamics of the multi-omic response to endurance exercise training across tissues Gay, N. R., Beltran, P., Amar, D., Montgomery, S. B., Carr, S. A., Motrpac Study Grp ELSEVIER. 2022: S31
  • European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. Journal of arrhythmia Wilde, A. A., Semsarian, C., Márquez, M. F., Sepehri Shamloo, A., Ackerman, M. J., Ashley, E. A., Sternick Eduardo, B., Barajas-Martinez, H., Behr, E. R., Bezzina, C. R., Breckpot, J., Charron, P., Chockalingam, P., Crotti, L., Gollob, M. H., Lubitz, S., Makita, N., Ohno, S., Ortiz-Genga, M., Sacilotto, L., Schulze-Bahr, E., Shimizu, W., Sotoodehnia, N., Tadros, R., Ware, J. S., Winlaw, D. S., Kaufman, E. S., Aiba, T., Bollmann, A., Choi, J. I., Dalal, A., Darrieux, F., Giudicessi, J., Guerchicoff, M., Hong, K., Krahn, A. D., Mac Intyre, C., Mackall, J. A., Mont, L., Napolitano, C., Ochoa Juan, P., Peichl, P., Pereira, A. C., Schwartz, P. J., Skinner, J., Stellbrink, C., Tfelt-Hansen, J., Deneke, T. 2022; 38 (4): 491-553

    View details for DOI 10.1002/joa3.12717

    View details for PubMedID 35936045

    View details for PubMedCentralID PMC9347209

  • ISARIC-COVID-19 dataset: A Prospective, Standardized, Global Dataset of Patients Hospitalized with COVID-19 SCIENTIFIC DATA Garcia-Gallo, E., Merson, L., Kennon, K., Kelly, S., Citarella, B., Fryer, D., Shrapnel, S., Lee, J., Duque, S., Fuentes, Y. V., Balan, V., Smith, S., Wei, J., Goncalves, B. P., Russell, C. D., Sigfrid, L., Dagens, A., Olliaro, P. L., Baruch, J., Kartsonaki, C., Dunning, J., Rojek, A., Rashan, A., Beane, A., Murthy, S., Reyes, L., ISARIC Clinical Characterization G 2022; 9 (1): 454

    Abstract

    The International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) COVID-19 dataset is one of the largest international databases of prospectively collected clinical data on people hospitalized with COVID-19. This dataset was compiled during the COVID-19 pandemic by a network of hospitals that collect data using the ISARIC-World Health Organization Clinical Characterization Protocol and data tools. The database includes data from more than 705,000 patients, collected in more than 60 countries and 1,500 centres worldwide. Patient data are available from acute hospital admissions with COVID-19 and outpatient follow-ups. The data include signs and symptoms, pre-existing comorbidities, vital signs, chronic and acute treatments, complications, dates of hospitalization and discharge, mortality, viral strains, vaccination status, and other data. Here, we present the dataset characteristics, explain its architecture and how to gain access, and provide tools to facilitate its use.

    View details for DOI 10.1038/s41597-022-01534-9

    View details for Web of Science ID 000833501200005

    View details for PubMedID 35908040

    View details for PubMedCentralID PMC9339000

  • Supporting undiagnosed participants when clinical genomics studies end. Nature genetics Halley, M. C., Ashley, E. A., Tabor, H. K. 2022

    View details for DOI 10.1038/s41588-022-01150-8

    View details for PubMedID 35902745

  • Author Correction: Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nature genetics Turner, A. W., Hu, S. S., Mosquera, J. V., Ma, W. F., Hodonsky, C. J., Wong, D., Auguste, G., Song, Y., Sol-Church, K., Farber, E., Kundu, S., Kundaje, A., Lopez, N. G., Ma, L., Ghosh, S. K., Onengut-Gumuscu, S., Ashley, E. A., Quertermous, T., Finn, A. V., Leeper, N. J., Kovacic, J. C., Björkegren, J. L., Zang, C., Miller, C. L. 2022

    View details for DOI 10.1038/s41588-022-01142-8

    View details for PubMedID 35768727

  • Wnt Signaling Interactor WTIP (Wilms Tumor Interacting Protein) Underlies Novel Mechanism for Cardiac Hypertrophy. Circulation. Genomic and precision medicine De Jong, H. N., Dewey, F. E., Cordero, P., Victorio, R. A., Kirillova, A., Huang, Y., Madhvani, R., Seo, K., Werdich, A. A., Lan, F., Orcholski, M., Robert Liu, W., Erbilgin, A., Wheeler, M. T., Chen, R., Pan, S., Kim, Y. M., Bommakanti, K., Marcou, C. A., Martijn Bos, J., Haddad, F., Ackerman, M., Vasan, R. S., MacRae, C., Wu, J. C., de Jesus Perez, V., Snyder, M., Parikh, V. N., Ashley, E. A. 2022: 101161CIRCGEN121003563

    Abstract

    BACKGROUND: The study of hypertrophic cardiomyopathy (HCM)-a severe Mendelian disease-can yield insight into the mechanisms underlying the complex trait of cardiac hypertrophy. To date, most genetic variants associated with HCM have been found in sarcomeric genes. Here, we describe a novel HCM-associated variant in the noncanonical Wnt signaling interactor WTIP (Wilms tumor interacting protein) and provide evidence of a role for WTIP in complex disease.METHODS: In a family affected by HCM, we used exome sequencing and identity-by-descent analysis to identify a novel variant in WTIP (p.Y233F). We knocked down WTIP in isolated neonatal rat ventricular myocytes with lentivirally delivered shRNAs and in Danio rerio via morpholino injection. We performed weighted gene coexpression network analysis for WTIP in human cardiac tissue, as well as association analysis for WTIP variation and left ventricular hypertrophy. Finally, we generated induced pluripotent stem cell-derived cardiomyocytes from patient tissue, characterized size and calcium cycling, and determined the effect of verapamil treatment on calcium dynamics.RESULTS: WTIP knockdown caused hypertrophy in neonatal rat ventricular myocytes and increased cardiac hypertrophy, peak calcium, and resting calcium in D rerio. Network analysis of human cardiac tissue indicated WTIP as a central coordinator of prohypertrophic networks, while common variation at the WTIP locus was associated with human left ventricular hypertrophy. Patient-derived WTIP p.Y233F-induced pluripotent stem cell-derived cardiomyocytes recapitulated cellular hypertrophy and increased resting calcium, which was ameliorated by verapamil.CONCLUSIONS: We demonstrate that a novel genetic variant found in a family with HCM disrupts binding to a known Wnt signaling protein, misregulating cardiomyocyte calcium dynamics. Further, in orthogonal model systems, we show that expression of the gene WTIP is important in complex cardiac hypertrophy phenotypes. These findings, derived from the observation of a rare Mendelian disease variant, uncover a novel disease mechanism with implications across diverse forms of cardiac hypertrophy.

    View details for DOI 10.1161/CIRCGEN.121.003563

    View details for PubMedID 35671065

  • Impact of SARS-Cov-2 infection in patients with hypertrophic cardiomyopathy: results of an international multicentre registry ESC HEART FAILURE Gimeno, J. R., Olivotto, I., Isabel Rodriguez, A., Ho, C. Y., Fernandez, A., Quiroga, A., Angeles Espinosa, M., Gomez-Gonzalez, C., Robledo, M., Tojal-Sierra, L., Day, S. M., Owens, A., Barriales-Villa, R., Maria Larranaga, J., Rodriguez-Palomares, J., Gonzalez-del-Hoyo, M., Piqueras-Flores, J., Reza, N., Chumakova, O., Ashley, E. A., Parikh, V., Wheeler, M., Jacoby, D., Pereira, A. C., Saberi, S., Helms, A. S., Villacorta, E., Gallego-Delgado, M., Castro, D., Dominguez, F., Ripoll-Vera, T., Zorio-Grima, E., Carlos Sanchez-Martinez, J., Garcia-Alvarez, A., Arbelo, E., Victoria Mogollon, M., Eugenia Fuentes-Canamero, M., Grande, E., Pena, C., Monserrat, L., Lakdawala, N. K., Dilema Int Cardiomyopathy Heart Fa 2022

    View details for DOI 10.1002/ehf2.13964

    View details for Web of Science ID 000805160500001

  • European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases JOURNAL OF ARRHYTHMIA Wilde, A. M., Semsarian, C., Marquez, M. F., Shamloo, A., Ackerman, M. J., Ashley, E. A., Eduardo, B., Barajas-Martinez, H., Behr, E. R., Bezzina, C. R., Breckpot, J., Charron, P., Chockalingam, P., Crotti, L., Gollob, M. H., Lubitz, S., Makita, N., Ohno, S., Ortiz-Genga, M., Sacilotto, L., Schulze-Bahr, E., Shimizu, W., Sotoodehnia, N., Tadros, R., Ware, J. S., Winlaw, D. S., Kaufman, E. S., Aiba, T., Bollmann, A., Choi, J., Dalal, A., Darrieux, F., Giudicessi, J., Guerchicoff, M., Hong, K., Krahn, A. D., Mac Intyre, C., Mackall, J. A., Mont, L., Napolitano, C., Ochoa Juan, P., Peichl, P., Pereira, A. C., Schwartz, P. J., Skinner, J., Stellbrink, C., Tfelt-Hansen, J., Deneke, T. 2022

    View details for DOI 10.1002/joa3.12717

    View details for Web of Science ID 000822658500001

  • Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk. Nature genetics Turner, A. W., Hu, S. S., Mosquera, J. V., Ma, W. F., Hodonsky, C. J., Wong, D., Auguste, G., Song, Y., Sol-Church, K., Farber, E., Kundu, S., Kundaje, A., Lopez, N. G., Ma, L., Ghosh, S. K., Onengut-Gumuscu, S., Ashley, E. A., Quertermous, T., Finn, A. V., Leeper, N. J., Kovacic, J. C., Björkgren, J. L., Zang, C., Miller, C. L. 2022

    Abstract

    Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements. Here, we applied single-nucleus assay for transposase-accessible chromatin with sequencing to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell-type-specific elements and transcription factors, and prioritized functional CAD risk variants. We identified elements in smooth muscle cell transition states (for example, fibromyocytes) and functional variants predicted to alter smooth muscle cell- and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single-nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.

    View details for DOI 10.1038/s41588-022-01069-0

    View details for PubMedID 35590109

  • European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology Wilde, A. A., Semsarian, C., Marquez, M. F., Sepehri Shamloo, A., Ackerman, M. J., Ashley, E. A., Sternick, E. B., Barajas-Martinez, H., Behr, E. R., Bezzina, C. R., Breckpot, J., Charron, P., Chockalingam, P., Crotti, L., Gollob, M. H., Lubitz, S., Makita, N., Ohno, S., Ortiz-Genga, M., Sacilotto, L., Schulze-Bahr, E., Shimizu, W., Sotoodehnia, N., Tadros, R., Ware, J. S., Winlaw, D. S., Kaufman, E. S., ESC Scientific Document Group, Aiba, T., Bollmann, A., Choi, J., Dalal, A., Darrieux, F., Giudicessi, J., Guerchicoff, M., Hong, K., Krahn, A. D., MacIntyre, C., Mackall, J. A., Mont, L., Napolitano, C., Ochoa, J. P., Peichl, P., Pereira, A. C., Schwartz, P. J., Skinner, J., Stellbrink, C., Tfelt-Hansen, J., Deneke, T. 2022

    View details for DOI 10.1093/europace/euac030

    View details for PubMedID 35373836

  • European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) Expert Consensus Statement on the state of genetic testing for cardiac diseases. Heart rhythm Wilde, A. A., Semsarian, C., Márquez, M. F., Shamloo, A. S., Ackerman, M. J., Ashley, E. A., Sternick, E. B., Barajas-Martinez, H., Behr, E. R., Bezzina, C. R., Breckpot, J., Charron, P., Chockalingam, P., Crotti, L., Gollob, M. H., Lubitz, S., Makita, N., Ohno, S., Ortiz-Genga, M., Sacilotto, L., Schulze-Bahr, E., Shimizu, W., Sotoodehnia, N., Tadros, R., Ware, J. S., Winlaw, D. S., Kaufman, E. S. 2022

    View details for DOI 10.1016/j.hrthm.2022.03.1225

    View details for PubMedID 35390533

  • ANALYZING PROGRESSION OF DISEASE IN HYPERTROPHIC CARDIOMYOPATHY UTILIZING SEQUENTIAL CARDIOPULMONARY EXERCISE TESTING Devareddy, A., Busque, V., Haddad, F., Myers, J. N., Christle, J., Ashley, E. A., Wheeler, M. ELSEVIER SCIENCE INC. 2022: 241
  • A call for an integrated approach to improve efficiency, equity and sustainability in rare disease research in the United States. Nature genetics Halley, M. C., Smith, H. S., Ashley, E. A., Goldenberg, A. J., Tabor, H. K. 2022

    View details for DOI 10.1038/s41588-022-01027-w

    View details for PubMedID 35256804

  • A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome medicine Marwaha, S., Knowles, J. W., Ashley, E. A. 2022; 14 (1): 23

    Abstract

    Rare diseases affect 30 million people in the USA and more than 300-400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25-35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.

    View details for DOI 10.1186/s13073-022-01026-w

    View details for PubMedID 35220969

  • High-Throughput Precision Phenotyping of Left Ventricular Hypertrophy With Cardiovascular Deep Learning. JAMA cardiology Duffy, G., Cheng, P. P., Yuan, N., He, B., Kwan, A. C., Shun-Shin, M. J., Alexander, K. M., Ebinger, J., Lungren, M. P., Rader, F., Liang, D. H., Schnittger, I., Ashley, E. A., Zou, J. Y., Patel, J., Witteles, R., Cheng, S., Ouyang, D. 2022

    Abstract

    Importance: Early detection and characterization of increased left ventricular (LV) wall thickness can markedly impact patient care but is limited by under-recognition of hypertrophy, measurement error and variability, and difficulty differentiating causes of increased wall thickness, such as hypertrophy, cardiomyopathy, and cardiac amyloidosis.Objective: To assess the accuracy of a deep learning workflow in quantifying ventricular hypertrophy and predicting the cause of increased LV wall thickness.Design, Settings, and Participants: This cohort study included physician-curated cohorts from the Stanford Amyloid Center and Cedars-Sinai Medical Center (CSMC) Advanced Heart Disease Clinic for cardiac amyloidosis and the Stanford Center for Inherited Cardiovascular Disease and the CSMC Hypertrophic Cardiomyopathy Clinic for hypertrophic cardiomyopathy from January 1, 2008, to December 31, 2020. The deep learning algorithm was trained and tested on retrospectively obtained independent echocardiogram videos from Stanford Healthcare, CSMC, and the Unity Imaging Collaborative.Main Outcomes and Measures: The main outcome was the accuracy of the deep learning algorithm in measuring left ventricular dimensions and identifying patients with increased LV wall thickness diagnosed with hypertrophic cardiomyopathy and cardiac amyloidosis.Results: The study included 23 745 patients: 12 001 from Stanford Health Care (6509 [54.2%] female; mean [SD] age, 61.6 [17.4] years) and 1309 from CSMC (808 [61.7%] female; mean [SD] age, 62.8 [17.2] years) with parasternal long-axis videos and 8084 from Stanford Health Care (4201 [54.0%] female; mean [SD] age, 69.1 [16.8] years) and 2351 from CSMS (6509 [54.2%] female; mean [SD] age, 69.6 [14.7] years) with apical 4-chamber videos. The deep learning algorithm accurately measured intraventricular wall thickness (mean absolute error [MAE], 1.2 mm; 95% CI, 1.1-1.3 mm), LV diameter (MAE, 2.4 mm; 95% CI, 2.2-2.6 mm), and posterior wall thickness (MAE, 1.4 mm; 95% CI, 1.2-1.5 mm) and classified cardiac amyloidosis (area under the curve [AUC], 0.83) and hypertrophic cardiomyopathy (AUC, 0.98) separately from other causes of LV hypertrophy. In external data sets from independent domestic and international health care systems, the deep learning algorithm accurately quantified ventricular parameters (domestic: R2, 0.96; international: R2, 0.90). For the domestic data set, the MAE was 1.7 mm (95% CI, 1.6-1.8 mm) for intraventricular septum thickness, 3.8 mm (95% CI, 3.5-4.0 mm) for LV internal dimension, and 1.8 mm (95% CI, 1.7-2.0 mm) for LV posterior wall thickness. For the international data set, the MAE was 1.7 mm (95% CI, 1.5-2.0 mm) for intraventricular septum thickness, 2.9 mm (95% CI, 2.4-3.3 mm) for LV internal dimension, and 2.3 mm (95% CI, 1.9-2.7 mm) for LV posterior wall thickness. The deep learning algorithm accurately detected cardiac amyloidosis (AUC, 0.79) and hypertrophic cardiomyopathy (AUC, 0.89) in the domestic external validation site.Conclusions and Relevance: In this cohort study, the deep learning model accurately identified subtle changes in LV wall geometric measurements and the causes of hypertrophy. Unlike with human experts, the deep learning workflow is fully automated, allowing for reproducible, precise measurements, and may provide a foundation for precision diagnosis of cardiac hypertrophy.

    View details for DOI 10.1001/jamacardio.2021.6059

    View details for PubMedID 35195663

  • Association of Titin Variations With Late-Onset Dilated Cardiomyopathy. JAMA cardiology Cannata, A., Merlo, M., Dal Ferro, M., Barbati, G., Manca, P., Paldino, A., Graw, S., Gigli, M., Stolfo, D., Johnson, R., Roy, D., Tharratt, K., Bromage, D. I., Jirikowic, J., Abbate, A., Goodwin, A., Rao, K., Marawan, A., Carr-White, G., Robert, L., Parikh, V., Ashley, E., McDonagh, T., Lakdawala, N. K., Fatkin, D., Taylor, M. R., Mestroni, L., Sinagra, G. 2022

    Abstract

    Importance: Dilated cardiomyopathy (DCM) is frequently caused by genetic factors. Studies identifying deleterious rare variants have predominantly focused on early-onset cases, and little is known about the genetic underpinnings of the growing numbers of patients with DCM who are diagnosed when they are older than 60 years (ie, late-onset DCM).Objective: To investigate the prevalence, type, and prognostic impact of disease-associated rare variants in patients with late-onset DCM.Design, Setting, and Participants: A population of patients with late-onset DCM who had undergone genetic testing in 7 international tertiary referral centers worldwide were enrolled from March 1990 to August 2020. A positive genotype was defined as the presence of pathogenic or likely pathogenic (P/LP) variants.Main Outcomes and Measures: The study outcome was all-cause mortality.Results: A total of 184 patients older than 60 years (103 female [56%]; mean [SD] age, 67[6] years; mean [SD] left ventricular ejection fraction, 32%[10%]) were studied. Sixty-six patients (36%) were carriers of a P/LP variant. Titin-truncating variants were the most prevalent (present in 46 [25%] of the total population and accounting for 46 [69%] of all genotype-positive patients). During a median (interquartile range) follow-up of 42 (10-115) months, 23 patients (13%) died; 17 (25%) of these were carriers of P/LP variants, while 6 patients (5.1%) were genotype-negative.Conclusions and Relevance: Late-onset DCM might represent a distinct subgroup characterized by and a high genetic variation burden, largely due to titin-truncating variants. Patients with a positive genetic test had higher mortality than genotype-negative patients. These findings support the extended use of genetic testing also in older patients.

    View details for DOI 10.1001/jamacardio.2021.5890

    View details for PubMedID 35138330

  • Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circulation. Genomic and precision medicine Gorzynski, J. E., Goenka, S. D., Shafin, K., Jensen, T. D., Fisk, D. G., Grove, M. E., Spiteri, E., Pesout, T., Monlong, J., Bernstein, J. A., Ceresnak, S., Chang, P., Christle, J. W., Chubb, H., Dunn, K., Garalde, D. R., Guillory, J., Ruzhnikov, M. R., Wright, C., Wusthoff, C. J., Xiong, K., Hollander, S. A., Berry, G. J., Jain, M., Sedlazeck, F. J., Carroll, A., Paten, B., Ashley, E. A. 2022: CIRCGEN121003591

    View details for DOI 10.1161/CIRCGEN.121.003591

    View details for PubMedID 35133172

  • Causative Variants for Inherited Cardiac Conditions in a Southeast Asian Population Cohort. Circulation. Genomic and precision medicine Tomar, S., Klinzing, D. C., Kit, C. C., Gan, L. H., Moscarello, T., Reuter, C., Ashley, E. A., Foo, R. 2022: CIRCGEN121003536

    Abstract

    BACKGROUND: Variable penetrance and late-onset phenotypes are key challenges for classifying causal as well as incidental findings in inherited cardiac conditions. Allele frequencies of variants in ancestry-specific populations, along with clinical variant analysis and interpretation, are critical to determine their true significance.METHODS: Here, we carefully reviewed and classified variants in genes associated with inherited cardiac conditions based on a population whole-genome sequencing cohort of 4810 Singaporeans representing Southeast Asian ancestries.RESULTS: Eighty-nine (1.85%) individuals carried either pathogenic or likely pathogenic variants across 25 genes. 51.7% had variants in causal genes for familial hyperlipidemia, but there were also recurrent variants in SCN5A and MYBPC3, causal genes for inherited arrhythmia and cardiomyopathy, which, despite previous reports, we determined to lack criteria for pathogenicity.CONCLUSIONS: Our findings highlight the incidence of disease-related variants in inherited cardiac conditions and emphasize the value of large-scale sequencing in specific ancestries. Follow-up detailed phenotyping and analysis of pedigrees are crucial because assigning pathogenicity will significantly affect clinical management for individuals and their family members.

    View details for DOI 10.1161/CIRCGEN.121.003536

    View details for PubMedID 35130036

  • Interactions of physical activity, muscular fitness, adiposity, and genetic risk for NAFLD. Hepatology communications Schnurr, T. M., Katz, S. F., Justesen, J. M., O'Sullivan, J. W., Saliba-Gustafsson, P., Assimes, T. L., Carcamo-Orive, I., Ahmed, A., Ashley, E. A., Hansen, T., Knowles, J. W. 2022

    Abstract

    Genetic predisposition and unhealthy lifestyle are risk factors for nonalcoholic fatty liver disease (NAFLD). We investigated whether the genetic risk of NAFLD is modified by physical activity, muscular fitness, and/or adiposity. In up to 242,524 UK Biobank participants without excessive alcohol intake or known liver disease, we examined cross-sectional interactions and joint associations of physical activity, muscular fitness, body mass index (BMI), and a genetic risk score (GRS) with alanine aminotransferase (ALT) levels and the proxy definition for suspected NAFLD of ALT levels > 30 U/L in women and >40 U/L in men. Genetic predisposition to NAFLD was quantified using a GRS consisting of 68 loci known to be associated with chronically elevated ALT. Physical activity was assessed using accelerometry, and muscular fitness was estimated by measuring handgrip strength. We found that increased physical activity and grip strength modestly attenuate genetic predisposition to elevation in ALT levels, whereas higher BMI markedly amplifies it (all p values < 0.001). Among those with normal weight and high level of physical activity, the odds of suspected NAFLD were 1.6-fold higher in those with high versus low genetic risk (reference group). In those with high genetic risk, the odds of suspected NAFLD were 12-fold higher in obese participants with low physical activity versus those with normal weight and high physical activity (odds ratio for NAFLD = 19.2 and 1.6, respectively, vs. reference group). Conclusion: In individuals with high genetic predisposition for NAFLD, maintaining a normal body weight and increased physical activity may reduce the risk of NAFLD.

    View details for DOI 10.1002/hep4.1932

    View details for PubMedID 35293152

  • Titin mutations and female sex characterize dilated cardiomyopathy in the elderly Cannata, A., Merlo, M., Dal Ferro, M., Manca, P., Paldino, A., Barbati, G., Graw, S., Bromage, D., Johnson, R., Roy, D., Gigli, M., Stolfo, D., Abbate, A., Parkih, V., Ashley, E., Lakdawala, N., Carr-White, G., Fatkin, D., Mcdonagh, T., Taylor, M., Mestroni, L., Sinagra, G. OXFORD UNIV PRESS. 2021: G153-+
  • Mono- and Biallelic Protein-Truncating Variants in Alpha-Actinin 2 Cause Cardiomyopathy Through Distinct Mechanisms. Circulation. Genomic and precision medicine Lindholm, M. E., Jimenez-Morales, D., Zhu, H., Seo, K., Amar, D., Zhao, C., Raja, A., Madhvani, R., Abramowitz, S., Espenel, C., Sutton, S., Caleshu, C., Berry, G. J., Motonaga, K. S., Dunn, K., Platt, J., Ashley, E. A., Wheeler, M. T. 2021: CIRCGEN121003419

    Abstract

    BACKGROUND: ACTN2 (alpha-actinin 2) anchors actin within cardiac sarcomeres. The mechanisms linking ACTN2 mutations to myocardial disease phenotypes are unknown. Here, we characterize patients with novel ACTN2 mutations to reveal insights into the physiological function of ACTN2.METHODS: Patients harboring ACTN2 protein-truncating variants were identified using a custom mutation pipeline. In patient-derived iPSC-cardiomyocytes, we investigated transcriptional profiles using RNA sequencing, contractile properties using video-based edge detection, and cellular hypertrophy using immunohistochemistry. Structural changes were analyzed through electron microscopy. For mechanistic studies, we used coimmunoprecipitation for ACTN2, followed by mass-spectrometry to investigate protein-protein interaction, and protein tagging followed by confocal microscopy to investigate introduction of truncated ACTN2 into the sarcomeres.RESULTS: Patient-derived iPSC-cardiomyocytes were hypertrophic, displayed sarcomeric structural disarray, impaired contractility, and aberrant Ca2+-signaling. In heterozygous indel cells, the truncated protein incorporates into cardiac sarcomeres, leading to aberrant Z-disc ultrastructure. In homozygous stop-gain cells, affinity-purification mass-spectrometry reveals an intricate ACTN2 interactome with sarcomere and sarcolemma-associated proteins. Loss of the C-terminus of ACTN2 disrupts interaction with ACTN1 and GJA1, 2 sarcolemma-associated proteins, which may contribute to the clinical arrhythmic and relaxation defects. The causality of the stop-gain mutation was verified using CRISPR-Cas9 gene editing.CONCLUSIONS: Together, these data advance our understanding of the role of ACTN2 in the human heart and establish recessive inheritance of ACTN2 truncation as causative of disease.

    View details for DOI 10.1161/CIRCGEN.121.003419

    View details for PubMedID 34802252

  • Designing clinically translatable artificial intelligence systems for high-dimensional medical imaging NATURE MACHINE INTELLIGENCE Shad, R., Cunningham, J. P., Ashley, E. A., Langlotz, C. P., Hiesinger, W. 2021; 3 (11): 929-935
  • Comparison of the FRIEND and Wasserman-Hansen Equations in Predicting Outcomes in Heart Failure. Journal of the American Heart Association Myers, J., de Souza E Silva, C. G., Arena, R., Kaminsky, L., Christle, J. W., Busque, V., Ashley, E., Moneghetti, K. 2021: e021246

    Abstract

    Background Percentage of age-predicted peak oxygen uptake (VO2) achieved (ppVO2) has been widely used to stratify risk in patients with heart failure. However, there are limitations to traditional normal standards. We compared the recently derived FRIEND (Fitness Registry and the Importance of Exercise: A National Data Base) equation to the widely used Wasserman-Hansen (WH) ppVO2 equation to predict outcomes in patients with heart failure. Methods and Results A subgroup of 4055 heart failure patients from the FRIEND registry (mean age 53±15years) was followed for a mean of 28±16months. The FRIEND and WH equations along with measured peak VO2 expressed in mL/kg-1 per min-1 were compared for mortality and composite cardiovascular events. ppVO2 was higher for the FRIEND versus the WH equation (66±30% versus 58±25%; P<0.001). The areas under the receiver operating characteristic curves were slightly but significantly higher for the FRIEND equation for mortality (0.74 versus 0.72; P=0.03) and cardiac events (0.70 versus 0.68; P=0.008). Area under the receiver operating characteristic curve for measured peak VO2 was 0.70 (P<0.001) for mortality and 0.73 (P<0.001) for cardiovascular events. For each 1-SD higher ppVO2 for the FRIEND equation, mortality was reduced by 18% (hazard ratio, 0.82; 95% CI, 0.69-0.97; P<0.02); for each 1-SD higher ppVO2 for the WH equation, the mortality was reduced by 17% (hazard ratio, 0.83; 95% CI, 0.71-0.97; P=0.02). The corresponding reductions in risk per 1 SD for cardiovascular events for the FRIEND and WH equations were 23 and 21%, respectively (both P<0.001). Conclusions Peak VO2 expressed as percentage of an age-predicted standard strongly predicts mortality and major cardiovascular events in patients with heart failure. The FRIEND registry equation exhibited test characteristics slightly superior to the commonly used WH equation.

    View details for DOI 10.1161/JAHA.121.021246

    View details for PubMedID 34689609

  • Deep learning evaluation of biomarkers from echocardiogram videos. EBioMedicine Hughes, J. W., Yuan, N., He, B., Ouyang, J., Ebinger, J., Botting, P., Lee, J., Theurer, J., Tooley, J. E., Nieman, K., Lungren, M. P., Liang, D. H., Schnittger, I., Chen, J. H., Ashley, E. A., Cheng, S., Ouyang, D., Zou, J. Y. 2021; 73: 103613

    Abstract

    BACKGROUND: Laboratory testing is routinely used to assay blood biomarkers to provide information on physiologic state beyond what clinicians can evaluate from interpreting medical imaging. We hypothesized that deep learning interpretation of echocardiogram videos can provide additional value in understanding disease states and can evaluate common biomarkers results.METHODS: We developed EchoNet-Labs, a video-based deep learning algorithm to detect evidence of anemia, elevated B-type natriuretic peptide (BNP), troponin I, and blood urea nitrogen (BUN), as well as values of ten additional lab tests directly from echocardiograms. We included patients (n=39,460) aged 18 years or older with one or more apical-4-chamber echocardiogram videos (n=70,066) from Stanford Healthcare for training and internal testing of EchoNet-Lab's performance in estimating the most proximal biomarker result. Without fine-tuning, the performance of EchoNet-Labs was further evaluated on an additional external test dataset (n=1,301) from Cedars-Sinai Medical Center. We calculated the area under the curve (AUC) of the receiver operating characteristic curve for the internal and external test datasets.FINDINGS: On the held-out test set of Stanford patients not previously seen during model training, EchoNet-Labs achieved an AUC of 0.80 (0.79-0.81) in detecting anemia (low hemoglobin), 0.86 (0.85-0.88) in detecting elevated BNP, 0.75 (0.73-0.78) in detecting elevated troponin I, and 0.74 (0.72-0.76) in detecting elevated BUN. On the external test dataset from Cedars-Sinai, EchoNet-Labs achieved an AUC of 0.80 (0.77-0.82) in detecting anemia, of 0.82 (0.79-0.84) in detecting elevated BNP, of 0.75 (0.72-0.78) in detecting elevated troponin I, and of 0.69 (0.66-0.71) in detecting elevated BUN. We further demonstrate the utility of the model in detecting abnormalities in 10 additional lab tests. We investigate the features necessary for EchoNet-Labs to make successful detection and identify potential mechanisms for each biomarker using well-known and novel explainability techniques.INTERPRETATION: These results show that deep learning applied to diagnostic imaging can provide additional clinical value and identify phenotypic information beyond current imaging interpretation methods.FUNDING: J.W.H. and B.H. are supported by the NSF Graduate Research Fellowship. D.O. is supported by NIH K99 HL157421-01. J.Y.Z. is supported by NSF CAREER 1942926, NIH R21 MD012867-01, NIH P30AG059307 and by a Chan-Zuckerberg Biohub Fellowship.

    View details for DOI 10.1016/j.ebiom.2021.103613

    View details for PubMedID 34656880

  • Disruption of Protein Quality Control of Human Ether-a-go-go Related Gene K+ Channel Results in Profound Long QT Syndrome. Heart rhythm Ledford, H. A., Ren, L., Thai, P. N., Park, S., Timofeyev, V., Sirish, P., Xu, W., Emigh, A. M., Priest, J. R., Perez, M. V., Ashley, E. A., Yarov-Yarovoy, V., Yamoah, E. N., Zhang, X., Chiamvimonvat, N. 2021

    Abstract

    BACKGROUND: Long QT syndrome (LQTS) is a hereditary disease that predisposes patients to life-threatening cardiac arrhythmias and sudden cardiac death. Our previously study of human ether-a-go-go related gene (hERG)-encoded K+ channel (Kv11.1) supports an association between hERG and RING Finger Protein 207 (RNF207) variants in aggravating the onset and severity of LQTS, specifically T613M hERG (hERGT613M) and RNF207 frameshift (RNF207G603fs) mutations. However, the underlying mechanistic underpinning remains unknown.OBJECTIVE: The purpose of the current study is to test the role of RNF207 on the function of hERG-encoded K+ channel subunits.METHODS AND RESULTS: Here, we demonstrate that RNF207 serves as an E3 ubiquitin ligase and targets misfolded hERGT613M proteins for degradation. RNF207G603fs exhibits decreased activity and hinders the normal degradation pathway; this increases the levels of hERGT613M subunits and their dominant-negative effect on the wild-type (WT) subunits, ultimately resulting in decreased current density. Similar findings are shown for hERGA614V, a known dominant-negative mutant subunit. Finally, the presence of RNF207G603fs with hERGT613M results in significantly prolonged action potential durations and reduced hERG current in human pluripotent stem cell-derived cardiomyocytes.CONCLUSIONS: Our study establishes RNF207 as an interacting protein serving as a ubiquitin ligase for hERG-encoded K+ channel subunits. Normal function of RNF207 is critical for the quality control of hERG subunits and, consequently, cardiac repolarization. Moreover, our study provides evidence for protein quality control as a new paradigm in life-threatening cardiac arrhythmias in LQTS patients.

    View details for DOI 10.1016/j.hrthm.2021.10.005

    View details for PubMedID 34634443

  • Worldwide differences in primary prevention implantable cardioverter defibrillator utilization and outcomes in hypertrophic cardiomyopathy. European heart journal Nauffal, V., Marstrand, P., Han, L., Parikh, V. N., Helms, A. S., Ingles, J., Jacoby, D., Lakdawala, N. K., Kapur, S., Michels, M., Owens, A. T., Ashley, E. A., Pereira, A. C., Rossano, J. W., Saberi, S., Semsarian, C., Ware, J. S., Wittekind, S. G., Day, S., Olivotto, I., Ho, C. Y. 2021; 42 (38): 3932-3944

    Abstract

    Risk stratification algorithms for sudden cardiac death (SCD) in hypertrophic cardiomyopathy (HCM) and regional differences in clinical practice have evolved over time. We sought to compare primary prevention implantable cardioverter defibrillator (ICD) implantation rates and associated clinical outcomes in US vs. non-US tertiary HCM centres within the international Sarcomeric Human Cardiomyopathy Registry.We included patients with HCM enrolled from eight US sites (n = 2650) and five non-US (n = 2660) sites and used multivariable Cox-proportional hazards models to compare outcomes between sites. Primary prevention ICD implantation rates in US sites were two-fold higher than non-US sites (hazard ratio (HR) 2.27 [1.89-2.74]), including in individuals deemed at high 5-year SCD risk (≥6%) based on the HCM risk-SCD score (HR 3.27 [1.76-6.05]). US ICD recipients also had fewer traditional SCD risk factors. Among ICD recipients, rates of appropriate ICD therapy were significantly lower in US vs. non-US sites (HR 0.52 [0.28-0.97]). No significant difference was identified in the incidence of SCD/resuscitated cardiac arrest among non-recipients of ICDs in US vs. non-US sites (HR 1.21 [0.74-1.97]).Primary prevention ICDs are implanted more frequently in patients with HCM in US vs. non-US sites across the spectrum of SCD risk. There was a lower rate of appropriate ICD therapy in US sites, consistent with a lower-risk population, and no significant difference in SCD in US vs. non-US patients who did not receive an ICD. Further studies are needed to understand what drives malignant arrhythmias, optimize ICD allocation, and examine the impact of different ICD utilization strategies on long-term outcomes in HCM.

    View details for DOI 10.1093/eurheartj/ehab598

    View details for PubMedID 36282238

  • Phenotypic Expression, Natural History and Risk Stratification of Cardiomyopathy Caused by Filamin C Truncating Variants. Circulation Gigli, M., Stolfo, D., Graw, S., Merlo, M., Gregorio, C., Chen, S. N., Dal Ferro, M., Paldino, A., De Angelis, G., Brun, F., Jirikowic, J., Salcedo, E. E., Turja, S., Fatkin, D., Johnson, R., van Tintelen, J. P., Te Riele, A. S., Wilde, A., Lakdawala, N. K., Picard, K., Miani, D., Muser, D., Severini, G. M., Calkins, H., James, C. A., Murray, B., Tichnell, C., Parikh, V. N., Ashley, E. A., Reuter, C., Song, J., Judge, D., McKenna, W. J., Taylor, M. R., Sinagra, G., Mestroni, L. 2021

    Abstract

    Background: Filamin C truncating variants (FLNCtv) cause a form of arrhythmogenic cardiomyopathy (ACM): the mode of presentation, natural history and risk stratification of FLNCtv remain incompletely explored. We sought to develop a risk profile for refractory heart failure and life-threatening arrhythmias in a multicenter cohort of FLNCtv carriers. Methods: FLNCtv carriers were identified from ten tertiary care centers for genetic cardiomyopathies. Clinical and outcome data were compiled. Composite outcomes were all-cause mortality/heart transplantation/left ventricle assist device (D/HT/LVAD), non-arrhythmic death/HT/LVAD and SCD/major ventricular arrhythmias (SCD/MVA). Previously established cohorts of 46 patients with LMNA and 60 with DSP-related ACM were used for prognostic comparison. Results: Eighty-five patients carrying FLNCtv were included (42±15 years, 53% males, 45% probands). Phenotypes were heterogeneous at presentation: 49% dilated cardiomyopathy, 25% arrhythmogenic left dominant cardiomyopathy, 3% arrhythmogenic right ventricular cardiomyopathy. Left ventricular ejection fraction (LVEF) was <50% in 64% of carriers and 34% had right ventricular fractional area changes (RVFAC=(right ventricular end-diastolic area - right ventricular end-systolic area)/ right ventricular end-diastolic area) <35%. During follow-up (median time 61 months), 19 (22%) carriers experienced D/HT/LVAD, 13 (15%) non-arrhythmic death/HT/LVAD and 23 (27%) SCD/MVA. The SCD/MVA incidence of FLNCtv carriers did not significantly differ from LMNA carriers and DSP carriers. In FLNCtv carriers, LVEF was associated with the risk of D/HT/LVAD and non-arrhythmic death/HT/LVAD. CConclusions: Among patients referred to tertiary referral centers, FLNCtv ACM is phenotypically heterogeneous and characterized by high risk of life-threatening arrhythmias, which does not seem to be associated with the severity of LV dysfunction.

    View details for DOI 10.1161/CIRCULATIONAHA.121.053521

    View details for PubMedID 34587765

  • Worldwide differences in primary prevention implantable cardioverter defibrillator utilization and outcomes in hypertrophic cardiomyopathy. European heart journal Nauffal, V., Marstrand, P., Han, L., Parikh, V. N., Helms, A. S., Ingles, J., Jacoby, D., Lakdawala, N. K., Kapur, S., Michels, M., Owens, A. T., Ashley, E. A., Pereira, A. C., Rossano, J. W., Saberi, S., Semsarian, C., Ware, J. S., Wittekind, S. G., Day, S., Olivotto, I., Ho, C. Y. 2021

    Abstract

    AIMS: Risk stratification algorithms for sudden cardiac death (SCD) in hypertrophic cardiomyopathy (HCM) and regional differences in clinical practice have evolved over time. We sought to compare primary prevention implantable cardioverter defibrillator (ICD) implantation rates and associated clinical outcomes in US vs. non-US tertiary HCM centres within the international Sarcomeric Human Cardiomyopathy Registry.METHODS AND RESULTS: We included patients with HCM enrolled from eight US sites (n = 2650) and five non-US (n = 2660) sites and used multivariable Cox-proportional hazards models to compare outcomes between sites. Primary prevention ICD implantation rates in US sites were two-fold higher than non-US sites (hazard ratio (HR) 2.27 [1.89-2.74]), including in individuals deemed at high 5-year SCD risk (≥6%) based on the HCM risk-SCD score (HR 3.27 [1.76-6.05]). US ICD recipients also had fewer traditional SCD risk factors. Among ICD recipients, rates of appropriate ICD therapy were significantly lower in US vs. non-US sites (HR 0.52 [0.28-0.97]). No significant difference was identified in the incidence of SCD/resuscitated cardiac arrest among non-recipients of ICDs in US vs. non-US sites (HR 1.21 [0.74-1.97]).CONCLUSION: Primary prevention ICDs are implanted more frequently in patients with HCM in US vs. non-US sites across the spectrum of SCD risk. There was a lower rate of appropriate ICD therapy in US sites, consistent with a lower-risk population, and no significant difference in SCD in US vs. non-US patients who did not receive an ICD. Further studies are needed to understand what drives malignant arrhythmias, optimize ICD allocation, and examine the impact of different ICD utilization strategies on long-term outcomes in HCM.

    View details for DOI 10.1093/eurheartj/ehab598

    View details for PubMedID 34491319

  • Genetic counselor roles in the undiagnosed diseases network research study: Clinical care, collaboration, and curation. Journal of genetic counseling Kohler, J. N., Kelley, E. G., Boyd, B. M., Sillari, C. H., Marwaha, S., Undiagnosed Diseases Network, Wheeler, M. T., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennet, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Sessions Cole, F., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Dayal, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kobren, S. N., Kohane, I. S., Kohler, J. N., Krakow, D., Krasnewich, D. M., Kravets, E., Korrick, S., Koziura, M., Krier, J. B., Lalani, S. R., Lam, B., Lam, C., LaMoure, G. L., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Mak, B. C., Maclidan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Lawrence Merritt, J., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Carl Pallais, J., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raskind, W., Raja, A. N., Rao, D. A., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Ron Scott, C., Schaechter, J., Schedl, T., Schoch, K., Scott, D. A., Shashi, V., Shin, J., Signer, R., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Solomon, B., Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. L., Tan, Q. K., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Wallace, S., Walley, N. M., Walsh, C. A., Walker, M., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K. W., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S. 2021

    Abstract

    Genetic counselors (GCs) are increasingly filling important positions on research study teams, but there is limited literature describing the roles of GCs in these settings. GCs on the Undiagnosed Diseases Network (UDN) study team serve in a variety of roles across the research network and provide an opportunity to better understand genetic counselor roles in research. To quantitatively characterize the tasks regularly performed and professional fulfillment derived from these tasks, two surveys were administered to UDN GCs in a stepwise fashion. Responses from the first, free-response survey elicited the scope of tasks which informed development of a second structured, multiple-select survey. In survey 2, respondents were asked to select which roles they performed. Across 19 respondents, roles in survey 2 received a total of 947 selections averaging approximately 10 selections per role. When asked to indicate what roles they performed, respondent selected a mean of 50 roles (range 22-70). Survey 2 data were analyzed via thematic coding of responses and hierarchical cluster analysis to identify patterns in responses. From the thematic analysis, 20 non-overlapping codes emerged in seven categories: clinical interaction and care, communication, curation, leadership, participant management, research, and team management. Three themes emerged from the categories that represented the roles of GCs in the UDN: clinical care, collaboration, and curation. Cluster analyses showed that responses were more similar among individuals at the same institution than between institutions. This study highlights the ways GCs apply their unique skill set in the context of a clinical translational research network. Additionally, findings from this study reinforce the wide applicability of core skills that are part of genetic counseling training. Clinical literacy, genomics expertise and analysis, interpersonal, psychosocial and counseling skills, education, professional practice skills, and an understanding of research processes make genetic counselors well suited for such roles and poised to positively impact research experiences and outcomes for participants.

    View details for DOI 10.1002/jgc4.1493

    View details for PubMedID 34374469

  • Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. The Journal of experimental medicine Wilk, A. J., Lee, M. J., Wei, B., Parks, B., Pi, R., Martinez-Colon, G. J., Ranganath, T., Zhao, N. Q., Taylor, S., Becker, W., Stanford COVID-19 Biobank, Jimenez-Morales, D., Blomkalns, A. L., O'Hara, R., Ashley, E. A., Nadeau, K. C., Yang, S., Holmes, S., Rabinovitch, M., Rogers, A. J., Greenleaf, W. J., Blish, C. A. 2021; 218 (8)

    Abstract

    Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-kappaB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.

    View details for DOI 10.1084/jem.20210582

    View details for PubMedID 34128959

  • Utility Of Cardiopulmonary Exercise Testing In Chronic Unexplained Dyspnea In A 77 Year Old Female Christle, J. W., Andruska, A. M., Moneghetti, K. J., Wheeler, M. T., Ashley, E. A., Myers, J., Ruoss, S. LIPPINCOTT WILLIAMS & WILKINS. 2021: 395
  • Respiratory Gas Kinetics After Maximal Exercise In Patients Referred For Cardiopulmonary Exercise Testing Christle, J. W., Patti, A., Blumberg, Y., Neunhaeuserer, D., Ashley, E. A., Haddad, F., Myers, J., Moneghetti, K. J. LIPPINCOTT WILLIAMS & WILKINS. 2021: 98-99
  • Predicting Peak VO2 In Clinical Populations With Obesity Busque, V., Monegheetti, K. J., Ashley, E. A., Wheeler, M. T., Haddad, F., Myers, J., Christle, J. W. LIPPINCOTT WILLIAMS & WILKINS. 2021: 446
  • Mulibrey Nanism and the Real Time Use of Genome and Biobank Engines to Inform Clinical Care in an Ultrarare Disease. Circulation. Genomic and precision medicine Weldy, C. S., Ashley, E. A. 2021: CIRCGEN121003430

    View details for DOI 10.1161/CIRCGEN.121.003430

    View details for PubMedID 34096331

  • Smartphone-Based VO2max Measurement With Heart Snapshot in Clinical and Real-world Settings With a Diverse Population: Validation Study. JMIR mHealth and uHealth Webster, D. E., Tummalacherla, M., Higgins, M., Wing, D., Ashley, E., Kelly, V. E., McConnell, M. V., Muse, E. D., Olgin, J. E., Mangravite, L. M., Godino, J., Kellen, M. R., Omberg, L. 2021; 9 (6): e26006

    Abstract

    BACKGROUND: Maximal oxygen consumption (VO2max) is one of the most predictive biometrics for cardiovascular health and overall mortality. However, VO2max is rarely measured in large-scale research studies or routine clinical care because of the high cost, participant burden, and requirement for specialized equipment and staff.OBJECTIVE: To overcome the limitations of clinical VO2max measurement, we aim to develop a digital VO2max estimation protocol that can be self-administered remotely using only the sensors within a smartphone. We also aim to validate this measure within a broadly representative population across a spectrum of smartphone devices.METHODS: Two smartphone-based VO2max estimation protocols were developed: a 12-minute run test (12-MRT) based on distance measured by GPS and a 3-minute step test (3-MST) based on heart rate recovery measured by a camera. In a 101-person cohort, balanced across age deciles and sex, participants completed a gold standard treadmill-based VO2max measurement, two silver standard clinical protocols, and the smartphone-based 12-MRT and 3-MST protocols in the clinic and at home. In a separate 120-participant cohort, the video-based heart rate measurement underlying the 3-MST was measured for accuracy in individuals across the spectrum skin tones while using 8 different smartphones ranging in cost from US $99 to US $999.RESULTS: When compared with gold standard VO2max testing, Lin concordance was pc=0.66 for 12-MRT and pc=0.61 for 3-MST. However, in remote settings, the 12-MRT was significantly less concordant with the gold standard (pc=0.25) compared with the 3-MST (pc=0.61), although both had high test-retest reliability (12-MRT intraclass correlation coefficient=0.88; 3-MST intraclass correlation coefficient=0.86). On the basis of the finding that 3-MST concordance was generalizable to remote settings whereas 12-MRT was not, the video-based heart rate measure within the 3-MST was selected for further investigation. Heart rate measurements in any of the combinations of the six Fitzpatrick skin tones and 8 smartphones resulted in a concordance of pc≥0.81. Performance did not correlate with device cost, with all phones selling under US $200 performing better than pc>0.92.CONCLUSIONS: These findings demonstrate the importance of validating mobile health measures in the real world across a diverse cohort and spectrum of hardware. The 3-MST protocol, termed as heart snapshot, measured VO2max with similar accuracy to supervised in-clinic tests such as the Tecumseh (pc=0.94) protocol, while also generalizing to remote and unsupervised measurements. Heart snapshot measurements demonstrated fidelity across demographic variation in age and sex, across diverse skin pigmentation, and between various iOS and Android phone configurations. This software is freely available for all validation data and analysis code.

    View details for DOI 10.2196/26006

    View details for PubMedID 34085945

  • A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases SCIENTIFIC DATA Kyle, J. E., Stratton, K. G., Zink, E. M., Kim, Y., Bloodsworth, K. J., Monroe, M. E., Bacino, C. A., Bacino, C. A., Hanchard, N. A., Lewis, R. A., Rosenfeld, J. A., Scott, D. A., Tran, A. A., Ward, P. A., Burrage, L. C., Clark, G. D., Alejandro, M. E., Posey, J. E., Wangler, M. F., Lee, B. H., Craigen, W. J., Bellen, H. J., Nicholas, S. K., Bostwick, B. L., Samson, S. L., Goldman, A. M., Moretti, P. M., Eng, C. M., Muzny, D. M., Orengo, J. P., Vogel, T. P., Lalani, S. R., Murdock, D. R., Azamian, M. S., Orange, J. S., Emrick, L. T., Dhar, S. U., Balasubramanyam, A., Potocki, L., Yamamoto, S., Yang, Y., Chen, S., Jamal, F., Karaviti, L., Marom, R., Lincoln, S. A., Walsh, C. A., Beggs, A. H., Rodan, L. H., Stoler, J. M., Berry, G. T., Cobban, L. A., MacRae, C. A., Krier, J. B., Silverman, E. K., Fieg, E. L., Maas, R. L., Loscalzo, J., Aday, A., Korrick, S., Goldstein, D. B., Stong, N., Sullivan, J. A., Spillmann, R. C., Pena, L. M., Tan, Q., Walley, N. M., Jiang, Y., McConkie-Rosell, A., Schoch, K., Shashi, V., Cope, H., Holm, I. A., Kohane, I. S., McCray, A. T., Esteves, C., LeBlanc, K., Might, M., Kelley, E., Worthey, E. A., Dorset, D. C., Boone, B. E., Levy, S. E., Birch, C. L., Jones, A. L., Brown, D. M., Bick, D. P., Newberry, J., Lazar, J., May, T., Sweetser, D. A., Briere, L. C., Pallais, J., Cooper, C. M., High, F., Walker, M., Colley, H. A., Mamounas, L. A., Manolio, T. A., Burke, E. A., Godfrey, R. A., Groden, C. A., Gahl, W. A., Wolfe, L. A., Markello, T. C., Lau, C., Draper, D. D., Gould, S. E., Nehrebecky, M. E., Wahl, C. E., Batzli, G. F., Macnamara, E. F., Dayal, J. G., Eckstein, D. J., Mulvihill, J. J., Tifft, C. J., Urv, T. K., Wise, A. L., Murphy, J. L., Gropman, A. L., Howerton, E. M., Krasnewich, D. M., Johnston, J. M., Pusey, B. N., Adams, D. R., Maduro, V. V., Malicdan, M. V., Davids, M., Estwick, T., Novacic, D., Sharma, P., Toro, C., Yu, G., Behnam, B., D'Souza, P., Ferreira, C., Morimoto, M., Baker, E. H., Yang, J., Gourdine, J. F., Brush, M., Haendel, M., Ashley, E. A., Bernstein, J. A., Sampson, J. B., Zastrow, D. B., Friedman, N. D., Merker, J. D., McCormack, C. E., Fisher, P. G., Davidson, J. M., Dries, A. M., Enns, G. M., Majcherska, M. M., Reuter, C. M., Waggott, D. M., Kohler, J. N., Coakley, T. R., Smith, K. S., Wheeler, M. T., Bonner, D., Fernandez, L., Hom, J., Huang, Y., Marwaha, S., Zhao, C., Martinez-Agosto, J. A., Dell'Angelica, E. C., Papp, J. C., Douine, E. D., Nelson, S. F., Martin, M. G., Palmer, C., Parker, N. H., Butte, M. J., Yoon, A. J., Loo, S. K., Fogel, B. L., Dipple, K. M., Sinsheimer, J. S., Allard, P., Barseghyan, H., Dorrani, N., Lee, H., Vilain, E., Eskin, A., Renteria, G., Signer, R., Wan, J., Zheng, A., Westerfield, M., Phillips, J. A., Cogan, J. D., Newman, J. H., Robertson, A. K., Hamid, R., Bican, A., Brokamp, E., Duncan, L., Kozuira, M., Rives, L., Shakachite, L., Waters, K. M., Webb-Robertson, B. M., Koeller, D. M., Metz, T. O., Undiagnosed Dis Network 2021; 8 (1): 114

    Abstract

    Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.

    View details for DOI 10.1038/s41597-021-00894-y

    View details for Web of Science ID 000642148100001

    View details for PubMedID 33883556

    View details for PubMedCentralID PMC8060404

  • Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain GENETICS IN MEDICINE Marbach, F., Stoyanov, G., Erger, F., Stratakis, C. A., Settas, N., London, E., Rosenfeld, J. A., Torti, E., Haldeman-Englert, C., Sklirou, E., Kessler, E., Ceulemans, S., Nelson, S. F., Martinez-Agosto, J. A., Palmer, C. S., Signer, R. H., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Daya, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Krier, J. B., LaMoure, G. L., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., MacRae, C. A., Macnamara, E. F., Maduro, V. V., Majcherska, M. M., Mak, B. C., Malicdan, M. V., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Merritt, J., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Moretti, P., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J., Palmer, C. S., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raja, A. N., Rao, D. A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, C., Scott, D. A., Shashi, V., Shin, J., Signer, R. H., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Ben Solomon, Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. M., Tan, Q., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Walsh, C. A., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S., Andrews, M. V., Grange, D. K., Willaert, R., Person, R., Telegrafi, A., Sievers, A., Laugsch, M., Theiss, S., Cheng, Y., Lichtarge, O., Katsonis, P., Stocco, A., Schaaf, C. P., Undiagnosed Diseases Network 2021

    Abstract

    We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA).Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development.Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs.Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.

    View details for DOI 10.1038/s41436-021-01152-7

    View details for Web of Science ID 000638059400001

    View details for PubMedID 33833410

  • Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation. Genetics in medicine : official journal of the American College of Medical Genetics Thompson, A. D., Helms, A. S., Kannan, A., Yob, J., Lakdawala, N. K., Wittekind, S. G., Pereira, A. C., Jacoby, D. L., Colan, S. D., Ashley, E. A., Saberi, S., Ware, J. S., Ingles, J., Semsarian, C., Michels, M., Mazzarotto, F., Olivotto, I., Ho, C. Y., Day, S. M. 2021

    Abstract

    PURPOSE: Variants in MYBPC3 causing loss of function are the most common cause of hypertrophic cardiomyopathy (HCM). However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will identify a subgroup of HCM patients with a MYBPC3 VUS associated with increased clinical risk.METHODS: Among 7,963 patients in the multicenter Sarcomeric Human Cardiomyopathy Registry (SHaRe), 120 unique missense VUS in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS.RESULTS: We demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM+, DeltaDeltaG ≤ -1.2kcal/mol) exhibited a higher rate of adverse events compared with those with a STRUM- VUS (hazard ratio=2.29, P=0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding.CONCLUSION: STRUM identifies patients with HCM and a MYBPC3 VUS who may be at higher clinical risk and provides supportive evidence for pathogenicity.

    View details for DOI 10.1038/s41436-021-01134-9

    View details for PubMedID 33782553

  • Clinical characteristics and outcomes in childhood-onset hypertrophic cardiomyopathy. European heart journal Marston, N. A., Han, L., Olivotto, I., Day, S. M., Ashley, E. A., Michels, M., Pereira, A. C., Ingles, J., Semsarian, C., Jacoby, D., Colan, S. D., Rossano, J. W., Wittekind, S. G., Ware, J. S., Saberi, S., Helms, A. S., Ho, C. Y. 2021

    Abstract

    AIMS: Childhood-onset hypertrophic cardiomyopathy (HCM) is far less common than adult-onset disease, thus natural history is not well characterized. We aim to describe the characteristics and outcomes of childhood-onset HCM.METHODS AND RESULTS: We performed an observational cohort study of 7677 HCM patients from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). Hypertrophic cardiomyopathy patients were stratified by age at diagnosis [<1 year (infancy), 1-18 years (childhood), >18 years (adulthood)] and assessed for composite endpoints reflecting heart failure (HF), life-threatening ventricular arrhythmias, atrial fibrillation (AF), and an overall composite that also included stroke and death. Stratifying by age of diagnosis, 184 (2.4%) patients were diagnosed in infancy; 1128 (14.7%) in childhood; and 6365 (82.9%) in adulthood. Childhood-onset HCM patients had an 2%/year event rate for the overall composite endpoint, with ventricular arrhythmias representing the most common event in the 1st decade following baseline visit, but HF and AF becoming more common by the end of the 2nd decade. Sarcomeric variants were more common in childhood-onset HCM (63%) and carried a worse prognosis than non-sarcomeric disease, including a greater than two-fold increased risk of HF [HRadj 2.39 (1.36-4.20), P = 0.003] and 67% increased risk of the overall composite outcome [HRadj 1.67 (1.16-2.41), P = 0.006]. When compared with adult-onset HCM, childhood-onset was 36% more likely to develop life-threatening ventricular arrhythmias [HRadj 1.36 (1.03-1.80)] and twice as likely to require transplant or ventricular assist device [HRadj 1.99 (1.23-3.23)].CONCLUSION: Patients with childhood-onset HCM are more likely to have sarcomeric disease, carry a higher risk of life-threatening ventricular arrythmias, and have greater need for advanced HF therapies. These findings provide insight into the natural history of disease and can help inform clinical risk stratification.

    View details for DOI 10.1093/eurheartj/ehab148

    View details for PubMedID 33769460

  • Genomic Context Differs Between Human Dilated Cardiomyopathy and Hypertrophic Cardiomyopathy. Journal of the American Heart Association Puckelwartz, M. J., Pesce, L. L., Dellefave-Castillo, L. M., Wheeler, M. T., Pottinger, T. D., Robinson, A. C., Kearns, S. D., Gacita, A. M., Schoppen, Z. J., Pan, W., Kim, G., Wilcox, J. E., Anderson, A. S., Ashley, E. A., Day, S. M., Cappola, T., Dorn, G. W., McNally, E. M. 2021: e019944

    Abstract

    Background Inherited cardiomyopathies display variable penetrance and expression, and a component of phenotypic variation is genetically determined. To evaluate the genetic contribution to this variable expression, we compared protein coding variation in the genomes of those with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). Methods and Results Nonsynonymous single-nucleotide variants (nsSNVs) were ascertained using whole genome sequencing from familial cases of HCM (n=56) or DCM (n=70) and correlated with echocardiographic information. Focusing on nsSNVs in 102 genes linked to inherited cardiomyopathies, we correlated the number of nsSNVs per person with left ventricular measurements. Principal component analysis and generalized linear models were applied to identify the probability of cardiomyopathy type as it related to the number of nsSNVs in cardiomyopathy genes. The probability of having DCM significantly increased as the number of cardiomyopathy gene nsSNVs per person increased. The increase in nsSNVs in cardiomyopathy genes significantly associated with reduced left ventricular ejection fraction and increased left ventricular diameter for individuals carrying a DCM diagnosis, but not for those with HCM. Resampling was used to identify genes with aberrant cumulative allele frequencies, identifying potential modifier genes for cardiomyopathy. Conclusions Participants with DCM had more nsSNVs per person in cardiomyopathy genes than participants with HCM. The nsSNV burden in cardiomyopathy genes did not correlate with the probability or manifestation of left ventricular measures in HCM. These findings support the concept that increased variation in cardiomyopathy genes creates a genetic background that predisposes to DCM and increased disease severity.

    View details for DOI 10.1161/JAHA.120.019944

    View details for PubMedID 33764162

  • Functional and structural analysis of cytokine selective IL6ST defects that cause recessive hyper-IgE syndrome. The Journal of allergy and clinical immunology Chen, Y., Zastrow, D. B., Metcalfe, R. D., Gartner, L., Krause, F., Morton, C. J., Marwaha, S., Fresard, L., Huang, Y., Zhao, C., McCormack, C., Bick, D., Worthey, E. A., Eng, C. M., Gold, J., Undiagnosed Diseases Network, Montgomery, S. B., Fisher, P. G., Ashley, E. A., Wheeler, M. T., Parker, M. W., Shanmugasundaram, V., Putoczki, T. L., Schmidt-Arras, D., Laurence, A., Bernstein, J. A., Griffin, M. D., Uhlig, H. H. 2021

    Abstract

    BACKGROUND: Biallelic variants in IL6ST cause a recessive form of hyper-IgE syndrome (HIES) characterized by high IgE, eosinophilia, defective acute phase response, susceptibility to bacterial infections and skeletal abnormalities due to cytokine selective loss-of-function in GP130 with defective IL-6 and IL-11, variable OSM and IL-27 but sparing LIF signaling.OBJECTIVE: To understand the functional and structural impact of recessive HIES-associated IL6ST variants.METHODS: We investigated a patient with HIES using exome, genome and RNA sequencing. Functional assays assessed IL-6, IL-11, IL-27, OSM, LIF, CT-1, CLC, and CNTF signaling. Molecular dynamic simulations and structural modeling of GP130 cytokine receptor complexes were performed.RESULTS: We identify a patient with compound heterozygous novel missense variants in IL6ST (p.Ala517Pro, and exon-skipping null variant p.Gly484_Pro518delinsArg). The p.Ala517Pro variant results in a more profound IL-6 and IL-11 dominated signaling defect compared to the previously identified recessive IL6ST variants p.Asn404Tyr, and p.Pro498Leu. Molecular dynamics simulations suggest that the p.Ala517Pro and p.Asn404Tyr variants result in increased flexibility of the extracellular membrane-proximal domains of GP130. We propose a structural model that explains the cytokine selectivity of pathogenic IL6ST variants that result in recessive HIES. The variants destabilize the hexameric cytokine receptor complexes whereas the trimeric LIF-GP130-LIFR complex remains stable by an additional membrane-proximal interaction. Deletion of this membrane-proximal interaction site in GP130 consequently causes additional defective LIF signaling and Stuve-Wiedemann syndrome.CONCLUSION: Our data provide a structural basis to understand clinical phenotypes in patients with IL6ST variants.

    View details for DOI 10.1016/j.jaci.2021.02.044

    View details for PubMedID 33771552

  • Generation of three induced pluripotent stem cell lines, SCVIi003-A, SCVIi004-A, SCVIi005-A, from patients with ARVD/C caused by heterozygous mutations in the PKP2 gene. Stem cell research Jahng, J. W., Black, K. E., Liu, L., Bae, H. R., Perez, M., Ashley, E. A., Sallam, K., Wu, J. C. 2021; 53: 102284

    Abstract

    Arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is an inherited heart disease which can cause life-threatening ventricular arrhythmias and cardiac dysfunction. The autosomal dominant form of ARVD/C is caused by mutations in the cardiac desmosome, such as those in the plakoglobin plakophilin-2 (PKP2) gene. Here, we generated three human induced pluripotent stem cell (iPSC) lines from the peripheral blood mononuclear cells (PBMCs) of three ARVD/C patients carrying pathogenic variants in their PKP2 genes (c.2065_2070delinsG; c.235C>T; c.1725_1728dup). All lines show the typical morphology of pluripotent stem cells, demonstrate high expression of pluripotent markers, display normal karyotype, and differentiate into all three germ layers in vitro. These lines are valuable resources for studying the pathological mechanisms of ARVD/C caused by PKP2 mutation.

    View details for DOI 10.1016/j.scr.2021.102284

    View details for PubMedID 33743362

  • Validation of an Integrated Risk Tool, Including Polygenic Risk Score, for Atherosclerotic Cardiovascular Disease in Multiple Ethnicities and Ancestries. The American journal of cardiology Weale, M. E., Riveros-Mckay, F., Selzam, S., Seth, P., Moore, R., Tarran, W. A., Gradovich, E., Giner-Delgado, C., Palmer, D., Wells, D., Saffari, A., Sivley, R. M., Lachapelle, A. S., Wand, H., Clarke, S. L., Knowles, J. W., O'Sullivan, J. W., Ashley, E. A., McVean, G., Plagnol, V., Donnelly, P. 2021

    Abstract

    The American College of Cardiology / American Heart Association pooled cohort equations tool (ASCVD-PCE) is currently recommended to assess 10-year risk for atherosclerotic cardiovascular disease (ASCVD). ASCVD-PCE does not currently include genetic risk factors. Polygenic risk scores (PRSs) have been shown to offer a powerful new approach to measuring genetic risk for common diseases, including ASCVD, and to enhance risk prediction when combined with ASCVD-PCE. Most work to date, including the assessment of tools, has focused on performance in individuals of European ancestries. Here we present evidence for the clinical validation of a new integrated risk tool (IRT), ASCVD-IRT, which combines ASCVD-PCE with PRS to predict 10-year risk of ASCVD across diverse ethnicity and ancestry groups. We demonstrate improved predictive performance of ASCVD-IRT over ASCVD-PCE, not only in individuals of self-reported White ethnicities (net reclassification improvement (NRI) (with 95% confidence interval) = 2.7% (1.1 - 4.2)) but also Black / African American / Black Caribbean / Black African (NRI = 2.5% (0.6 - 4.3)) and South Asian (Indian, Bangladeshi or Pakistani) ethnicities (NRI = 8.7% (3.1 - 14.4)). NRI confidence intervals were wider and included zero for ethnicities with smaller sample sizes, including Hispanic (NRI = 7.5% (-1.4 - 16.5)), but PRS effect sizes in these ethnicities were significant and of comparable size to those seen in individuals of White ethnicities. Comparable results were obtained when individuals were analysed by genetically inferred ancestry. Together, these results validate the performance of ASCVD-IRT in multiple ethnicities and ancestries, and favour their generalisation to all ethnicities and ancestries.

    View details for DOI 10.1016/j.amjcard.2021.02.032

    View details for PubMedID 33675770

  • An Integrated Polygenic Tool Substantially Enhances Coronary Artery Disease Prediction. Circulation. Genomic and precision medicine Riveros-Mckay, F., Weale, M. E., Moore, R., Selzam, S., Krapohl, E., Sivley, R. M., Tarran, W. A., Sorensen, P., Lachapelle, A. S., Griffiths, J. A., Saffari, A., Deanfield, J., Spencer, C. C., Hippisley-Cox, J., Hunter, D. J., O'Sullivan, J. W., Ashley, E. A., Plagnol, V., Donnelly, P. 2021

    Abstract

    Background - There is considerable interest in whether genetic data can be used to improve standard cardiovascular disease risk calculators, as the latter are routinely used in clinical practice to manage preventative treatment. Methods - Using the UK Biobank (UKB) resource, we developed our own polygenic risk score (PRS) for coronary artery disease (CAD). We used an additional 60,000 UKB individuals to develop an integrated risk tool (IRT) that combined our PRS with established risk tools (either the American Heart Association/American College of Cardiology's Pooled Cohort Equations (PCE) or UK's QRISK3), and we tested our IRT in an additional, independent, set of 186,451 UKB individuals. Results - The novel CAD PRS shows superior predictive power for CAD events, compared to other published PRSs and is largely uncorrelated with PCE and QRISK3. When combined with PCE into an integrated risk tool, it has superior predictive accuracy. Overall, 10.4% of incident CAD cases were misclassified as low risk by PCE and correctly classified as high risk by the IRT, compared to 4.4% misclassified by the IRT and correctly classified by PCE. The overall net reclassification improvement for the IRT was 5.9% (95% CI 4.7-7.0). When individuals were stratified into age-by-sex subgroups the improvement was larger for all subgroups (range 8.3%-15.4%), with best performance in 40-54yo men (15.4%, 95% CI 11.6-19.3). Comparable results were found using a different risk tool (QRISK3), and also a broader definition of cardiovascular disease. Use of the IRT is estimated to avoid up to 12,000 deaths in the USA over a 5-year period. Conclusions - An integrated risk tool that includes polygenic risk outperforms current risk stratification tools and offers greater opportunity for early interventions. Given the plummeting costs of genetic tests, future iterations of CAD risk tools would be enhanced with the addition of a person's polygenic risk.

    View details for DOI 10.1161/CIRCGEN.120.003304

    View details for PubMedID 33651632

  • Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC bioinformatics Krishnan, V., Utiramerur, S., Ng, Z., Datta, S., Snyder, M. P., Ashley, E. A. 2021; 22 (1): 85

    Abstract

    BACKGROUND: Benchmarking the performance of complex analytical pipelines is an essential part of developing Lab Developed Tests (LDT). Reference samples and benchmark calls published by Genome in a Bottle (GIAB) consortium have enabled the evaluation of analytical methods. The performance of such methods is not uniform across the different genomic regions of interest and variant types. Several benchmarking methods such as hap.py, vcfeval, and vcflib are available to assess the analytical performance characteristics of variant calling algorithms. However, assessing the performance characteristics of an overall LDT assay still requires stringing together several such methods and experienced bioinformaticians to interpret the results. In addition, these methods are dependent on the hardware, operating system and other software libraries, making it impossible to reliably repeat the analytical assessment, when any of the underlying dependencies change in the assay. Here we present a scalable and reproducible, cloud-based benchmarking workflow that is independent of the laboratory and the technician executing the workflow, or the underlying compute hardware used to rapidly and continually assess the performance of LDT assays, across their regions of interest and reportable range, using a broad set of benchmarking samples.RESULTS: The benchmarking workflow was used to evaluate the performance characteristics for secondary analysis pipelines commonly used by Clinical Genomics laboratories in their LDT assays such as the GATK HaplotypeCaller v3.7 and the SpeedSeq workflow based on FreeBayes v0.9.10. Five reference sample truth sets generated by Genome in a Bottle (GIAB) consortium, six samples from the Personal Genome Project (PGP) and several samples with validated clinically relevant variants from the Centers for Disease Control were used in this work. The performance characteristics were evaluated and compared for multiple reportable ranges, such as whole exome and the clinical exome.CONCLUSIONS: We have implemented a benchmarking workflow for clinical diagnostic laboratories that generates metrics such as specificity, precision and sensitivity for germline SNPs and InDels within a reportable range using whole exome or genome sequencing data. Combining these benchmarking results with validation using known variants of clinical significance in publicly available cell lines, we were able to establish the performance of variant calling pipelines in a clinical setting.

    View details for DOI 10.1186/s12859-020-03934-3

    View details for PubMedID 33627090

  • Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases. Genetics in medicine : official journal of the American College of Medical Genetics Kobren, S. N., Baldridge, D., Velinder, M., Krier, J. B., LeBlanc, K., Esteves, C., Pusey, B. N., Zuchner, S., Blue, E., Lee, H., Huang, A., Bastarache, L., Bican, A., Cogan, J., Marwaha, S., Alkelai, A., Murdock, D. R., Liu, P., Wegner, D. J., Paul, A. J., Undiagnosed Diseases Network, Sunyaev, S. R., Kohane, I. S., Acosta, M. T., Adam, M., Adams, D. R., Agrawal, P. B., Alejandro, M. E., Alvey, J., Amendola, L., Andrews, A., Ashley, E. A., Azamian, M. S., Bacino, C. A., Bademci, G., Baker, E., Balasubramanyam, A., Baldridge, D., Bale, J., Bamshad, M., Barbouth, D., Bayrak-Toydemir, P., Beck, A., Beggs, A. H., Behrens, E., Bejerano, G., Bennett, J., Berg-Rood, B., Bernstein, J. A., Berry, G. T., Bican, A., Bivona, S., Blue, E., Bohnsack, J., Bonnenmann, C., Bonner, D., Botto, L., Boyd, B., Briere, L. C., Brokamp, E., Brown, G., Burke, E. A., Burrage, L. C., Butte, M. J., Byers, P., Byrd, W. E., Carey, J., Carrasquillo, O., Chang, T. C., Chanprasert, S., Chao, H., Clark, G. D., Coakley, T. R., Cobban, L. A., Cogan, J. D., Coggins, M., Cole, F. S., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., Crouse, A. B., Cunningham, M., D'Souza, P., Dai, H., Dasari, S., Davis, J., Daya, J. G., Deardorff, M., Dell'Angelica, E. C., Dhar, S. U., Dipple, K., Doherty, D., Dorrani, N., Doss, A. L., Douine, E. D., Draper, D. D., Duncan, L., Earl, D., Eckstein, D. J., Emrick, L. T., Eng, C. M., Esteves, C., Falk, M., Fernandez, L., Ferreira, C., Fieg, E. L., Findley, L. C., Fisher, P. G., Fogel, B. L., Forghani, I., Fresard, L., Gahl, W. A., Glass, I., Gochuico, B., Godfrey, R. A., Golden-Grant, K., Goldman, A. M., Goldrich, M. P., Goldstein, D. B., Grajewski, A., Groden, C. A., Gutierrez, I., Hahn, S., Hamid, R., Hanchard, N. A., Hassey, K., Hayes, N., High, F., Hing, A., Hisama, F. M., Holm, I. A., Hom, J., Horike-Pyne, M., Huang, A., Huang, Y., Huryn, L., Isasi, R., Jamal, F., Jarvik, G. P., Jarvik, J., Jayadev, S., Karaviti, L., Kennedy, J., Kiley, D., Kohane, I. S., Kohler, J. N., Korrick, S., Kozuira, M., Krakow, D., Krasnewich, D. M., Kravets, E., Krier, J. B., LaMoure, G. L., Lalani, S. R., Lam, B., Lam, C., Lanpher, B. C., Lanza, I. R., Latham, L., LeBlanc, K., Lee, B. H., Lee, H., Levitt, R., Lewis, R. A., Lincoln, S. A., Liu, P., Liu, X. Z., Longo, N., Loo, S. K., Loscalzo, J., Maas, R. L., MacDowall, J., MacRae, C. A., Macnamara, E. F., Maduro, V. V., Majcherska, M. M., Mak, B. C., Malicdan, M. C., Mamounas, L. A., Manolio, T. A., Mao, R., Maravilla, K., Markello, T. C., Marom, R., Marth, G., Martin, B. A., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., McCauley, J., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., McGee, E., Mefford, H., Merritt, J. L., Might, M., Mirzaa, G., Morava, E., Moretti, P. M., Moretti, P., Mosbrook-Davis, D., Mulvihill, J. J., Murdock, D. R., Nagy, A., Nakano-Okuno, M., Nath, A., Nelson, S. F., Newman, J. H., Nicholas, S. K., Nickerson, D., Nieves-Rodriguez, S., Novacic, D., Oglesbee, D., Orengo, J. P., Pace, L., Pak, S., Pallais, J. C., Palmer, C. G., Papp, J. C., Parker, N. H., Phillips, J. A., Posey, J. E., Potocki, L., Power, B., Pusey, B. N., Quinlan, A., Raja, A. N., Rao, D. A., Raskind, W., Renteria, G., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Rosenwasser, N., Rossignol, F., Ruzhnikov, M., Sacco, R., Sampson, J. B., Samson, S. L., Saporta, M., Schaechter, J., Schedl, T., Schoch, K., Scott, C. R., Scott, D. A., Shashi, V., Shin, J., Signer, R. H., Silverman, E. K., Sinsheimer, J. S., Sisco, K., Smith, E. C., Smith, K. S., Solem, E., Solnica-Krezel, L., Ben Solomon, S., Spillmann, R. C., Stoler, J. M., Sullivan, J. A., Sullivan, K., Sun, A., Sutton, S., Sweetser, D. A., Sybert, V., Tabor, H. K., Tan, A. L., Tan, Q. K., Tekin, M., Telischi, F., Thorson, W., Thurm, A., Tifft, C. J., Toro, C., Tran, A. A., Tucker, B. M., Urv, T. K., Vanderver, A., Velinder, M., Viskochil, D., Vogel, T. P., Wahl, C. E., Walker, M., Wallace, S., Walley, N. M., Walsh, C. A., Wambach, J., Wan, J., Wang, L., Wangler, M. F., Ward, P. A., Wegner, D., Wener, M., Wenger, T., Perry, K. W., Westerfield, M., Wheeler, M. T., Whitlock, J., Wolfe, L. A., Woods, J. D., Yamamoto, S., Yang, J., Yousef, M., Zastrow, D. B., Zein, W., Zhao, C., Zuchner, S. 2021

    Abstract

    PURPOSE: Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful.METHODS: We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols.RESULTS: We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases.CONCLUSION: The largest differences across diagnostic workflows suggest that advances in structural variant detection, noncoding variant interpretation, and integration of additional biomedical data may be especially promising for solving chronically undiagnosed cases.

    View details for DOI 10.1038/s41436-020-01084-8

    View details for PubMedID 33580225

  • Whole-Transcriptome Profiling of Human Heart Tissues Reveals the Potential Novel Players and Regulatory Networks in Different Cardiomyopathy Subtypes of Heart Failure. Circulation. Genomic and precision medicine Liu, C., Ni, Y., Moravec, C. S., Morley, M., Ashley, E. A., Cappola, T. P., Margulies, K. B., Tang, W. H. 2021: CIRCGEN120003142

    View details for DOI 10.1161/CIRCGEN.120.003142

    View details for PubMedID 33517678

  • Graphical analysis for phenome-wide causal discovery in genotyped population-scale biobanks. Nature communications Amar, D., Sinnott-Armstrong, N., Ashley, E. A., Rivas, M. A. 2021; 12 (1): 350

    Abstract

    Causal inference via Mendelian randomization requires making strong assumptions about horizontal pleiotropy, where genetic instruments are connected to the outcome not only through the exposure. Here, we present causal Graphical Analysis Using Genetics (cGAUGE), a pipeline that overcomes these limitations using instrument filters with provable properties. This is achievable by identifying conditional independencies while examining multiple traits. cGAUGE also uses ExSep (Exposure-based Separation), a novel test for the existence of causal pathways that does not require selecting instruments. In simulated data we illustrate how cGAUGE can reduce the empirical false discovery rate by up to 30%, while retaining the majority of true discoveries. On 96 complex traits from 337,198 subjects from the UK Biobank, our results cover expected causal links and many new ones that were previously suggested by correlation-based observational studies. Notably, we identify multiple risk factors for cardiovascular disease, including red blood cell distribution width.

    View details for DOI 10.1038/s41467-020-20516-2

    View details for PubMedID 33441555

  • SARS-CoV-2 RNAemia predicts clinical deterioration and extrapulmonary complications from COVID-19. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Ram-Mohan, N. n., Kim, D. n., Zudock, E. J., Hashemi, M. M., Tjandra, K. C., Rogers, A. J., Blish, C. A., Nadeau, K. C., Newberry, J. A., Quinn, J. V., O'Hara, R. n., Ashley, E. n., Nguyen, H. n., Jiang, L. n., Hung, P. n., Blomkalns, A. L., Yang, S. n. 2021

    Abstract

    The determinants of COVID-19 disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between SARS-CoV-2 RNAemia and disease severity, clinical deterioration, and specific EPCs.We used quantitative (qPCR) and digital (dPCR) PCR to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the Emergency Department (ED) with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression.23.0% (44/191) of SARS-CoV-2 positive patients had viral RNA detected in plasma by dPCR, compared to 1.4% (2/147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAaemic patients were more likely to manifest severe disease (OR 6.72 [95% CI, 2.45 - 19.79]), worsening of disease severity (OR 2.43 [95% CI, 1.07 - 5.38]), and EPCs (OR 2.81 [95% CI, 1.26 - 6.36]). RNA load correlated with maximum severity (r = 0.47 [95% CI, 0.20 - 0.67]).dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Since many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.

    View details for DOI 10.1093/cid/ciab394

    View details for PubMedID 33949665

  • Combining Clinical and Polygenic Risk Improves Stroke Prediction Among Individuals with Atrial Fibrillation. Circulation. Genomic and precision medicine O'Sullivan, J. W., Shcherbina, A., Justesen, J. M., Turakhia, M., Perez, M., Wand, H., Tcheandjieu, C., Clarke, S. L., Rivas, M. A., Ashley, E. A. 2021

    Abstract

    Background - Atrial fibrillation (AF) is associated with a five-fold increased risk of ischemic stroke. A portion of this risk is heritable, however current risk stratification tools (CHA2DS2-VASc) don't include family history or genetic risk. We hypothesized that we could improve ischemic stroke prediction in patients with AF by incorporating polygenic risk scores (PRS). Methods - Using data from the largest available GWAS in Europeans, we combined over half a million genetic variants to construct a PRS to predict ischemic stroke in patients with AF. We externally validated this PRS in independent data from the UK Biobank, both independently and integrated with clinical risk factors. The integrated PRS and clinical risk factors risk tool had the greatest predictive ability. Results - Compared with the currently recommended risk tool (CHA2DS2-VASc), the integrated tool significantly improved net reclassification (NRI: 2.3% (95%CI: 1.3% to 3.0%)), and fit (χ2 P =0.002). Using this improved tool, >115,000 people with AF would have improved risk classification in the US. Independently, PRS was a significant predictor of ischemic stroke in patients with AF prospectively (Hazard Ratio: 1.13 per 1 SD (95%CI: 1.06 to 1.23)). Lastly, polygenic risk scores were uncorrelated with clinical risk factors (Pearson's correlation coefficient: -0.018). Conclusions - In patients with AF, there appears to be a significant association between PRS and risk of ischemic stroke. The greatest predictive ability was found with the integration of PRS and clinical risk factors, however the prediction of stroke remains challenging.

    View details for DOI 10.1161/CIRCGEN.120.003168

    View details for PubMedID 34029116

  • Time trajectories in the transcriptomic response to exercise - a meta-analysis. Nature communications Amar, D., Lindholm, M. E., Norrbom, J., Wheeler, M. T., Rivas, M. A., Ashley, E. A. 2021; 12 (1): 3471

    Abstract

    Exercise training prevents multiple diseases, yet the molecular mechanisms that drive exercise adaptation are incompletely understood. To address this, we create a computational framework comprising data from skeletal muscle or blood from 43 studies, including 739 individuals before and after exercise or training. Using linear mixed effects meta-regression, we detect specific time patterns and regulatory modulators of the exercise response. Acute and long-term responses are transcriptionally distinct and we identify SMAD3 as a central regulator of the exercise response. Exercise induces a more pronounced inflammatory response in skeletal muscle of older individuals and our models reveal multiple sex-associated responses. We validate seven of our top genes in a separate human cohort. In this work, we provide a powerful resource ( www.extrameta.org ) that expands the transcriptional landscape of exercise adaptation by extending previously known responses and their regulatory networks, and identifying novel modality-, time-, age-, and sex-associated changes.

    View details for DOI 10.1038/s41467-021-23579-x

    View details for PubMedID 34108459

  • Towards precision medicine in heart failure. Nature reviews. Cardiology Weldy, C. S., Ashley, E. A. 2021

    Abstract

    The number of therapies for heart failure (HF) with reduced ejection fraction has nearly doubled in the past decade. In addition, new therapies for HF caused by hypertrophic and infiltrative disease are emerging rapidly. Indeed, we are on the verge of a new era in HF in which insights into the biology of myocardial disease can be matched to an understanding of the genetic predisposition in an individual patient to inform precision approaches to therapy. In this Review, we summarize the biology of HF, emphasizing the causal relationships between genetic contributors and traditional structure-based remodelling outcomes, and highlight the mechanisms of action of traditional and novel therapeutics. We discuss the latest advances in our understanding of both the Mendelian genetics of cardiomyopathy and the complex genetics of the clinical syndrome presenting as HF. In the phenotypic domain, we discuss applications of machine learning for the subcategorization of HF in ways that might inform rational prescribing of medications. We aim to bridge the gap between the biology of the failing heart, its diverse clinical presentations and the range of medications that we can now use to treat it. We present a roadmap for the future of precision medicine in HF.

    View details for DOI 10.1038/s41569-021-00566-9

    View details for PubMedID 34108678

  • Combining digital data and artificial intelligence for cardiovascular health. Cardiovascular research Soto, J. T., Hershman, S. G., Ashley, E. A. 2021; 117 (9): e116-e117

    View details for DOI 10.1093/cvr/cvab211

    View details for PubMedID 34320165

  • Cardiopulmonary Exercise Testing With Echocardiography to Assess Recovery in Patients With Ventricular Assist Devices. ASAIO journal (American Society for Artificial Internal Organs : 1992) Christle, J. W., Moneghetti, K. J., Duclos, S., Mueller, S., Moayedi, Y., Khush, K. K., Haddad, F., Hiesinger, W., Myers, J., Ashley, E. A., Teuteberg, J. J., Wheeler, M. T., Banerjee, D. 2021; 67 (10): 1134-1138

    Abstract

    The left ventricular assist device (LVAD) is an established treatment for select patients with end-stage heart failure. Some patients recovered and are considered for explantation. Assessing recovery involves exercise testing and echo ramping on full and minimal LVAD support. Combined cardiopulmonary exercise testing with simultaneous echo ramping (CPET-R) has not been well studied. Patients were included if they had CPET within the previous 6 months, were clinically stable, and had an INR >2.0 on the day of examination. Patients had CPET-R on two occasions within 14 days: (a) with LVAD at therapeutic speed and (b) with LVAD at the lowest speed possible. Six patients were between 29 and 75 years (two female). One patient did not complete a turn-down test due to evidence of ischemia on initial CPET-R subsequently confirmed as a significant coronary artery stenosis on angiography. There were no significant differences in CPET or echo metrics between LVAD speeds. Two patients were explanted due to presumed LV recovery and remained event free for 30 and 47 months, respectively. Serial CPET-R seems safe and feasible for the evaluation of LV and global function and may result in improved clinical decision making for LVAD explantation.

    View details for DOI 10.1097/MAT.0000000000001383

    View details for PubMedID 34570726

  • Clinical utility of genomic sequencing: a measurement toolkit. NPJ genomic medicine Hayeems, R. Z., Dimmock, D., Bick, D., Belmont, J. W., Green, R. C., Lanpher, B., Jobanputra, V., Mendoza, R., Kulkarni, S., Grove, M. E., Taylor, S. L., Ashley, E., Medical Genome Initiative 2020; 5 (1): 56

    Abstract

    Whole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder's perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.

    View details for DOI 10.1038/s41525-020-00164-7

    View details for PubMedID 33319814

  • Associations Between Female Sex, Sarcomere Variants and Clinical Outcomes in Hypertrophic Cardiomyopathy. Circulation. Genomic and precision medicine Lakdawala, N. K., Olivotto, I., Day, S. M., Han, L., Ashley, E. A., Michels, M., Ingles, J., Semsarian, C., Jacoby, D., Jefferies, J. L., Colan, S. D., Pereira, A. C., Rossano, J. W., Wittekind, S., Ware, J. S., Saberi, S., Helms, A. S., Cirino, A. L., Leinwand, L. A., Seidman, C. E., Ho, C. Y. 2020

    Abstract

    Background - The impact of sex on phenotypic expression in hypertrophic cardiomyopathy (HCM) has not been well characterized in genotyped cohorts. Methods - Retrospective cohort study from an international registry of patients receiving care at experienced HCM centers. Sex-based differences in baseline characteristics and clinical outcomes were assessed. Results - Of 5,873 patients (3,788 genotyped), 2,226 (37.9%) were women. At baseline, women were older (49.0±19.9 vs. 42.9±18.4 years, p<0.001) and more likely to have pathogenic/likely-pathogenic sarcomeric variants (SARC+; 51% vs 43%, p<0.001) despite equivalent utilization of genetic testing. Age at diagnosis varied by sex and genotype despite similar distribution of causal genes. Women were 3.6 to 7.1 years older at diagnosis (p<0.02) except for patients with MYH7 variants where age at diagnosis was comparable for women and men (n=492; 34.8±19.2 vs 33.3±16.8 years, p=0.39). Over 7.7 median years of follow up, NYHA III-IV heart failure (HF) was more common in women (HR 1.87, CI 1.48-2.36, p<0.001), after controlling for their higher burden of symptoms and outflow tract obstruction at baseline, reduced ejection fraction, SARC+, age and hypertension. All-cause mortality was increased in women (HR 1.50, CI 1.13-1.99, p<0.01), but neither ICD utilization nor ventricular arrhythmia varied by sex. Conclusions - In HCM, women are older at diagnosis, partly modified by genetic substrate. Regardless of genotype, women were at higher risk of mortality and developing severe HF symptoms. This points to a sex-effect on long-term myocardial performance in HCM, which should be investigated further.

    View details for DOI 10.1161/CIRCGEN.120.003062

    View details for PubMedID 33284039

  • Clinical utility of genomic sequencing: A measurement toolkit Hayeems, R. Z., Dimmock, D., Bick, D., Belmont, J., Green, R., Lanpher, B., Mendoza, R., Jobanputra, V., Taylor, S., Kulkarni, S., Grove, M., Ashley, E., Med Genome Initiative SPRINGERNATURE. 2020: 787
  • Digital Health Applications for Pharmacogenetic Clinical Trials. Genes Naik, H., Palaniappan, L., Ashley, E. A., Scott, S. A. 2020; 11 (11)

    Abstract

    Digital health (DH) is the use of digital technologies and data analytics to understand health-related behaviors and enhance personalized clinical care. DH is increasingly being used in clinical trials, and an important field that could potentially benefit from incorporating DH into trial design is pharmacogenetics. Prospective pharmacogenetic trials typically compare a standard care arm to a pharmacogenetic-guided therapeutic arm. These trials often require large sample sizes, are challenging to recruit into, lack patient diversity, and can have complicated workflows to deliver therapeutic interventions to both investigators and patients. Importantly, the use of DH technologies could mitigate these challenges and improve pharmacogenetic trial design and operation. Some DH use cases include (1) automatic electronic health record-based patient screening and recruitment; (2) interactive websites for participant engagement; (3) home- and tele-health visits for patient convenience (e.g., samples for lab tests, physical exams, medication administration); (4) healthcare apps to collect patient-reported outcomes, adverse events and concomitant medications, and to deliver therapeutic information to patients; and (5) wearable devices to collect vital signs, electrocardiograms, sleep quality, and other discrete clinical variables. Given that pharmacogenetic trials are inherently challenging to conduct, future pharmacogenetic utility studies should consider implementing DH technologies and trial methodologies into their design and operation.

    View details for DOI 10.3390/genes11111261

    View details for PubMedID 33114567

  • Patient-Specific Induced Pluripotent Stem Cells Implicate Intrinsic Impaired Contractility in Hypoplastic Left Heart Syndrome. Circulation Paige, S. L., Galdos, F. X., Lee, S., Chin, E. T., Ranjbarvaziri, S., Feyen, D. A., Darsha, A. K., Xu, S., Ryan, J. A., Beck, A. L., Qureshi, M. Y., Miao, Y., Gu, M., Bernstein, D., Nelson, T. J., Mercola, M., Rabinovitch, M., Ashley, E. A., Parikh, V. N., Wu, S. M. 2020; 142 (16): 1605–8

    View details for DOI 10.1161/CIRCULATIONAHA.119.045317

    View details for PubMedID 33074758

  • Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions. Genetics in medicine : official journal of the American College of Medical Genetics Zhang, X., Walsh, R., Whiffin, N., Buchan, R., Midwinter, W., Wilk, A., Govind, R., Li, N., Ahmad, M., Mazzarotto, F., Roberts, A., Theotokis, P. I., Mazaika, E., Allouba, M., de Marvao, A., Pua, C. J., Day, S. M., Ashley, E., Colan, S. D., Michels, M., Pereira, A. C., Jacoby, D., Ho, C. Y., Olivotto, I., Gunnarsson, G. T., Jefferies, J. L., Semsarian, C., Ingles, J., O'Regan, D. P., Aguib, Y., Yacoub, M. H., Cook, S. A., Barton, P. J., Bottolo, L., Ware, J. S. 2020

    Abstract

    PURPOSE: Accurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning variant prioritization tools are imprecise and ignore important parameters defining gene-disease relationships, e.g., distinct consequences of gain-of-function versus loss-of-function variants. We hypothesized that incorporating disease-specific information would improve tool performance.METHODS: We developed a disease-specific variant classifier, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias. We assessed CardioBoost's ability to discriminate known pathogenic from benign variants, prioritize disease-associated variants, and stratify patient outcomes.RESULTS: CardioBoost has high global discrimination accuracy (precision recall area under the curve [AUC] 0.91 for cardiomyopathies; 0.96 for arrhythmias), outperforming existing tools (4-24% improvement). CardioBoost obtains excellent accuracy (cardiomyopathies 90.2%; arrhythmias 91.9%) for variants classified with >90% confidence, and increases the proportion of variants classified with high confidence more than twofold compared with existing tools. Variants classified as disease-causing are associated with both disease status and clinical severity, including a 21% increased risk (95% confidence interval [CI] 11-29%) of severe adverse outcomes by age 60 in patients with hypertrophic cardiomyopathy.CONCLUSIONS: A disease-specific variant classifier outperforms state-of-the-art genome-wide tools for rare missense variants in inherited cardiac conditions ( https://www.cardiodb.org/cardioboost/ ), highlighting broad opportunities for improved pathogenicity prediction through disease specificity.

    View details for DOI 10.1038/s41436-020-00972-3

    View details for PubMedID 33046849

  • Multi-task deep learning for cardiac rhythm detection in wearable devices. NPJ digital medicine Torres-Soto, J., Ashley, E. A. 2020; 3 (1): 116

    Abstract

    Wearable devices enable theoretically continuous, longitudinal monitoring of physiological measurements such as step count, energy expenditure, and heart rate. Although the classification of abnormal cardiac rhythms such as atrial fibrillation from wearable devices has great potential, commercial algorithms remain proprietary and tend to focus on heart rate variability derived from green spectrum LED sensors placed on the wrist, where noise remains an unsolved problem. Here we develop DeepBeat, a multitask deep learning method to jointly assess signal quality and arrhythmia event detection in wearable photoplethysmography devices for real-time detection of atrial fibrillation. The model is trained on approximately one million simulated unlabeled physiological signals and fine-tuned on a curated dataset of over 500 K labeled signals from over 100 individuals from 3 different wearable devices. We demonstrate that, in comparison with a single-task model, our architecture using unsupervised transfer learning through convolutional denoising autoencoders dramatically improves the performance of atrial fibrillation detection from a F1 score of 0.54 to 0.96. We also include in our evaluation a prospectively derived replication cohort of ambulatory participants where the algorithm performed with high sensitivity (0.98), specificity (0.99), and F1 score (0.93). We show that two-stage training can help address the unbalanced data problem common to biomedical applications, where large-scale well-annotated datasets are hard to generate due to the expense of manual annotation, data acquisition, and participant privacy.

    View details for DOI 10.1038/s41746-020-00320-4

    View details for PubMedID 34497341

  • Temporal Trend of Age at Diagnosis in Hypertrophic Cardiomyopathy: An Analysis of the International Sarcomeric Human Cardiomyopathy Registry. Circulation. Heart failure Canepa, M., Fumagalli, C., Tini, G., Vincent-Tompkins, J., Day, S. M., Ashley, E. A., Mazzarotto, F., Ware, J. S., Michels, M., Jacoby, D., Ho, C. Y., Olivotto, I., SHaRe Investigators 2020: CIRCHEARTFAILURE120007230

    Abstract

    BACKGROUND: Over the last 50 years, the epidemiology of hypertrophic cardiomyopathy (HCM) has changed because of increased awareness and availability of advanced diagnostic tools. We aim to describe the temporal trends in age, sex, and clinical characteristics at HCM diagnosis over >4 decades.METHODS: We retrospectively analyzed records from the ongoing multinational Sarcomeric Human Cardiomyopathy Registry. Overall, 7286 patients with HCM diagnosed at an age ≥18 years between 1961 and 2019 were included in the analysis and divided into 3 eras of diagnosis (<2000, 2000-2010, >2010).RESULTS: Age at diagnosis increased markedly over time (40±14 versus 47±15 versus 51±16 years, P<0.001), both in US and non-US sites, with a stable male-to-female ratio of about 3:2. Frequency of familial HCM declined over time (38.8% versus 34.3% versus 32.7%, P<0.001), as well as heart failure symptoms at presentation (New York Heart Association III/IV: 18.1% versus 15.8% versus 12.6%, P<0.001). Left ventricular hypertrophy became less marked over time (maximum wall thickness: 20±6 versus 18±5 versus 17±5 mm, P<0.001), while prevalence of obstructive HCM was greater in recent cohorts (peak gradient >30 mm Hg: 31.9% versus 39.3% versus 39.0%, P=0.001). Consistent with decreasing phenotypic severity, yield of pathogenic/likely pathogenic variants at genetic testing decreased over time (57.7% versus 45.6% versus 38.4%, P<0.001).CONCLUSIONS: Evolving HCM populations include progressively greater representation of older patients with sporadic disease, mild phenotypes, and genotype-negative status. Such trend suggests a prominent role of imaging over genetic testing in promoting HCM diagnoses and urges efforts to understand genotype-negative disease eluding the classic monogenic paradigm.

    View details for DOI 10.1161/CIRCHEARTFAILURE.120.007230

    View details for PubMedID 32894986

  • Apelin increases atrial conduction velocity, refractoriness, and prevents inducibility of atrial fibrillation. JCI insight Kim, Y. M., Lakin, R., Zhang, H., Liu, J., Sachedina, A., Singh, M., Wilson, E., Perez, M., Verma, S., Quertermous, T., Olgin, J., Backx, P. H., Ashley, E. A. 2020; 5 (17)

    Abstract

    Previous studies have shown an association between elevated atrial NADPH-dependent oxidative stress and decreased plasma apelin in patients with atrial fibrillation (AF), though the basis for this relationship is unclear. In the current study, RT-PCR and immunofluorescence studies of human right atrial appendages (RAAs) showed expression of the apelin receptor, APJ, and reduced apelin content in the atria, but not in plasma, of patients with AF versus normal sinus rhythm. Disruption of the apelin gene in mice increased (2.4-fold) NADPH-stimulated superoxide levels and slowed atrial conduction velocities in optical mapping of a Langendorff-perfused isolated heart model, suggesting that apelin levels may influence AF vulnerability. Indeed, in mice with increased AF vulnerability (induced by chronic intense exercise), apelin administration reduced the incidence and duration of induced atrial arrhythmias in association with prolonged atrial refractory periods. Moreover, apelin decreased AF induction in isolated atria from exercised mice while accelerating conduction velocity and increasing action potential durations. At the cellular level, these changes were associated with increased atrial cardiomyocyte sodium currents. These findings support the conclusion that reduced atrial apelin is maladaptive in fibrillating human atrial myocardium and that increasing apelin bioavailability may be a worthwhile therapeutic strategy for treating and preventing AF.

    View details for DOI 10.1172/jci.insight.126525

    View details for PubMedID 32879139

  • Spatial and Functional Distribution of MYBPC3 Pathogenic Variants and Clinical Outcomes in Patients with Hypertrophic Cardiomyopathy. Circulation. Genomic and precision medicine Helms, A. S., Thompson, A. D., Glazier, A. A., Hafeez, N., Kabani, S., Rodriguez, J., Yob, J. M., Woolcock, H., Mazzarotto, F., Lakdawala, N. K., Wittekind, S. G., Pereira, A. C., Jacoby, D. L., Colan, S. D., Ashley, E. A., Saberi, S., Ware, J. S., Ingles, J., Semsarian, C., Michels, M., Olivotto, I., Ho, C. Y., Day, S. M. 2020

    Abstract

    Background - Pathogenic variants in MYBPC3, encoding cardiac MyBP-C, are the most common cause of familial hypertrophic cardiomyopathy. A large number of unique MYBPC3 variants and relatively small genotyped HCM cohorts have precluded detailed genotype-phenotype correlations. Methods - Patients with HCM and MYBPC3 variants were identified from the Sarcomeric Human Cardiomyopathy Registry (SHaRe). Variant types and locations were analyzed, morphologic severity was assessed, and time-event analysis was performed (composite clinical outcome of sudden death, class III/IV heart failure, LVAD/transplant, atrial fibrillation). For selected missense variants falling in enriched domains, myofilament localization and degradation rates were measured in vitro. Results - Among 4,756 genotyped HCM patients in SHaRe, 1,316 patients were identified with adjudicated pathogenic truncating (N=234 unique variants, 1047 patients) or non-truncating (N=22 unique variants, 191 patients) variants in MYBPC3. Truncating variants were evenly dispersed throughout the gene, and hypertrophy severity and outcomes were not associated with variant location (grouped by 5' - 3' quartiles or by founder variant subgroup). Non-truncating pathogenic variants clustered in the C3, C6, and C10 domains (18 of 22, 82%, p<0.001 vs. gnomAD common variants) and were associated with similar hypertrophy severity and adverse event rates as observed with truncating variants. MyBP-C with variants in the C3, C6, and C10 domains was expressed in rat ventricular myocytes. C10 mutant MyBP-C failed to incorporate into myofilaments and degradation rates were accelerated by ~90%, while C3 and C6 mutant MyBP-C incorporated normally with degradation rate similar to wild-type. Conclusions - Truncating variants account for 91% of MYBPC3 pathogenic variants and cause similar clinical severity and outcomes regardless of location, consistent with locus-independent loss-of-function. Non-truncating MYBPC3 pathogenic variants are regionally clustered, and a subset also cause loss-of-function through failure of myofilament incorporation and rapid degradation. Cardiac morphology and clinical outcomes are similar in patients with truncating vs. non-truncating variants.

    View details for DOI 10.1161/CIRCGEN.120.002929

    View details for PubMedID 32841044

  • Silencing of MYH7 ameliorates disease phenotypes in human iPSC-Cardiomyocytes. Physiological genomics Dainis, A., Zaleta-Rivera, K., Ribeiro, A., Chang, A. C., Shang, C., Lan, F., Burridge, P. W., Liu, W. R., Wu, J. C., Chang, A. C., Pruitt, B. L., Wheeler, M., Ashley, E. A. 2020

    Abstract

    Allele-specific RNA silencing has been shown to be an effective therapeutic treatment in a number of diseases, including neurodegenerative disorders. Studies of allele-specific silencing in hypertrophic cardiomyopathy (HCM) to date have focused on mouse models of disease. We here examine allele-specific silencing in a human-cell model of HCM. We investigate two methods of silencing, short hairpin RNA (shRNA) and antisense oligonucleotide (ASO) silencing, using a human induced pluripotent stem cell-derived cardiomyocyte (hiPSC-CM) model. We used cellular micropatterning devices with traction force microscopy and automated video analysis to examine each strategy's effects on contractile defects underlying disease. We find that shRNA silencing ameliorates contractile phenotypes of disease, reducing disease-associated increases in cardiomyocyte velocity, force, and power. We find that ASO silencing, while better able to target and knockdown a specific disease-associated allele, showed more modest improvements in contractile phenotypes. These findings are the first exploration of allele-specific silencing in a human HCM model and provide a foundation for further exploration of silencing as a therapeutic treatment for MYH7-mutation-associated cardiomyopathy.

    View details for DOI 10.1152/physiolgenomics.00021.2020

    View details for PubMedID 32567507

  • The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic. Genome medicine Marshall, C. R., Bick, D., Belmont, J. W., Taylor, S. L., Ashley, E., Dimmock, D., Jobanputra, V., Kearney, H. M., Kulkarni, S., Rehm, H., Medical Genome Initiative 2020; 12 (1): 48

    Abstract

    Clinical whole-genome sequencing (WGS) offers clear diagnostic benefits for patients with rare disease. However, there are barriers to its widespread adoption, including a lack of standards for clinical practice. The Medical Genome Initiative consortium was formed to provide practical guidance and support the development of standards for the use of clinical WGS.

    View details for DOI 10.1186/s13073-020-00748-z

    View details for PubMedID 32460895

  • CLINICAL, CELLULAR AND MOLECULAR FEATURES OF THE IL6ST - RELATED IMMUNODEFICIENCY SYNDROME Zastrow, D. B., Kohler, J., Bonner, D., Reuter, C., Fernandez, L., Chen, H., Laurence, A., Fresard, L., Marwaha, S., McCormack, C., Majcherska, M., Velez-Bartolomei, F., Yang, Y., Eng, C. M., Fisher, P. G., Ashley, E. A., Uhlig, H. H., Montgomery, S. B., Wheeler, M. T., Bernstein, J. A., Undiagnosed Dis Network WILEY. 2020: 937
  • Variant Interpretation for Dilated Cardiomyopathy: Refinement of the American College of Medical Genetics and Genomics/ClinGen Guidelines for the DCM Precision Medicine Study. Circulation. Genomic and precision medicine Morales, A., Kinnamon, D. D., Jordan, E., Platt, J., Vatta, M., Dorschner, M. O., Starkey, C. A., Mead, J. O., Ai, T., Burke, W., Gastier-Foster, J., Jarvik, G. P., Rehm, H. L., Nickerson, D. A., Hershberger, R. E., DCM Precision Medicine study of the DCM Consortium, DCM Consortium institutions and personnel participating in this study: Study Principal Investigator and Co-Investigators, D. C., Bowen, D. J., Haas, G., Abraham, W. T., Binkley, P. F., Hasan, A., Host, J., Lampert, B., Smith, S., Huggins, G. S., DeNofrio, D. D., Kiernan, M., Fishbein, D., Cheng, R., Dardas, T., Levy, W., Mahr, C., Masri, S., Stempien-Otero, A., Gottlieb Ste Pl, S. S., Wheeler, M., Ashley, E., Hofmeyer, M., Tang, W. H., Starling, R., Owens, A., Marguilies, K. B., Cappola, T., Goldberg, L. R., McLean, R., Moore, C. K., Long, R. C., Jimenez Carcamo, J., Trachtenberg, B., Ashrith, G., Bhimarahj, A., Sweitzer, N. K., Shah, P., Lowes, B., Stoller, D., Smart, F., Morris, A. A., Wilcox, J., Pan, S., Ewald, G. A., Aaronson, K. D., Wang, J. J., Pamboukian, S., Judge, D. P., Kransdorf, E. P., Garg, S., Desvigne-Nickens, P., Troendle, J., Fu, Y., Hindorff, L. 2020; 13 (2): e002480

    Abstract

    BACKGROUND: The hypothesis of the Dilated Cardiomyopathy Precision Medicine Study is that most dilated cardiomyopathy has a genetic basis. The study returns results to probands and, when indicated, to relatives. While both the American College of Medical Genetics and Genomics/Association for Molecular Pathology and ClinGen's MYH7-cardiomyopathy specifications provide relevant guidance for variant interpretation, further gene- and disease-specific considerations were required for dilated cardiomyopathy. To this end, we tailored the ClinGen MYH7-cardiomyopathy variant interpretation framework; the specifications implemented for the study are presented here.METHODS: Modifications were created and approved by an external Variant Adjudication Oversight Committee. After a pilot using 81 probands, further adjustments were made, resulting in 27 criteria (9 modifications of the ClinGen MYH7 framework and reintroduction of 2 American College of Medical Genetics and Genomics/Association of Molecular Pathology criteria that were deemed not applicable by the ClinGen MYH7 working group).RESULTS: These criteria were applied to 2059 variants in a test set of 97 probands. Variants were classified as benign (n=1702), likely benign (n=33), uncertain significance (n=71), likely pathogenic (likely pathogenic; n=12), and pathogenic (P; n=3). Only 2/15 likely pathogenic/P variants were identified in Non-Hispanic African ancestry probands.CONCLUSIONS: We tailored the ClinGen MYH7 criteria for our study. Our preliminary data show that 15/97 (15.5%) probands have likely pathogenic/P variants, most of which were identified in probands of Non-Hispanic European ancestry. We anticipate continued evolution of our approach, one that will be informed by new insights on variant interpretation and a greater understanding of the genetic architecture of dilated cardiomyopathy.CLINICAL TRIAL REGISTRATION: URL: https://www.clinicaltrials.gov; Unique identifier: NCT03037632.

    View details for DOI 10.1161/CIRCGEN.119.002480

    View details for PubMedID 32160020

  • Hypertrophic Cardiomyopathy with Left Ventricular Systolic Dysfunction: Insights from the SHaRe Registry. Circulation Marstrand, P., Han, L., Day, S. M., Olivotto, I., Ashley, E. A., Michels, M., Pereira, A. C., Wittekind, S. G., Helms, A., Saberi, S., Jacoby, D., Ware, J. S., Colan, S. D., Semsarian, C., Ingles, J., Lakdawala, N. K., Ho, C. Y., SHaRe Investigators 2020

    Abstract

    Background: The terminology "end-stage" has been used to describe hypertrophic cardiomyopathy (HCM) with left ventricular systolic dysfunction (herein referred to as HCM-LVSD), defined when left ventricular ejection fraction (LVEF) <50% is present. The prognosis of HCM-LVSD has reportedly been poor, but due to its relative rarity, natural history remains incompletely characterized. Methods: Data from eleven high-volume HCM specialty centers comprising the international Sarcomeric Human Cardiomyopathy Registry (SHaRe) were used to describe the natural history of patients with HCM-LVSD. Cox proportional hazards models were used to identify predictors of prognosis and incident development. Results: From a cohort of 6,793 HCM patients, 553 (8%) met criteria for HCM-LVSD. Overall, 75% of HCM-LVSD patients experienced clinically relevant events and 35% met the composite outcome (all-cause death (n=128), cardiac transplantation (n=55) or left ventricular assist device implantation (n=9). After recognition of HCM-LVSD, the median time to composite outcome was 8.4 years. However, there was substantial individual variation in natural history. Significant predictors of the composite outcome included the presence of multiple pathogenic/likely pathogenic sarcomeric variants (Hazard Ratio (HR) 5.6 [95% Confidence Interval 2.3-13.5]), atrial fibrillation (HR 2.6 [1.7, 3.5]), LVEF <35% (HR 2.0 [1.3, 2.8]). The incidence of new HCM-LVSD was ~7.5% over 15 years. Significant predictors of developing incident HCM-LVSD included greater LV cavity size (HR 1.1 [1.0-1.3] and wall thickness (HR 1.3 [1.1, 1.4]), LVEF 50-60% (HR 1.8 [1.2, 2.8]-2.8 [1.8, 4.2]) at baseline evaluation, the presence of late gadolinium enhancement on cardiac magnetic resonance imaging (HR 2.3 [1.0, 4.9]), and the presence of a pathogenic/likely pathogenic sarcomeric variant, particularly in thin filament genes (HR 1.5 [1.0, 2.1] and 2.5 [1.2, 5.1], respectively). Conclusions: HCM-LVSD affects approximately 8% of HCM patients. Although the natural history of HCM-LVSD was variable, 75% of patients experienced adverse events, including 35% experiencing a death-equivalent with an estimated median time of 8.4 years after developing systolic dysfunction. In addition to clinical features, genetic substrate appears to play a role in both prognosis (multiple sarcomeric variants) and in the risk for incident development of HCM-LVSD (thin filament variants).

    View details for DOI 10.1161/CIRCULATIONAHA.119.044366

    View details for PubMedID 32228044

  • A DEEP LEARNING ALGORITHM ACCURATELY DETECTS PERICARDIAL EFFUSION ON ECHOCARDIOGRAPHY Nayak, A., Ouyang, D., Ashley, E. A. ELSEVIER SCIENCE INC. 2020: 1563
  • Deep learning interpretation of echocardiograms. NPJ digital medicine Ghorbani, A., Ouyang, D., Abid, A., He, B., Chen, J. H., Harrington, R. A., Liang, D. H., Ashley, E. A., Zou, J. Y. 2020; 3 (1): 10

    Abstract

    Echocardiography uses ultrasound technology to capture high temporal and spatial resolution images of the heart and surrounding structures, and is the most common imaging modality in cardiovascular medicine. Using convolutional neural networks on a large new dataset, we show that deep learning applied to echocardiography can identify local cardiac structures, estimate cardiac function, and predict systemic phenotypes that modify cardiovascular risk but not readily identifiable to human interpretation. Our deep learning model, EchoNet, accurately identified the presence of pacemaker leads (AUC = 0.89), enlarged left atrium (AUC = 0.86), left ventricular hypertrophy (AUC = 0.75), left ventricular end systolic and diastolic volumes ([Formula: see text] = 0.74 and [Formula: see text] = 0.70), and ejection fraction ([Formula: see text] = 0.50), as well as predicted systemic phenotypes of age ([Formula: see text] = 0.46), sex (AUC = 0.88), weight ([Formula: see text] = 0.56), and height ([Formula: see text] = 0.33). Interpretation analysis validates that EchoNet shows appropriate attention to key cardiac structures when performing human-explainable tasks and highlights hypothesis-generating regions of interest when predicting systemic phenotypes difficult for human interpretation. Machine learning on echocardiography images can streamline repetitive tasks in the clinical workflow, provide preliminary interpretation in areas with insufficient qualified cardiologists, and predict phenotypes challenging for human evaluation.

    View details for DOI 10.1038/s41746-019-0216-8

    View details for PubMedID 33483633

  • Classifying Drugs by their Arrhythmogenic Risk Using Machine Learning. Biophysical journal Sahli-Costabal, F., Seo, K., Ashley, E., Kuhl, E. 2020

    Abstract

    All medications have adverse effects. Among the most serious of these are cardiac arrhythmias. Current paradigms for drug safety evaluation are costly, lengthy, conservative, and impede efficient drug development. Here, we combine multiscale experiment and simulation, high-performance computing, and machine learning to create a risk estimator to stratify new and existing drugs according to their proarrhythmic potential. We capitalize on recent developments in machine learning and integrate information across 10 orders of magnitude in space and time to provide a holistic picture of the effects of drugs, either individually or in combination with other drugs. We show, both experimentally and computationally, that drug-induced arrhythmias are dominated by the interplay between two currents with opposing effects: the rapid delayed rectifier potassium current and the L-type calcium current. Using Gaussian process classification, we create a classifier that stratifies drugs into safe and arrhythmic domains for any combinations of these two currents. We demonstrate that our classifier correctly identifies the risk categories of 22 common drugs exclusively on the basis of their concentrations at 50% current block. Our new risk assessment tool explains under which conditions blocking the L-type calcium current can delay or even entirely suppress arrhythmogenic events. Using machine learning in drug safety evaluation can provide a more accurate and comprehensive mechanistic assessment of the proarrhythmic potential of new drugs. Our study paves the way toward establishing science-based criteria to accelerate drug development, design safer drugs, and reduce heart rhythm disorders.

    View details for DOI 10.1016/j.bpj.2020.01.012

    View details for PubMedID 32023435

  • Association of Obesity With Adverse Long-term Outcomes in Hypertrophic Cardiomyopathy JAMA CARDIOLOGY Fumagalli, C., Maurizi, N., Day, S. M., Ashley, E. A., Michels, M., Colan, S. D., Jacoby, D., Marchionni, N., Vincent-Tompkins, J., Ho, C. Y., Olivotto, I., Pereira, A., Cirino, A., Ware, J., Fox, J., Lakdawala, N., Caleshu, C., Girolami, F., Cecchi, F., Seidman, C., Sajeev, G., Signorovitch, J., Green, E., SHARE Investigators 2020; 5 (1): 65–72
  • SARS-CoV-2 RNAaemia predicts clinical deterioration and extrapulmonary complications from COVID-19. medRxiv : the preprint server for health sciences Ram-Mohan, N. n., Kim, D. n., Zudock, E. J., Hashemi, M. M., Tjandra, K. C., Rogers, A. J., Blish, C. A., Nadeau, K. C., Newberry, J. A., Quinn, J. V., O'Hara, R. n., Ashley, E. n., Nguyen, H. n., Jiang, L. n., Hung, P. n., Blomkalns, A. L., Yang, S. n. 2020

    Abstract

    The determinants of COVID-19 disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterise the relationships between SARS-CoV-2 RNAaemia and disease severity, clinical deterioration, and specific EPCs.We used quantitative (qPCR) and digital (dPCR) PCR to quantify SARS-CoV-2 RNA from nasopharyngeal swabs and plasma in 191 patients presenting to the Emergency Department (ED) with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterised the role of RNAaemia in predicting clinical severity and EPCs using elastic net regression.23·0% (44/191) of SARS-CoV-2 positive patients had viral RNA detected in plasma by dPCR, compared to 1·4% (2/147) by qPCR. Most patients with serial measurements had undetectable RNAaemia 10 days after onset of symptoms, but took 16 days to reach maximum severity, and 33 days for symptoms to resolve. Initially RNAaemic patients were more likely to manifest severe disease (OR 6·72 [95% CI, 2·45 - 19·79]), worsening of disease severity (OR 2·43 [95% CI, 1·07 - 5·38]), and EPCs (OR 2·81 [95% CI, 1·26 - 6·36]). RNA load correlated with maximum severity ( r = 0·47 [95% CI, 0·20 - 0·67]).dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAaemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Since many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAaemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.NIH/NIAID (Grants R01A153133, R01AI137272, and 3U19AI057229 - 17W1 COVID SUPP #2) and a donation from Eva Grove.Evidence before this study: The varied clinical manifestations of COVID-19 have directed attention to the distribution of SARS-CoV-2 in the body. Although most concentrated and tested for in the nasopharynx, SARS-CoV-2 RNA has been found in blood, stool, and numerous tissues, raising questions about dissemination of viral RNA throughout the body, and the role of this process in disease severity and extrapulmonary complications. Recent studies have detected low levels of SARS-CoV-2 RNA in blood using either quantitative reverse transcriptase real-time PCR (qPCR) or droplet digital PCR (dPCR), and have associated RNAaemia with disease severity and biomarkers of dysregulated immune response.Added value of this study: We quantified SARS-CoV-2 RNA in the nasopharynx and plasma of patients presenting to the Emergency Department with COVID-19, and found an array-based dPCR platform to be markedly more sensitive than qPCR for detection of SARS-CoV-2 RNA, with a simplified workflow well-suited to clinical adoption. We collected serial plasma samples during patients' course of illness, and showed that SARS-CoV-2 RNAaemia peaks early, while clinical condition often continues to worsen. Our findings confirm the association between RNAaemia and disease severity, and additionally demonstrate a role for RNAaemia in predicting future deterioration and specific extrapulmonary complications.Implications of all the available evidence: Variation in SARS-CoV-2 RNAaemia may help explain disparities in disease severity and extrapulmonary complications from COVID-19. Testing for RNAaemia with dPCR early in the course of illness may help guide patient triage and management.

    View details for DOI 10.1101/2020.12.19.20248561

    View details for PubMedID 33398290

    View details for PubMedCentralID PMC7781329

  • Mobile Health Monitoring of Cardiac Status ANNUAL REVIEW OF BIOMEDICAL DATA SCIENCE, VOL 3, 2020 Christle, J. W., Hershman, S. G., Soto, J., Ashley, E. A., Altman, R. B. 2020; 3: 243–63
  • Accuracy of Smartphone Camera Applications for Detecting Atrial Fibrillation: A Systematic Review and Meta-analysis. JAMA network open O'Sullivan, J. W., Grigg, S. n., Crawford, W. n., Turakhia, M. P., Perez, M. n., Ingelsson, E. n., Wheeler, M. T., Ioannidis, J. P., Ashley, E. A. 2020; 3 (4): e202064

    Abstract

    Atrial fibrillation (AF) affects more than 6 million people in the United States; however, much AF remains undiagnosed. Given that more than 265 million people in the United States own smartphones (>80% of the population), smartphone applications have been proposed for detecting AF, but the accuracy of these applications remains unclear.To determine the accuracy of smartphone camera applications that diagnose AF.MEDLINE and Embase were searched until January 2019 for studies that assessed the accuracy of any smartphone applications that use the smartphone's camera to measure the amplitude and frequency of the user's fingertip pulse to diagnose AF.Bivariate random-effects meta-analyses were constructed to synthesize data. The study followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) of Diagnostic Test Accuracy Studies reporting guideline.Sensitivity and specificity were measured with bivariate random-effects meta-analysis. To simulate the use of these applications as a screening tool, the positive predictive value (PPV) and negative predictive value (NPV) for different population groups (ie, age ≥65 years and age ≥65 years with hypertension) were modeled. Lastly, the association of methodological limitations with outcomes were analyzed with sensitivity analyses and metaregressions.A total of 10 primary diagnostic accuracy studies, with 3852 participants and 4 applications, were included. The oldest studies were published in 2016 (2 studies [20.0%]), while most studies (4 [40.0%]) were published in 2018. The applications analyzed the pulsewave signal for a mean (range) of 2 (1-5) minutes. The meta-analyzed sensitivity and specificity for all applications combined were 94.2% (95% CI, 92.2%-95.7%) and 95.8% (95% CI, 92.4%-97.7%), respectively. The PPV for smartphone camera applications detecting AF in an asymptomatic population aged 65 years and older was between 19.3% (95% CI, 19.2%-19.4%) and 37.5% (95% CI, 37.4%-37.6%), and the NPV was between 99.8% (95% CI, 99.83%-99.84%) and 99.9% (95% CI, 99.94%-99.95%). The PPV and NPV increased for individuals aged 65 years and older with hypertension (PPV, 20.5% [95% CI, 20.4%-20.6%] to 39.2% [95% CI, 39.1%-39.3%]; NPV, 99.8% [95% CI, 99.8%-99.8%] to 99.9% [95% CI, 99.9%-99.9%]). There were methodological limitations in a number of studies that did not appear to be associated with diagnostic performance, but this could not be definitively excluded given the sparsity of the data.In this study, all smartphone camera applications had relatively high sensitivity and specificity. The modeled NPV was high for all analyses, but the PPV was modest, suggesting that using these applications in an asymptomatic population may generate a higher number of false-positive than true-positive results. Future research should address the accuracy of these applications when screening other high-risk population groups, their ability to help monitor chronic AF, and, ultimately, their associations with patient-important outcomes.

    View details for DOI 10.1001/jamanetworkopen.2020.2064

    View details for PubMedID 32242908

  • Stretch-Induced Biased Signaling in Angiotensin II Type 1 and Apelin Receptors for the Mediation of Cardiac Contractility and Hypertrophy. Frontiers in physiology Seo, K., Parikh, V. N., Ashley, E. A. 2020; 11: 181

    Abstract

    The myocardium has an intrinsic ability to sense and respond to mechanical load in order to adapt to physiological demands. Primary examples are the augmentation of myocardial contractility in response to increased ventricular filling caused by either increased venous return (Frank-Starling law) or aortic resistance to ejection (the Anrep effect). Sustained mechanical overload, however, can induce pathological hypertrophy and dysfunction, resulting in heart failure and arrhythmias. It has been proposed that angiotensin II type 1 receptor (AT1R) and apelin receptor (APJ) are primary upstream actors in this acute myocardial autoregulation as well as the chronic maladaptive signaling program. These receptors are thought to have mechanosensing capacity through activation of intracellular signaling via G proteins and/or the multifunctional transducer protein, beta-arrestin. Importantly, ligand and mechanical stimuli can selectively activate different downstream signaling pathways to promote inotropic, cardioprotective or cardiotoxic signaling. Studies to understand how AT1R and APJ integrate ligand and mechanical stimuli to bias downstream signaling are an important and novel area for the discovery of new therapeutics for heart failure. In this review, we provide an up-to-date understanding of AT1R and APJ signaling pathways activated by ligand versus mechanical stimuli, and their effects on inotropy and adaptive/maladaptive hypertrophy. We also discuss the possibility of targeting these signaling pathways for the development of novel heart failure therapeutics.

    View details for DOI 10.3389/fphys.2020.00181

    View details for PubMedID 32231588

  • Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genetics in medicine : official journal of the American College of Medical Genetics Schoch, K. n., Esteves, C. n., Bican, A. n., Spillmann, R. n., Cope, H. n., McConkie-Rosell, A. n., Walley, N. n., Fernandez, L. n., Kohler, J. N., Bonner, D. n., Reuter, C. n., Stong, N. n., Mulvihill, J. J., Novacic, D. n., Wolfe, L. n., Abdelbaki, A. n., Toro, C. n., Tifft, C. n., Malicdan, M. n., Gahl, W. n., Liu, P. n., Newman, J. n., Goldstein, D. B., Hom, J. n., Sampson, J. n., Wheeler, M. T., Cogan, J. n., Bernstein, J. A., Adams, D. R., McCray, A. T., Shashi, V. n. 2020

    Abstract

    The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices.We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods.Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling.Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.

    View details for DOI 10.1038/s41436-020-00984-z

    View details for PubMedID 33093671

  • Cardiac Imaging of Aortic Valve Area from 34,287 UK Biobank Participants Reveal Novel Genetic Associations and Shared Genetic Comorbidity with Multiple Disease Phenotypes. Circulation. Genomic and precision medicine Córdova-Palomera, A. n., Tcheandjieu, C. n., Fries, J. n., Varma, P. n., Chen, V. S., Fiterau, M. n., Xiao, K. n., Tejeda, H. n., Keavney, B. n., Cordell, H. J., Tanigawa, Y. n., Venkataraman, G. n., Rivas, M. n., Ré, C. n., Ashley, E. A., Priest, J. R. 2020

    Abstract

    Background - The aortic valve is an important determinant of cardiovascular physiology and anatomic location of common human diseases. Methods - From a sample of 34,287 white British-ancestry participants, we estimated functional aortic valve area by planimetry from prospectively obtained cardiac MRI sequences of the aortic valve. Aortic valve area measurements were submitted to genome-wide association testing, followed by polygenic risk scoring and phenome-wide screening to identify genetic comorbidities. Results - A genome-wide association study of aortic valve area in these UK Biobank participants showed three significant associations, indexed by rs71190365 (chr13:50764607, DLEU1, p=1.8×10-9), rs35991305 (chr12:94191968, CRADD, p=3.4×10-8) and chr17:45013271:C:T (GOSR2, p=5.6×10-8). Replication on an independent set of 8,145 unrelated European-ancestry participants showed consistent effect sizes in all three loci, although rs35991305 did not meet nominal significance. We constructed a polygenic risk score for aortic valve area, which in a separate cohort of 311,728 individuals without imaging demonstrated that smaller aortic valve area is predictive of increased risk for aortic valve disease (Odds Ratio 1.14, p=2.3×10-6). After excluding subjects with a medical diagnosis of aortic valve stenosis (remaining n=308,683 individuals), phenome-wide association of >10,000 traits showed multiple links between the polygenic score for aortic valve disease and key health-related comorbidities involving the cardiovascular system and autoimmune disease. Genetic correlation analysis supports a shared genetic etiology with between aortic valve area and birthweight along with other cardiovascular conditions. Conclusions - These results illustrate the use of automated phenotyping of cardiac imaging data from the general population to investigate the genetic etiology of aortic valve disease, perform clinical prediction, and uncover new clinical and genetic correlates of cardiac anatomy.

    View details for DOI 10.1161/CIRCGEN.120.003014

    View details for PubMedID 33125279

  • Impact of the distance from the chest wall to the heart on surface ECG voltage in athletes. BMJ open sport & exercise medicine Hedman, K., Patti, A., Moneghetti, K. J., Hsu, D., Christle, J. W., Ashley, E., Hadley, D., Haddad, F., Froelicher, V. 2020; 6 (1): e000696

    Abstract

    Objective: Available ECG criteria for detection of left ventricular (LV) hypertrophy have been reported to have limited diagnostic capability. Our goal was to describe how the distance between the chest wall and the left ventricle determined by echocardiography affected the relationship between ECG voltage and LV mass (LVM) in athletes.Methods: We retrospectively evaluated digitised ECG data from college athletes undergoing routine echocardiography as part of their preparticipation evaluation. Along with LV mass and volume, we determined the chest wall-LV distance in the parasternal short-axis and long-axis views from two-dimensional transthoracic echocardiographic images and explored the relation with ECG QRS voltages in all leads, as well as summed voltages as included in six major ECG-LVH criteria.Results: 239 athletes (43 women) were included (age 19±1years). In men, greater LV-chest wall distance was associated with higher R-wave amplitudes in leads aVL and I (R=0.20and R=0.25, both p<0.01), while in women greater distance was associated with higher R-amplitudes in V5 and V6 (R=0.42and R=0.34, both p<0.01). In women, the chest wall-LV distance was the only variable independently (and positively) associated with R V5 voltage, while LVM, height and weight contributed to the relationship in men.Conclusions: The chest wall-LV distance was weakly associated with ECG voltage in athletes. Inconsistent associations in men and women imply different intrathoracic factors affecting impedance and conductance between sexes. This may help explain the poor relationship between QRS voltage and LVM in athletes.

    View details for DOI 10.1136/bmjsem-2019-000696

    View details for PubMedID 32201618

  • De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. American journal of human genetics Mao, D. n., Reuter, C. M., Ruzhnikov, M. R., Beck, A. E., Farrow, E. G., Emrick, L. T., Rosenfeld, J. A., Mackenzie, K. M., Robak, L. n., Wheeler, M. T., Burrage, L. C., Jain, M. n., Liu, P. n., Calame, D. n., Küry, S. n., Sillesen, M. n., Schmitz-Abe, K. n., Tonduti, D. n., Spaccini, L. n., Iascone, M. n., Genetti, C. A., Koenig, M. K., Graf, M. n., Tran, A. n., Alejandro, M. n., Lee, B. H., Thiffault, I. n., Agrawal, P. B., Bernstein, J. A., Bellen, H. J., Chao, H. T. 2020

    Abstract

    EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.

    View details for DOI 10.1016/j.ajhg.2020.02.016

    View details for PubMedID 32197074

  • TANGO2 DEFICIENCY: A CASE SERIES HIGHLIGHTING INTRAFAMILIAL VARIABILITY AND REVIEW OF THE LITERATURE Schymick, J., Bonner, D., Leahy, P., Cowan, T., Ruzhnikov, M., Kohler, J., McCormack, C., Fernandez, L., Matalon, D., Yarlagadda, V., Fisher, P., Ashley, E., Wheeler, M., Enns, G., Bernstein, J., Lee, C. BMJ PUBLISHING GROUP. 2020: A116
  • Deep learning interpretation of echocardiograms. NPJ digital medicine Ghorbani, A., Ouyang, D., Abid, A., He, B., Chen, J. H., Harrington, R. A., Liang, D. H., Ashley, E. A., Zou, J. Y. 2020; 3: 10

    Abstract

    Echocardiography uses ultrasound technology to capture high temporal and spatial resolution images of the heart and surrounding structures, and is the most common imaging modality in cardiovascular medicine. Using convolutional neural networks on a large new dataset, we show that deep learning applied to echocardiography can identify local cardiac structures, estimate cardiac function, and predict systemic phenotypes that modify cardiovascular risk but not readily identifiable to human interpretation. Our deep learning model, EchoNet, accurately identified the presence of pacemaker leads (AUC=0.89), enlarged left atrium (AUC=0.86), left ventricular hypertrophy (AUC=0.75), left ventricular end systolic and diastolic volumes ( R 2 =0.74 and R 2 =0.70), and ejection fraction ( R 2 =0.50), as well as predicted systemic phenotypes of age ( R 2 =0.46), sex (AUC=0.88), weight ( R 2 =0.56), and height ( R 2 =0.33). Interpretation analysis validates that EchoNet shows appropriate attention to key cardiac structures when performing human-explainable tasks and highlights hypothesis-generating regions of interest when predicting systemic phenotypes difficult for human interpretation. Machine learning on echocardiography images can streamline repetitive tasks in the clinical workflow, provide preliminary interpretation in areas with insufficient qualified cardiologists, and predict phenotypes challenging for human evaluation.

    View details for DOI 10.1038/s41746-019-0216-8

    View details for PubMedID 31993508

  • Myosin Sequestration Regulates Sarcomere Function, Cardiomyocyte Energetics, and Metabolism, Informing the Pathogenesis of Hypertrophic Cardiomyopathy. Circulation Toepfer, C. N., Garfinkel, A. C., Venturini, G. n., Wakimoto, H. n., Repetti, G. n., Alamo, L. n., Sharma, A. n., Agarwal, R. n., Ewoldt, J. F., Cloonan, P. n., Letendre, J. n., Lun, M. n., Olivotto, I. n., Colan, S. n., Ashley, E. n., Jacoby, D. n., Michels, M. n., Redwood, C. S., Watkins, H. C., Day, S. M., Staples, J. F., Padrón, R. n., Chopra, A. n., Ho, C. Y., Chen, C. S., Pereira, A. C., Seidman, J. G., Seidman, C. E. 2020

    Abstract

    Background: Hypertrophic cardiomyopathy (HCM) is caused by pathogenic variants in sarcomere protein genes that evoke hypercontractility, poor relaxation, and increased energy consumption by the heart and increased patient risks for arrhythmias and heart failure. Recent studies show that pathogenic missense variants in myosin, the molecular motor of the sarcomere, are clustered in residues that participate in dynamic conformational states of sarcomere proteins. We hypothesized that these conformations are essential to adapt contractile output for energy conservation and that pathophysiology of HCM results from destabilization of these conformations. Methods: We assayed myosin ATP binding to define the proportions of myosin in SRX or DRX conformations in healthy rodent and human hearts, at baseline and in response to reduced hemodynamic demands of hibernation or pathogenic HCM variants. To determine the relationships between myosin conformations, sarcomere function, and cell biology we assessed contractility, relaxation, and cardiomyocyte morphology and metabolism, with and without an allosteric modulator of myosin ATPase activity. We then tested whether the positions of myosin variants with unknown clinical significance (VUS) that were identified in HCM patients, predicted functional consequences and associations with heart failure and arrhythmias. Results: Myosins undergo physiologic shifts between SRX conformations that maximized energy-conservation and active states (DRX) that enable cross-bridge formation with greater ATP consumption. Systemic hemodynamic requirements, pharmacologic modulators of myosin, and pathogenic myosin missense mutations influenced the proportions of these conformations. Hibernation increased SRX conformations while pathogenic variants destabilized these and increased the proportion of DRX myosins, which enhanced cardiomyocyte contractility but impaired relaxation, and evoked hypertrophic remodeling with increased energetic stress. Using structural locations to stratify VUS, we showed that variants that unbalanced myosin conformations were associated with higher rates of heart failure and arrhythmias in HCM patients. Conclusions: Myosin conformations establish work-energy equipoise that is essential for life-long cellular homeostasis and heart function. Destabilization of myosin energy conserving states promotes contractile abnormalities, morphological and metabolic remodeling and adverse clinical outcomes in HCM patients. Therapeutic restabilization corrects cellular contractile and metabolic phenotypes and may limit these adverse clinical outcomes in HCM patients.

    View details for DOI 10.1161/CIRCULATIONAHA.119.042339

    View details for PubMedID 31983222

  • Association of Race With Disease Expression and Clinical Outcomes Among Patients With Hypertrophic Cardiomyopathy. JAMA cardiology Eberly, L. A., Day, S. M., Ashley, E. A., Jacoby, D. L., Jefferies, J. L., Colan, S. D., Rossano, J. W., Semsarian, C., Pereira, A. C., Olivotto, I., Ingles, J., Seidman, C. E., Channaoui, N., Cirino, A. L., Han, L., Ho, C. Y., Lakdawala, N. K. 2019

    Abstract

    Importance: Racial differences are recognized in multiple cardiovascular parameters, including left ventricular hypertrophy and heart failure, which are 2 major manifestations of hypertrophic cardiomyopathy. The association of race with disease expression and outcomes among patients with hypertrophic cardiomyopathy is not well characterized.Objective: To assess the association between race, disease expression, care provision, and clinical outcomes among patients with hypertrophic cardiomyopathy.Design, Setting, and Participants: This retrospective cohort study included data on black and white patients with hypertrophic cardiomyopathy from the US-based sites of the Sarcomeric Human Cardiomyopathy Registry from 1989 through 2018.Exposures: Self-identified race.Main Outcomes and Measures: Baseline characteristics; genetic architecture; adverse outcomes, including cardiac arrest, cardiac transplantation or left ventricular assist device implantation, implantable cardioverter-defibrillator therapy, all-cause mortality, atrial fibrillation, stroke, and New York Heart Association (NYHA) functional class III or IV heart failure; and septal reduction therapies. The overall composite outcome consists of the first occurrence of any component of the ventricular arrhythmic composite end point, cardiac transplantation, left ventricular assist device implantation, NYHA class III or IV heart failure, atrial fibrillation, stroke, or all-cause mortality.Results: Of 2467 patients with hypertrophic cardiomyopathy at the time of analysis, 205 (8.3%) were black (130 male [63.4%]; mean [SD] age, 40.0 [18.6] years) and 2262 (91.7%) were white (1351 male [59.7%]; mean [SD] age, 45.5 [20.5] years). Compared with white patients, black patients were younger at the time of diagnosis (mean [SD], 36.5 [18.2] vs 41.9 [20.2] years; P<.001), had higher prevalence of NYHA class III or IV heart failure at presentation (36 of 205 [22.6%] vs 174 of 2262 [15.8%]; P=.001), had lower rates of genetic testing (111 [54.1%] vs 1404 [62.1%]; P=.03), and were less likely to have sarcomeric mutations identified by genetic testing (29 [26.1%] vs 569 [40.5%]; P=.006). Implantation of implantable cardioverter-defibrillators did not vary by race; however, invasive septal reduction was less common among black patients (30 [14.6%] vs 521 [23.0%]; P=.007). Black patients had less incident atrial fibrillation (35 [17.1%] vs 608 [26.9%]; P<.001). Black race was associated with increased development of NYHA class III or IV heart failure (hazard ratio, 1.45; 95% CI, 1.08-1.94) which persisted on multivariable Cox proportional hazards regression (hazard ratio, 1.97; 95% CI, 1.34-2.88). There were no differences in the associations of race with stroke, ventricular arrhythmias, all-cause mortality, or the overall composite outcome.Conclusions and Relevance: The findings suggest that black patients with hypertrophic cardiomyopathy are diagnosed at a younger age, are less likely to carry a sarcomere mutation, have a higher burden of functionally limited heart failure, and experience inequities in care with lower use of invasive septal reduction therapy and genetic testing compared with white patients. Further study is needed to assess whether higher rates of heart failure may be associated with underlying ancestry-based disease pathways, clinical management, or structural inequities.

    View details for DOI 10.1001/jamacardio.2019.4638

    View details for PubMedID 31799990

  • Echocardiographic Assessment of Left Ventricular Remodeling in American Style Footballers. International journal of sports medicine Moneghetti, K. J., Singh, T., Hedman, K., Christle, J. W., Kooreman, Z., Kobayashi, Y., Bouajila, S., Amsallem, M., Wheeler, M., Gerche, A. L., Ashley, E., Haddad, F. 2019

    Abstract

    Several athletic programs incorporate echocardiography during pre-participation screening of American Style Football (ASF) players with great variability in reported echocardiographic values. Pre-participation screening was performed in National Collegiate Athletic Association Division I ASF players from 2008 to 2016 at the Division of Sports Cardiology. The echocardiographic protocol focused on left ventricular (LV) mass, mass-to-volume ratio, sphericity, ejection fraction, and longitudinal Lagrangian strain. LV mass was calculated using the area-length method in end-diastole and end-systole. A total of two hundred and thirty players were included (18±1 years, 57% were Caucasian, body mass index 29±4kg/m2) after four players (2%) were excluded for pathological findings. Although there was no difference in indexed LV mass by race (Caucasian 78±11 vs. African American 81±10g/m2, p=0.089) or sphericity (Caucasian 1.81±0.13 vs. African American 1.78±0.14, p=0.130), the mass-to-volume ratio was higher in African Americans (0.91±0.09 vs. 0.83±0.08, p<0.001). No race-specific differences were noted in LV longitudinal Lagrangian strain. Player position appeared to have a limited role in defining LV remodeling. In conclusion, significant echocardiographic differences were observed in mass-to-volume ratio between African American and Caucasian players. These demographics should be considered as part of pre-participation screening.

    View details for DOI 10.1055/a-1014-2994

    View details for PubMedID 31791086

  • Temporal trend in age at diagnosis of hypertrophic cardiomyopathy: an analysis of the share registry Canepa, M., Fumagalli, C., Tini, G., Mazzarotto, F., Vincent-Tompkins, J., Day, S., Ashley, E., Michels, M., Colan, S. D., Jacoby, D., Ho, C., Olivotto, I. OXFORD UNIV PRESS. 2019: J181–J182
  • The effect of digital physical activity interventions on daily step count: a randomised controlled crossover substudy of the MyHeart Counts Cardiovascular Health Study. The Lancet. Digital health Shcherbina, A., Hershman, S. G., Lazzeroni, L., King, A. C., O'Sullivan, J. W., Hekler, E., Moayedi, Y., Pavlovic, A., Waggott, D., Sharma, A., Yeung, A., Christle, J. W., Wheeler, M. T., McConnell, M. V., Harrington, R. A., Ashley, E. A. 2019; 1 (7): e344-e352

    Abstract

    Smartphone apps might enable interventions to increase physical activity, but few randomised trials testing this hypothesis have been done. The MyHeart Counts Cardiovascular Health Study is a longitudinal smartphone-based study with the aim of elucidating the determinants of cardiovascular health. We aimed to investigate the effect of four different physical activity coaching interventions on daily step count in a substudy of the MyHeart Counts Study.In this randomised, controlled crossover trial, we recruited adults (aged ≥18 years) in the USA with access to an iPhone smartphone (Apple, Cupertino, CA, USA; version 5S or newer) who had downloaded the MyHeart Counts app (version 2.0). After completion of a 1 week baseline period of interaction with the MyHeart Counts app, participants were randomly assigned to receive one of 24 permutations (four combinations of four 7 day interventions) in a crossover design using a random number generator built into the app. Interventions consisted of either daily prompts to complete 10 000 steps, hourly prompts to stand following 1 h of sitting, instructions to read the guidelines from the American Heart Association website, or e-coaching based upon the individual's personal activity patterns from the baseline week of data collection. Participants completed the trial in a free-living setting. Due to the nature of the interventions, participants could not be masked from the intervention. Investigators were not masked to intervention allocation. The primary outcome was change in mean daily step count from baseline for each of the four interventions, assessed in the modified intention-to-treat analysis set, which included all participants who had completed 7 days of baseline monitoring and at least 1 day of one of the four interventions. This trial is registered with ClinicalTrials.gov, NCT03090321.Between Dec 12, 2016, and June 6, 2018, 2783 participants consented to enrol in the coaching study, of whom 1075 completed 7 days of baseline monitoring and at least 1 day of one of the four interventions and thus were included in the modified intention-to-treat analysis set. 493 individuals completed the full set of assigned interventions. All four interventions significantly increased mean daily step count from baseline (mean daily step count 2914 [SE 74]): mean step count increased by 319 steps (75) for participants in the American Heart Association website prompt group (p<0·0001), 267 steps (74) for participants in the hourly stand prompt group (p=0·0003), 254 steps (74) for participants in the cluster-specific prompts group (p=0·0006), and by 226 steps (75) for participants in the 10 000 daily step prompt group (p=0·0026 vs baseline).Four smartphone-based physical activity coaching interventions significantly increased daily physical activity. These findings suggests that digital interventions delivered via a mobile app have the ability to increase short-term physical activity levels in a free-living cohort.Stanford Data Science Initiative.

    View details for DOI 10.1016/S2589-7500(19)30129-3

    View details for PubMedID 33323209

  • Broad Genetic Testing in a Clinical Setting Uncovers a High Prevalence of Titin Loss-of-Function Variants in Very Early-Onset Atrial Fibrillation. Circulation. Genomic and precision medicine Goodyer, W. R., Dunn, K., Caleshu, C., Jackson, M., Wylie, J., Moscarello, T., Platt, J., Reuter, C., Smith, A., Trela, A., Ceresnak, S. R., Motonaga, K. S., Ashley, E., Yang, P., Dubin, A. M., Perez, M. 2019

    Abstract

    Atrial fibrillation (AF) is the most common sustained arrhythmia, affecting approximately 34 million worldwide. The pathophysiology of AF remains incompletely understood but is clearly complex with multiple underlying genetic, physiologic and environmental factors. Very early-onset AF (vEAF) (defined here as onset <45 years and without significant comorbidities), while rare (only ~0.5-3% of AF cases), is highly heritable, with a greater prevalence of rare variants in genes previously associated with AF. Patients with vEAF, therefore, represent an ideal population for discovering novel genes involved in the underlying genetic basis of AF. Notably, the Framingham study showed that patients with AF without comorbidities have a three-fold higher risk for heart failure. Conversely, several forms of inherited cardiomyopathy have been strongly associated with AF suggestive of a shared etiology.

    View details for DOI 10.1161/CIRCGEN.119.002713

    View details for PubMedID 31638414

  • Multiomics Approach to Diagnosing Undiagnosed Patients Wheeler, M. T., Kohler, J. N., Bonner, D. E., Zastrow, D. B., Reuter, C., Majcherska, M., Fernandez, L., McCormack, C., Marwaha, S., Curnin, C., Dries, A., Ruzhnikov, M., Hom, J., Sampson, J., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Undiagnosed Dis Network NATURE PUBLISHING GROUP. 2019: 1163–64
  • Structural variants in Alpha-actinin 2 are associated with cardiomyopathy and hypertrophy in human cardiac tissue and iPSC-derived cardiomyocytes Lindholm, M. E., Zhu, H., Huang, Y., Ashley, E. A., Wheeler, M. NATURE PUBLISHING GROUP. 2019: 1310
  • Pathological overlap of Arrhythmogenic Right Ventricular Cardiomyopathy and Cardiac Sarcoidosis. Circulation. Genomic and precision medicine Kerkar, A., Hazard, F., Caleshu, C. A., Shah, R. L., Reuter, C., Ashley, E. A., Parikh, V. N. 2019

    Abstract

    A previously healthy 50-year-old female long-distance runner initially presented to the emergency room with sustained palpitations and was found to be in a hemodynamically stable wide complex tachycardia at 220 bpm. Initial electrocardiogram (ECG) demonstrated monomorphic tachycardia with a right inferoapical ventricular origin (Figure 1A). Echocardiogram revealed normal left ventricular (LV) size and moderately reduced function, but severe right ventricular (RV) enlargement and systolic dysfunction in the absence of elevated pulmonary pressures (Figure 1B). Her ECG in normal sinus rhythm showed T wave inversions in V1-V4 (Figure 1C) and her signal averaged ECG was abnormal with a filtered QRS duration of 150 msec, root mean square amplitude of the last 40 msec of late potentials (RMS40) of 2.16 mV and duration of low amplitude signal (LAS) of 92.5msec. Electrophysiology study confirmed inducible ventricular arrhythmias from the RV, and internal cardiac defibrillator (ICD) was placed.

    View details for DOI 10.1161/CIRCGEN.119.002638

    View details for PubMedID 31542937

  • Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. Journal of genetic counseling Reuter, C. M., Kohler, J. N., Bonner, D., Zastrow, D., Fernandez, L., Dries, A., Marwaha, S., Davidson, J., Brokamp, E., Herzog, M., Hong, J., Macnamara, E., Rosenfeld, J. A., Schoch, K., Spillmann, R., Undiagnosed Diseases Network, Loscalzo, J., Krier, J., Stoler, J., Sweetser, D., Palmer, C. G., Phillips, J. A., Shashi, V., Adams, D. A., Yang, Y., Ashley, E. A., Fisher, P. G., Mulvihill, J. J., Bernstein, J. A., Wheeler, M. T. 2019

    Abstract

    BACKGROUND: Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored.METHODS: We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated.RESULTS: Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%).CONCLUSIONS: These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.

    View details for DOI 10.1002/jgc4.1161

    View details for PubMedID 31478310

  • Genomic Context Predicts Dilated but Not Hypertrophic Cardiomyopathy Puckelwartz, M. J., Pesce, L. L., Dellefave-Castillo, L. M., Wheeler, M. T., Pottinger, T. D., Robinson, A. C., Gacita, A. M., Schoppen, Z. J., Pan Wenyu, Kim, G., Wilcox, J. E., Anderson, A. S., Ashley, E. A., Day, S. M., Cappola, T., Dorn, G. W., McNally, E. M. LIPPINCOTT WILLIAMS & WILKINS. 2019
  • Limitations of Electrocardiography for Detecting Left Ventricular Hypertrophy or Concentric Remodeling in Athletes. The American journal of medicine Hedman, K., Moneghetti, K. J., Hsu, D., Christle, J. W., Patti, A., Ashley, E., Hadley, D., Haddad, F., Froelicher, V. 2019

    Abstract

    BACKGROUND: Electrocardiography (ECG) is used to screen for left ventricular hypertrophy (LVH), but common ECG-LVH criteria have been found less effective in athletes. The purpose of this study was to comprehensively evaluate the value of ECG for identifying athletes with left ventricular hypertrophy and/or a concentric cardiac phenotype.METHODS: A retrospective analysis of 196 male division 1 college athletes routinely screened with ECG and echocardiography within The Stanford Athletic Cardiovascular Screening Program was performed. Left-ventricular mass and volume were determined using echocardiography. Left ventricular hypertrophy was defined as left ventricular mass >102 g/m2; a concentric cardiac phenotype as left ventricular mass/volume (M/V) ≥1.05 g/mL. Twelve-lead ECGs including high-resolution time intervals and QRS voltages were obtained. 37 previously published ECG-LVH criteria were applied, of which the majority have never been evaluated in athletes. C-statistics, including area under the receiver operating curve (AUC), and likelihood ratios were calculated.RESULTS: ECG lead voltages were poorly associated with left ventricular mass (r=0.18-0.30) and M/V (r=0.15-0.25). The proportion of athletes with ECG-LVH was 0-74% across criteria, with sensitivity and specificity ranging between 0-91% and 27-99.5%, respectively. The average AUC of the criteria in identifying the 11 athletes with left ventricular hypertrophy was 0.57 (95% CI 0.56-0.59), while the average AUC for identifying the eight athletes with a concentric phenotype was 0.59 (95% CI 0.56-0.62).CONCLUSION: The diagnostic capacity of all ECG-LVH criteria were inadequate and therefore not clinically useful in screening for left ventricular hypertrophy or a concentric phenotype in athletes. This is probably due to the weak association between left ventricular mass and ECG voltage.

    View details for DOI 10.1016/j.amjmed.2019.06.028

    View details for PubMedID 31738876

  • Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review AMERICAN JOURNAL OF MEDICAL GENETICS PART A Kumar, A., Zastrow, D. B., Kravets, E. J., Beleford, D., Ruzhnikov, M. Z., Grove, M. E., Dries, A. M., Kohler, J. N., Waggott, D. M., Yang, Y., Huang, Y., Mackenzie, K. M., Eng, C. M., Fisher, P. G., Ashley, E. A., Teng, J. M., Stevenson, D. A., Shieh, J. T., Wheeler, M. T., Bernstein, J. A., Adams, D. R., Aday, A., Alejandro, M. E., Allard, P., Azamian, M. S., Bacino, C. A., Baker, E., Balasubramanyam, A., Barseghyan, H., Batzli, G. F., Beggs, A. H., Behnam, B., Bellen, H. J., Bican, A., Bick, D. P., Birch, C. L., Bonner, D., Boone, B. E., Bostwick, B. L., Briere, L. C., Brokamp, E., Brown, D. M., Brush, M., Burke, E. A., Burrage, L. C., Butte, M. J., Chen, S., Clark, G. D., Coakley, T. R., Cogan, J. D., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., D'Souza, P., Davids, M., Davidson, J. M., Dayal, J. G., Dell'Angelica, E. C., Dhar, S. U., Dipple, K. M., Donnell-Fink, L. A., Dorrani, N., Dorset, D. C., Douine, E. D., Draper, D. D., Eckstein, D. J., Emrick, L. T., Enns, G. M., Eskin, A., Esteves, C., Estwick, T., Fairbrother, L., Fernandez, L., Ferreira, C., Fieg, E. L., Fogel, B. L., Friedman, N. D., Gahl, W. A., Glanton, E., Godfrey, R. A., Goldman, A. M., Goldstein, D. B., Gould, S. E., Gourdine, J. F., Groden, C. A., Gropman, A. L., Haendel, M., Hamid, R., Hanchard, N. A., High, F., Holm, I. A., Hom, J., Howerton, E. M., Jamal, F., Jiang, Y., Johnston, J. M., Jones, A. L., Karaviti, L., Koeller, D. M., Kohane, I. S., Krasnewich, D. M., Korrick, S., Koziura, M., Krier, J. B., Kyle, J. E., Lalani, S. R., Lau, C., Lazar, J., LeBlanc, K., Lee, B. H., Lee, H., Levy, S. E., Lewis, R. A., Lincoln, S. A., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Malicdan, M., Mamounas, L. A., Manolio, T. A., Markello, T. C., Marom, R., Martin, M. G., Martinez-Agosto, J. A., Marwaha, S., May, T., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., Merker, J. D., Metz, T. O., Might, M., Moretti, P. M., Morimoto, M., Mulvihill, J. J., Murdock, D. R., Murphy, J. L., Muzny, D. M., Nehrebecky, M. E., Nelson, S. F., Newberry, J., Newman, J. H., Nicholas, S. K., Novacic, D., Orange, J. S., Orengo, J. P., Pallais, J., Palmer, C. S., Papp, J. C., Parker, N. H., Pena, L. M., Phillips, J. A., Posey, J. E., Postlethwait, J. H., Potocki, L., Pusey, B. N., Reuter, C. M., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Sampson, J. B., Samson, S. L., Schoch, K., Scott, D. A., Shakachite, L., Sharma, P., Shashi, V., Signer, R., Silverman, E. K., Sinsheimer, J. S., Smith, K. S., Spillmann, R. C., Staler, J. M., Stong, N., Sullivan, J. A., Sweetser, D. A., Tan, Q., Tifft, C. J., Toro, C., Tran, A. A., Urv, T. K., Vilain, E., Vogel, T. P., Wahl, C. E., Walley, N. M., Walsh, C. A., Walker, M., Wan, J., Wangler, M. F., Ward, P. A., Waters, K. M., Webb-Robertson, B. M., Westerfield, M., Wise, A. L., Wolfe, L. A., Worthey, E. A., Yamamoto, S., Yang, J., Yoon, A. J., Yu, G., Zhao, C., Zheng, A., Undiagnosed Dis Network 2019; 179 (6): 966–77
  • Comparison of QT Interval Measurement Methods and Correction Formulas in Atrial Fibrillation AMERICAN JOURNAL OF CARDIOLOGY Tooley, J., Ouyang, D., Hadley, D., Turakhia, M., Wang, P., Ashley, E., Froelicher, V., Perez, M. 2019; 123 (11): 1822–27
  • A Patient with Sjogren's Syndrome and Subsequent Diagnosis of Inclusion Body Myositis and Light-Chain Amyloidosis JOURNAL OF GENERAL INTERNAL MEDICINE Hom, J., Marwaha, S., Postolova, A., Kittle, J., Vasquez, R., Davidson, J., Kohler, J., Dries, A., Fernandez-Betancourt, L., Majcherska, M., Dearlove, J., Raghavan, S., Vogel, H., Bernstein, J. A., Fisher, P., Ashley, E., Sampson, J., Wheeler, M., Undiagnosed Dis Network 2019; 34 (6): 1058–62
  • Rapid Genome Sequencing in the Critically Ill CLINICAL CHEMISTRY Buchan, J. G., White, S., Joshi, R., Ashley, E. A. 2019; 65 (6): 723–26
  • Blood pressure in athletic preparticipation evaluation and the implication for cardiac remodelling. Heart (British Cardiac Society) Hedman, K., Moneghetti, K. J., Christle, J. W., Bagherzadeh, S. P., Amsallem, M., Ashley, E., Froelicher, V., Haddad, F. 2019

    Abstract

    OBJECTIVES: To explore blood pressure (BP) in athletes at preparticipation evaluation (PPE) in the context of recently updated US and European hypertension guidelines, and to determine the relationship between BP and left ventricular (LV) remodelling.METHODS: In this retrospective study, athletes aged 13-35 years who underwent PPE facilitated by the Stanford Sports Cardiology programme were considered. Resting BP was measured in both arms; repeated once if ≥140/90mm Hg. Athletes with abnormal ECGs or known hypertension were excluded. BP was categorised per US/European hypertension guidelines. In a separate cohort of athletes undergoing routine PPE echocardiography, we explored the relationship between BP and LV remodelling (LV mass, mass/volume ratio, sphericity index) and LV function.RESULTS: In cohort 1 (n=2733, 65.5% male), 34.3% of athletes exceeded US hypertension thresholds. Male sex (B=3.17, p<0.001), body mass index (BMI) (B=0.80, p<0.001) and height (B=0.25, p<0.001) were the strongest independent correlates of systolic BP. In the second cohort (n=304, ages 17-26), systolic BP was an independent correlate of LV mass/volume ratio (B=0.002, p=0.001). LV longitudinal strain was similar across BP categories, while higher BP was associated with slower early diastolic relaxation.CONCLUSION: In a large contemporary cohort of athletes, one-third presented with BP levels above the current US guidelines' thresholds for hypertension, highlighting that lowering the BP thresholds at PPE warrants careful consideration as well as efforts to standardise measurements. Higher systolic BP was associated with male sex, BMI and height and with LV remodelling and diastolic function, suggesting elevated BP in athletes during PPE may signify a clinically relevant condition.

    View details for DOI 10.1136/heartjnl-2019-314815

    View details for PubMedID 31142598

  • Targeted Long-Read RNA Sequencing Demonstrates Transcriptional Diversity Driven by Splice-Site Variation in MYBPC3. Circulation. Genomic and precision medicine Dainis, A., Tseng, E., Clark, T. A., Hon, T., Wheeler, M., Ashley, E. 2019; 12 (5): e002464

    View details for DOI 10.1161/CIRCGEN.119.002464

    View details for PubMedID 31112421

  • Athletic Remodeling in Female College Athletes: The "Morganroth Hypothesis" Revisited CLINICAL JOURNAL OF SPORT MEDICINE Kooreman, Z., Giraldeau, G., Finocchiaro, G., Kobayashi, Y., Wheeler, M., Perez, M., Moneghetti, K., Oxborough, D., George, K. P., Myers, J., Ashley, E., Haddad, F. 2019; 29 (3): 224–31
  • Physical activity, sleep and cardiovascular health data for 50,000 individuals from the MyHeart Counts Study SCIENTIFIC DATA Hershman, S. G., Bot, B. M., Shcherbina, A., Doerr, M., Moayedi, Y., Pavlovic, A., Waggott, D., Cho, M. K., Rosenberger, M. E., Haskell, W. L., Myers, J., Champagne, M., Mignot, E., Salvi, D., Landray, M., Tarassenko, L., Harrington, R. A., Yeung, A. C., McConnell, M. V., Ashley, E. A. 2019; 6
  • Physical activity, sleep and cardiovascular health data for 50,000 individuals from the MyHeart Counts Study. Scientific data Hershman, S. G., Bot, B. M., Shcherbina, A., Doerr, M., Moayedi, Y., Pavlovic, A., Waggott, D., Cho, M. K., Rosenberger, M. E., Haskell, W. L., Myers, J., Champagne, M. A., Mignot, E., Salvi, D., Landray, M., Tarassenko, L., Harrington, R. A., Yeung, A. C., McConnell, M. V., Ashley, E. A. 2019; 6 (1): 24

    Abstract

    Studies have established the importance of physical activity and fitness for long-term cardiovascular health, yet limited data exist on the association between objective, real-world large-scale physical activity patterns, fitness, sleep, and cardiovascular health primarily due to difficulties in collecting such datasets. We present data from the MyHeart Counts Cardiovascular Health Study, wherein participants contributed data via an iPhone application built using Apple's ResearchKit framework and consented to make this data available freely for further research applications. In this smartphone-based study of cardiovascular health, participants recorded daily physical activity, completed health questionnaires, and performed a 6-minute walk fitness test. Data from English-speaking participants aged 18 years or older with a US-registered iPhone who agreed to share their data broadly and who enrolled between the study's launch and the time of the data freeze for this data release (March 10 2015-October 28 2015) are now available for further research. It is anticipated that releasing this large-scale collection of real-world physical activity, fitness, sleep, and cardiovascular health data will enable the research community to work collaboratively towards improving our understanding of the relationship between cardiovascular indicators, lifestyle, and overall health, as well as inform mobile health research best practices.

    View details for PubMedID 30975992

  • Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students JOURNAL OF GENETIC COUNSELING Grove, M. E., White, S., Fisk, D. G., Rego, S., Dagan-Rosenfeld, O., Kohler, J. N., Reuter, C. M., Bonner, D., Wheeler, M. T., Bernstein, J. A., Ormond, K. E., Hanson-Kahn, A. K., Undiagnosed Dis Network 2019; 28 (2): 466–76

    View details for DOI 10.1002/jgc4.1094

    View details for Web of Science ID 000463993600030

  • PHACOMATOSIS PIGMENTOVASCULARIS AND EXTRACUTANEOUS MANIFESTATIONS: CASE SERIES, LITERATURE REVIEW AND CONSIDERATIONS FOR MANAGEMENT Kumar, A., Zastrow, D. B., Beleford, D., Ruzhnikov, M. Z., Grove, M. E., Dries, A. M., Kohler, J. N., Waggott, D. M., Yang, Y., Huang, Y., Mackenzie, K. M., Eng, C. M., Fisher, P. G., Ashley, E. A., Teng, J. M., Stevenson, D. A., Shieh, J. T., Wheeler, M. T., Bernstein, J. A., Undiagnosed Dis Network WILEY. 2019: 718–19
  • A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing JOURNAL OF GENETIC COUNSELING Zastrow, D. B., Kohler, J. N., Bonner, D., Reuter, C. M., Fernandez, L., Grove, M. E., Fisk, D. G., Yang, Y., Eng, C. M., Ward, P. A., Bick, D., Worthey, E. A., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T., Adams, D. R., Aday, A., Alejandro, M. E., Allard, P., Ashley, E. A., Azamian, M. S., Bacino, C. A., Baker, E., Balasubramanyam, A., Barseghyan, H., Batzli, G. F., Beggs, A. H., Behnam, B., Bellen, H. J., Bernstein, J. A., Bican, A., Bick, D. P., Birch, C. L., Boone, B. E., Bostwick, B. L., Briere, L. C., Brokamp, E., Brown, D. M., Brush, M., Burke, E. A., Burrage, L. C., Butte, M. J., Chen, S., Clark, G. D., Coakley, T. R., Cogan, J. D., Colley, H. A., Cooper, C. M., Cope, H., Craigen, W. J., D'Souza, P., Davids, M., Dayal, J. G., Dell'Angelica, E. C., Dhar, S. U., Dipple, K. M., Donnell-Fink, L. A., Dorrani, N., Dorset, D. C., Douine, E. D., Draper, D. D., Dries, A. M., Eckstein, D. J., Emrick, L. T., Eng, C. M., Enns, G. M., Eskin, A., Esteves, C., Estwick, T., Fairbrother, L., Ferreira, C., Fieg, E. L., Fisher, P. G., Fogel, B. L., Gahl, W. A., Glanton, E., Godfrey, R. A., Goldman, A. M., Goldstein, D. B., Gould, S. E., Gourdine, J. F., Groden, C. A., Gropman, A. L., Haendel, M., Hamid, R., Hanchard, N. A., High, F., Holm, I. A., Hom, J., Howerton, E. M., Huang, Y., Jamal, F., Jiang, Y., Johnston, J. M., Jones, A. L., Karaviti, L., Koeller, D. M., Kohane, I. S., Krasnewich, D. M., Korrick, S., Koziura, M., Krier, J. B., Kyle, J. E., Lalani, S. R., Lau, C., Lazar, J., LeBlanc, K., Lee, B. H., Lee, H., Levy, S. E., Lewis, R. A., Lincoln, S. A., Loo, S. K., Loscalzo, J., Maas, R. L., Macnamara, E. F., MacRae, C. A., Maduro, V. V., Majcherska, M. M., Malicdan, M. V., Mamounas, L. A., Manolio, T. A., Markello, T. C., Marom, R., Martin, G., Martinez-Agosto, J. A., Marwaha, S., May, T., McConkie-Rosell, A., McCormack, C. E., McCray, A. T., Merker, J. D., Metz, T. O., Might, M., Moretti, P. M., Morimoto, M., Nehrebecky, M. E., Nelson, S. F., Newberry, J., Newman, J. H., Nicholas, S. K., Novacic, D., Orange, J. S., Orengo, J. P., Pallais, J., Palmer, C. S., Papp, J. C., Postlethwait, J. H., Potocki, L., Pusey, B. N., Rives, L., Robertson, A. K., Rodan, L. H., Rosenfeld, J. A., Sampson, J. B., Samson, S. L., Schoch, K., Scott, D. A., Shakachite, L., Sharma, P., Shashi, V., Signer, R., Silverman, E. K., Sinsheimer, J. S., Smith, K. S., Spillmann, R. C., Stoler, J. M., Stong, N., Sullivan, J. A., Sweetser, D. A., Tan, Q., Tifft, C. J., Toro, C., Tran, A. A., Urv, T. K., Vilain, E., Vogel, T. P., Waggott, D. M., Wahl, C. E., Walley, N. M., Walsh, C. A., Walker, M., Wan, J., Wangler, M. F., Ward, P. A., Waters, K. M., Webb-Robertson, B. M., Westerfield, M., Wheeler, M. T., Wise, A. L., Wolfe, L. A., Worthey, E. A., Yamamoto, S., Yang, J., Yang, Y., Yoon, A. J., Yu, G., Zhao, C., Zheng, A., Undiagnosed Dis Network 2019; 28 (2): 213–28

    View details for DOI 10.1002/jgc4.1119

    View details for Web of Science ID 000463993600005

  • Targeting ferroptosis: A novel therapeutic strategy for the treatment of mitochondrial disease-related epilepsy. PloS one Kahn-Kirby, A. H., Amagata, A., Maeder, C. I., Mei, J. J., Sideris, S., Kosaka, Y., Hinman, A., Malone, S. A., Bruegger, J. J., Wang, L., Kim, V., Shrader, W. D., Hoff, K. G., Latham, J. C., Ashley, E. A., Wheeler, M. T., Bertini, E., Carrozzo, R., Martinelli, D., Dionisi-Vici, C., Chapman, K. A., Enns, G. M., Gahl, W., Wolfe, L., Saneto, R. P., Johnson, S. C., Trimmer, J. K., Klein, M. B., Holst, C. R. 2019; 14 (3): e0214250

    Abstract

    Mitochondrial disease is a family of genetic disorders characterized by defects in the generation and regulation of energy. Epilepsy is a common symptom of mitochondrial disease, and in the vast majority of cases, refractory to commonly used antiepileptic drugs. Ferroptosis is a recently-described form of iron- and lipid-dependent regulated cell death associated with glutathione depletion and production of lipid peroxides by lipoxygenase enzymes. Activation of the ferroptosis pathway has been implicated in a growing number of disorders, including epilepsy. Given that ferroptosis is regulated by balancing the activities of glutathione peroxidase-4 (GPX4) and 15-lipoxygenase (15-LO), targeting these enzymes may provide a rational therapeutic strategy to modulate seizure. The clinical-stage therapeutic vatiquinone (EPI-743, α-tocotrienol quinone) was reported to reduce seizure frequency and associated morbidity in children with the mitochondrial disorder pontocerebellar hypoplasia type 6. We sought to elucidate the molecular mechanism of EPI-743 and explore the potential of targeting 15-LO to treat additional mitochondrial disease-associated epilepsies.Primary fibroblasts and B-lymphocytes derived from patients with mitochondrial disease-associated epilepsy were cultured under standardized conditions. Ferroptosis was induced by treatment with the irreversible GPX4 inhibitor RSL3 or a combination of pharmacological glutathione depletion and excess iron. EPI-743 was co-administered and endpoints, including cell viability and 15-LO-dependent lipid oxidation, were measured.EPI-743 potently prevented ferroptosis in patient cells representing five distinct pediatric disease syndromes with associated epilepsy. Cytoprotection was preceded by a dose-dependent decrease in general lipid oxidation and the specific 15-LO product 15-hydroxyeicosatetraenoic acid (15-HETE).These findings support the continued clinical evaluation of EPI-743 as a therapeutic agent for PCH6 and other mitochondrial diseases with associated epilepsy.

    View details for DOI 10.1371/journal.pone.0214250

    View details for PubMedID 30921410

    View details for PubMedCentralID PMC6438538

  • Extracutaneous manifestations in phacomatosis cesioflammea and cesiomarmorata: Case series and literature review. American journal of medical genetics. Part A Kumar, A., Zastrow, D. B., Kravets, E. J., Beleford, D., Ruzhnikov, M. R., Grove, M. E., Dries, A. M., Kohler, J. N., Waggott, D. M., Yang, Y., Huang, Y., Undiagnosed Diseases Network, Mackenzie, K. M., Eng, C. M., Fisher, P. G., Ashley, E. A., Teng, J. M., Stevenson, D. A., Shieh, J. T., Wheeler, M. T., Bernstein, J. A. 2019

    Abstract

    Phacomatosis pigmentovascularis (PPV) comprises a family of rare conditions that feature vascular abnormalities and melanocytic lesions that can be solely cutaneous or multisystem in nature. Recently published work has demonstrated that both vascular and melanocytic abnormalities in PPV of the cesioflammea and cesiomarmorata subtypes can result from identical somatic mosaic activating mutations in the genes GNAQ and GNA11. Here, we present three new cases of PPV with features of the cesioflammea and/or cesiomarmorata subtypes and mosaic mutations in GNAQ or GNA11. To better understand the risk of potentially occult complications faced by such patients we additionally reviewed 176 cases published in the literature. We report the frequency of clinical findings, their patterns of co-occurrence as well as published recommendations for surveillance after diagnosis. Features assessed include: capillary malformation; dermal and ocular melanocytosis; glaucoma; limb asymmetry; venous malformations; and central nervous system (CNS) anomalies, such as ventriculomegaly and calcifications. We found that ocular findings are common in patients with phacomatosis cesioflammea and cesiomarmorata. Facial vascular involvement correlates with a higher risk of seizures (p=.0066). Our genetic results confirm the role of mosaic somatic mutations in GNAQ and GNA11 in phacomatosis cesioflammea and cesiomarmorata. Their clinical and molecular findings place these conditions on a clinical spectrum encompassing other GNAQ and GNA11 related disorders and inform recommendations for their management.

    View details for PubMedID 30920161

  • Targeting ferroptosis: A novel therapeutic strategy for the treatment of mitochondrial disease-related epilepsy PLOS ONE Kahn-Kirby, A. H., Amagata, A., Maeder, C. I., Mei, J. J., Sideris, S., Kosaka, Y., Hinman, A., Malone, S. A., Bruegger, J. J., Wang, L., Kim, V., Shrader, W. D., Hoff, K. G., Latham, J. C., Ashley, E. A., Wheeler, M. T., Bertini, E., Carrozzo, R., Martinelli, D., Dionisi-Vici, C., Chapman, K. A., Enns, G. M., Gahl, W., Wolfe, L., Saneto, R. P., Johnson, S. C., Trimmer, J. K., Klein, M. B., Holst, C. R. 2019; 14 (3)
  • Response by Ho et al to Letter Regarding Article, "Genotype and Lifetime Burden of Disease in Hypertrophic Cardiomyopathy: Insights From the Sarcomeric Human Cardiomyopathy Registry (SHaRe)". Circulation Ho, C. Y., Day, S. M., Ashley, E. A., Michels, M., Pereira, A. C., Jacoby, D., Lakdawala, N. K., Ware, J. S., Helms, A. S., Colan, S. D., Seidman, C. E., Olivotto, I., SHaRe Investigators 2019; 139 (12): 1559–60

    View details for DOI 10.1161/CIRCULATIONAHA.118.039069

    View details for PubMedID 30883221

  • Comparison of QT Interval Measurement Methods and Correction Formulas in Atrial Fibrillation. The American journal of cardiology Tooley, J., Ouyang, D., Hadley, D., Turakhia, M., Wang, P., Ashley, E., Froelicher, V., Perez, M. 2019

    Abstract

    Antiarrhythmic drugs used in atrial fibrillation (AF) cause QT prolongation and are associated with torsades de pointes, a deadly ventricular arrhythmia. No consensus exists on the optimal method of QT measurement or correction in AF. Therefore, we compared common methods to measure and correct QT in AF to identify the most accurate approach. We identified patients who had electrocardiograms done at Stanford Hospital (Stanford, California) between January 2014 and October 2016 with conversion from AF to sinus rhythm (SR) within a 24-hour period. QT intervals were determined using different measurement methods and corrected using the Bazett's, Framingham, Fridericia, or Hodges formulas for heart rate (HR). Comparisons were made between QT in a patient's last instance of AF to SR. Computerized measurements were taken from 715 patients. Manual measurements were taken from a 50-patient subset. Bazett's formula produced the longest corrected QT in AF compared with other formulas (p <0.005). Measuring QT as an average over multiple beats resulted in a smaller difference between AF and SR than choosing a single beat. Determining QT from a 5-beat average resulted in a QTc that was 19.0ms higher (interquartile range 0.30 to 43.7) in AF than SR. After correcting for residual effect of HR on QTc, there was not a significant difference between QTc in AF to SR. In conclusion, measuring QT over multiple beats produces a more accurate measurement of QT in AF. Differences between QTc in AF and SR exist because of imperfect HR correction formula and not due to an independent effect of AF.

    View details for PubMedID 30961909

  • COMPARISON OF UNITED STATES AND EUROPEAN CRITERIA FOR HYPERTENSION IN A LARGE COHORT OF COMPETITIVE ATHLETES EXAMINED AS PART OF PRE-PARTICIPATION EVALUATION Hedman, K., Moneghetti, K., Christle, J. W., Bagherzadeh, S. P., Haddad, F., Ashley, E. A., Froelicher, V. ELSEVIER SCIENCE INC. 2019: 446
  • INDEPENDENT PROGNOSTIC VALUES OF CLINICAL RISK SCORES, RIGHT VENTRICULAR SYSTOLIC PRESSURE, AND N-TERMINAL PRO-B-TYPE PEPTIDE IN HEART FAILURE WITH PRESERVED EJECTION FRACTION: INSIGHTS FROM SUPERVISED AND UNSUPERVISED MODELS Tremblay-Gravel, M., Kobayashi, Y., Boralkar, K., Li, X., Bouajila, S., Nishi, T., Amsallem, M., Moneghetti, K., Selej, M., Ozen, M., Demirci, U., Ashley, E. A., Wheeler, M., Knowlton, K., Kouznetsova, T., Haddad, F. ELSEVIER SCIENCE INC. 2019: 718
  • NOVEL ALPHA-ACTININ 2 MUTATIONS ARE ASSOCIATED WITH CARDIOMYOPATHY AND HYPERTROPHY IN HUMAN CARDIAC TISSUE AND IPSC-DERIVED CARDIOMYOCYTES Lindholm, M., Zhu, H., Huang, Y., Ashley, E. A., Wheeler, M. ELSEVIER SCIENCE INC. 2019: 1027
  • RESTING BLOOD PRESSURE IN 2881 ATHLETES AGED 9-35 YEARS OF AGE AND THE RELATION TO SEX, AGE, BODY SIZE, AND AFRO-AMERICAN DESCENT Bagherzadeh, S. P., Hedman, K., Christle, J. W., Moneghetti, K., Ashley, E. A., Haddad, F., Froelicher, V. ELSEVIER SCIENCE INC. 2019: 447
  • Rapid Genome Sequencing in the Critically lll. Clinical chemistry Buchan, J. G., White, S., Joshi, R., Ashley, E. A. 2019

    View details for PubMedID 30842082

  • Loss of function, missense, and intronic variants in NOTCH1 confer different risks for left ventricular outflow tract obstructive heart defects in two European cohorts GENETIC EPIDEMIOLOGY Helle, E., Cordova-Palomera, A., Ojala, T., Saha, P., Potiny, P., Gustafsson, S., Ingelsson, E., Bamshad, M., Nickerson, D., Chong, J. X., Ashley, E., Priest, J. R., Univ Washington Ctr Mendelia 2019; 43 (2): 215–26

    View details for DOI 10.1002/gepi.22176

    View details for Web of Science ID 000462061900008

  • Time based versus strain based myocardial performance indices in hypertrophic cardiomyopathy, the merging role of left atrial strain EUROPEAN HEART JOURNAL-CARDIOVASCULAR IMAGING Kobayashi, Y., Moneghetti, K. J., Bouajila, S., Stolfo, D., Finocchiaro, G., Kuznetsova, T., Liang, D., Schnittger, I., Ashley, E., Wheeler, M., Haddad, F. 2019; 20 (3): 334–42
  • Regional Variation in RBM20 Causes a Highly Penetrant Arrhythmogenic Cardiomyopathy. Circulation. Heart failure Parikh, V. N., Caleshu, C., Reuter, C., Lazzeroni, L. C., Ingles, J., Garcia, J., McCaleb, K., Adesiyun, T., Sedaghat-Hamedani, F., Kumar, S., Graw, S., Gigli, M., Stolfo, D., Dal Ferro, M., Ing, A. Y., Nussbaum, R., Funke, B., Wheeler, M. T., Hershberger, R. E., Cook, S., Steinmetz, L. M., Lakdawala, N. K., Taylor, M. R., Mestroni, L., Merlo, M., Sinagra, G., Semsarian, C., Meder, B., Judge, D. P., Ashley, E. 2019; 12 (3): e005371

    Abstract

    Background Variants in the cardiomyocyte-specific RNA splicing factor RBM20 have been linked to familial cardiomyopathy, but the causative genetic architecture and clinical consequences of this disease are incompletely defined. Methods and Results To define the genetic architecture of RBM20 cardiomyopathy, we first established a database of RBM20 variants associated with cardiomyopathy and compared these to variants observed in the general population with respect to their location in the RBM20 coding transcript. We identified 2 regions significantly enriched for cardiomyopathy-associated variants in exons 9 and 11. We then assembled a registry of 74 patients with RBM20 variants from 8 institutions across the world (44 index cases and 30 from cascade testing). This RBM20 patient registry revealed highly prevalent family history of sudden cardiac death (51%) and cardiomyopathy (72%) among index cases and a high prevalence of composite arrhythmias (including atrial fibrillation, nonsustained ventricular tachycardia, implantable cardiac defibrillator discharge, and sudden cardiac arrest, 43%). Patients harboring variants in cardiomyopathy-enriched regions identified by our variant database analysis were enriched for these findings. Further, these characteristics were more prevalent in the RBM20 registry than in large cohorts of patients with dilated cardiomyopathy and TTNtv cardiomyopathy and not significantly different from a cohort of patients with LMNA-associated cardiomyopathy. Conclusions Our data establish RBM20 cardiomyopathy as a highly penetrant and arrhythmogenic cardiomyopathy. These findings underline the importance of arrhythmia surveillance and family screening in this disease and represent the first step in defining the genetic architecture of RBM20 disease causality on a population level.

    View details for PubMedID 30871351

  • Regional Variation in RBM20 Causes a Highly Penetrant Arrhythmogenic Cardiomyopathy CIRCULATION-HEART FAILURE Parikh, V. N., Caleshu, C., Reuter, C., Lazzeroni, L. C., Ingles, J., Garcia, J., McCaleb, K., Adesiyun, T., Sedaghat-Hamedani, F., Kumar, S., Graw, S., Gigli, M., Stolfo, D., Dal Ferro, M., Ing, A. Y., Nussbaum, R., Funke, B., Wheeler, M. T., Hershberger, R. E., Cook, S., Steinmetz, L. M., Lakdawala, N. K., Taylor, M. G., Mestroni, L., Merlo, M., Sinagra, G., Semsarian, C., Meder, B., Judge, D. P., Ashley, E. 2019; 12 (3)
  • A Premature Termination Codon Mutation in MYBPC3 Causes Hypertrophic Cardiomyopathy via Chronic Activation of Nonsense-Mediated Decay CIRCULATION Seeger, T., Shrestha, R., Lam, C., Chen, C., McKeithan, W. L., Lau, E., Wnorowski, A., McMullen, G., Greenhaw, M., Lee, J., Oikonomopoulos, A., Lee, S., Yang, H., Mercola, M., Wheeler, M., Ashley, E. A., Yang, F., Karakikes, I., Wu, J. C. 2019; 139 (6): 799–811
  • Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy. Genome medicine Walsh, R., Mazzarotto, F., Whiffin, N., Buchan, R., Midwinter, W., Wilk, A., Li, N., Felkin, L., Ingold, N., Govind, R., Ahmad, M., Mazaika, E., Allouba, M., Zhang, X., de Marvao, A., Day, S. M., Ashley, E., Colan, S. D., Michels, M., Pereira, A. C., Jacoby, D., Ho, C. Y., Thomson, K. L., Watkins, H., Barton, P. J., Olivotto, I., Cook, S. A., Ware, J. S. 2019; 11 (1): 5

    Abstract

    BACKGROUND: International guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false-positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework.METHODS: We compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts (up to 6179 cases) to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). We analysed the distribution of variants using a bespoke unsupervised clustering algorithm to identify gene regions in which variants are significantly clustered in cases.RESULTS: Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF ≥0.95 were identified in five established HCM genes. Applying this approach leads to an estimated 14-20% increase in cases with actionable HCM variants, i.e. variants classified as pathogenic/likely pathogenic that might be used for predictive testing in probands' relatives.CONCLUSIONS: When found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a "likely pathogenic" classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent and unbiased approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner.

    View details for PubMedID 30696458

  • Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: the case of hypertrophic cardiomyopathy GENOME MEDICINE Walsh, R., Mazzarotto, F., Whiffin, N., Buchan, R., Midwinter, W., Wilk, A., Li, N., Felkin, L., Ingold, N., Govind, R., Ahmad, M., Mazaika, E., Allouba, M., Zhang, X., de Marvao, A., Day, S. M., Ashley, E., Colan, S. D., Michels, M., Pereira, A. C., Jacoby, D., Ho, C. Y., Thomson, K. L., Watkins, H., Barton, P. R., Olivotto, I., Cook, S. A., Ware, J. S. 2019; 11
  • Approaching Higher Dimension Imaging Data Using Cluster-Based Hierarchical Modeling in Patients with Heart Failure Preserved Ejection Fraction. Scientific reports Kobayashi, Y. n., Tremblay-Gravel, M. n., Boralkar, K. A., Li, X. n., Nishi, T. n., Amsallem, M. n., Moneghetti, K. J., Bouajila, S. n., Selej, M. n., Ozen, M. O., Demirci, U. n., Ashley, E. n., Wheeler, M. n., Knowlton, K. U., Kouznetsova, T. n., Haddad, F. n. 2019; 9 (1): 10431

    Abstract

    Heart failure with preserved ejection fraction (HFpEF) is a major cause of morbidity and mortality, accounting for the majority of heart failure (HF) hospitalization. To identify the most complementary predictors of mortality among clinical, laboratory and echocardiographic data, we used cluster based hierarchical modeling. Using Stanford Translational Research Database, we identified patients hospitalized with HFpEF between 2005 and 2016 in whom echocardiogram and NT-proBNP were both available at the time of admission. Comprehensive echocardiographic assessment including left ventricular longitudinal strain (LVLS), right ventricular function and right ventricular systolic pressure (RVSP) was performed. The outcome was defined as all-cause mortality. Among patients identified, 186 patients with complete echocardiographic assessment were included in the analysis. The cohort included 58% female, with a mean age of 78.7 ± 13.5 years, LVLS of -13.3 ± 2.5%, an estimated RVSP of 38 ± 13 mmHg. Unsupervised cluster analyses identified six clusters including ventricular systolic-function cluster, diastolic-hemodynamic cluster, end-organ function cluster, vital-sign cluster, complete blood count and sodium clusters. Using a stepwise hierarchical selection from each cluster, we identified NT-proBNP (standard hazard ratio [95%CI] = 1.56 [1.17-2.08]) and RVSP (1.37 [1.09-1.78]) as independent correlates of outcome. When adding these parameters to the well validated Get with the Guideline Heart Failure risk score, the Chi-square was significantly improved (p = 0.01). In conclusion, NT-proBNP and RVSP were independently predictive in HFpEF among clinical, imaging, and biomarker parameters. Cluster-based hierarchical modeling may help identify the complementally predictive parameters in small cohorts with higher dimensional clinical data.

    View details for DOI 10.1038/s41598-019-46873-7

    View details for PubMedID 31320698

  • A novel noninvasive method for remote heart failure monitoring: the EuleriAn video Magnification apPLications In heart Failure studY (AMPLIFY). NPJ digital medicine Abnousi, F., Kang, G., Giacomini, J., Yeung, A., Zarafshar, S., Vesom, N., Ashley, E., Harrington, R., Yong, C. 2019; 2: 80

    Abstract

    Current remote monitoring devices for heart failure have been shown to reduce hospitalizations but are invasive and costly; accurate non-invasive options remain limited. The EuleriAn Video Magnification ApPLications In Heart Failure StudY (AMPLIFY) pilot aimed to evaluate the accuracy of a novel noninvasive method that uses Eulerian video magnification. Video recordings were performed on the neck veins of 50 patients who were scheduled for right heart catheterization at the Palo Alto VA Medical Center. The recorded jugular venous pulsations were then enhanced by applying Eulerian phase-based motion magnification. Assessment of jugular venous pressure was compared across three categories: (1) physicians who performed bedside exams, (2) physicians who reviewed both the amplified and unamplified videos, and (3) direct invasive measurement of right atrial pressure from right heart catheterization. Motion magnification reduced inaccuracy of the clinician assessment of central venous pressure compared to the gold standard of right heart catheterization (mean discrepancy of -0.80cm H2O; 95% CI -2.189 to 0.612, p=0.27) when compared to both unamplified video (-1.84cm H2O; 95% CI -3.22 to -0.46, p=0.0096) and the bedside exam (-2.90cm H2O; 95% CI -4.33 to 1.40, p=0.0002). Major categorical disagreements with right heart catheterization were significantly reduced with motion magnification (12%) when compared to unamplified video (25%) or the bedside exam (27%). This novel method of assessing jugular venous pressure improves the accuracy of the clinical exam and may enable accurate remote monitoring of heart failure patients with minimal patient risk.

    View details for DOI 10.1038/s41746-019-0159-0

    View details for PubMedID 31453375

  • Cardiopulmonary Exercise Testing, Impedance Cardiography and Reclassification of Risk in Patients Referred for Heart Failure Evaluation. Journal of cardiac failure Myers, J. n., Christle, J. W., Tun, A. n., Yilmaz, B. n., Moneghetti, K. J., Yuen, E. n., Soofi, M. n., Ashley, E. n. 2019

    Abstract

    An impaired cardiac output response to exercise is a hallmark of chronic heart failure (HF). We determined the extent to which impedance cardiography (ICG) during exercise in combination with cardiopulmonary exercise test (CPX) responses reclassified risk for adverse events in patients with HF.CPX and ICG were performed in 1,236 consecutive patients (48±15 years) evaluated for HF. Clinical, ICG and CPX variables were acquired at baseline and subjects were followed for the composite outcome of cardiac-related death, hospitalization for worsening HF, cardiac transplantation, and left ventricular assist device (LVAD) implantation. Cox proportional hazards analyses including clinical, non-invasive hemodynamic, and CPX variables were performed to determine their association with the composite endpoint. Net reclassification improvement (NRI) was calculated to quantify the impact of adding hemodynamic responses to a model including established CPX risk markers on reclassifying risk. There were 422 events. Among CPX variables, peak VO2 and indices of ventilatory inefficiency (VE/VCO2 slope, oxygen uptake efficiency slope) were significant predictors of risk for adverse events. Among hemodynamic variables, change in cardiac index, peak cardiac time interval, and peak left cardiac work index were the strongest predictors of risk. Having five impaired CPX and ICG responses to exercise yielded a seven-fold higher risk for adverse events compared to having no abnormal responses. Combining ICG responses to CPX resulted in NRIs ranging between 0.34 to 0.89, attributable to better reclassification of events.Cardiac hemodynamics determined by ICG complement established CPX measures in reclassifying risk among patients with HF.

    View details for DOI 10.1016/j.cardfail.2019.08.013

    View details for PubMedID 31454685

  • Genomics in medicine: a novel elective rotation for internal medicine residents. Postgraduate medical journal Geng, L. N., Kohler, J. N., Levonian, P. n., Bernstein, J. A., Ford, J. M., Ahuja, N. n., Witteles, R. n., Hom, J. n., Wheeler, M. n. 2019

    Abstract

    It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in 'Genomic Medicine and Undiagnosed Diseases' for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.

    View details for DOI 10.1136/postgradmedj-2018-136355

    View details for PubMedID 31439813

  • Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD. PloS one Dinstag, G. n., Amar, D. n., Ingelsson, E. n., Ashley, E. n., Shamir, R. n. 2019; 14 (8): e0219728

    Abstract

    The 2017 guidelines of the American College of Cardiology and the American Heart Association propose substantial changes to hypertension management. The guidelines lower the blood pressure threshold defining hypertension and promote more aggressive treatments. Thus, more individuals are now classified as hypertensive and as a result, medication usage may become more extensive. An inevitable byproduct of greater medication use is higher incidence of adverse effects. Here, we examined these issues by developing models that predict both cardiovascular events and other adverse events based on the treatment chosen and other patient's data.We used data from the SPRINT trial to produce patient-specific predictions of the risks for adverse cardiovascular or kidney outcomes. Unlike prior models, we used both the baseline characteristics collected upon recruitment and the longitudinal data during the follow-up. Importantly, our cardiovascular predictor outperformed extant models on SPRINT participants, achieving AUC = 0.765, and was validated with good performance in an independent cohort of the ACCORD trial.Our study illustrates the importance of including longitudinal data for assessing personalized risk and provides means for recommending personalized treatment decisions.

    View details for DOI 10.1371/journal.pone.0219728

    View details for PubMedID 31393900

  • IL6ST RELATED IMMUNODEFICIENCY DISORDER: A CASE REPORT AND REVIEW OF LITERATURE Velez-Bartolomei, F., Zastrow, D., McCormack, C., Kohler, J., Ud, N., Fisher, P., Ashley, E., Wheeler, M., Bernstein, J. BMJ PUBLISHING GROUP. 2019: 208
  • DNASE1L3 RELATED AUTOIMMUNE SYNDROME: A CASE REPORT AND REVIEW OF THE LITERATURE Schymick, J., Bonner, D., Majcherska, M., McCormack, C., Fresard, L., Smith, K., Montgomery, S., Fisher, P., Ashley, E., Ud, N., Maller, J., Hsu, J., Balboni, I., Wheeler, M., Bernstein, J. BMJ PUBLISHING GROUP. 2019: 80–81
  • Athletic Remodeling in Female College Athletes: The "Morganroth Hypothesis" Revisited. Clinical journal of sport medicine : official journal of the Canadian Academy of Sport Medicine Kooreman, Z. n., Giraldeau, G. n., Finocchiaro, G. n., Kobayashi, Y. n., Wheeler, M. n., Perez, M. n., Moneghetti, K. n., Oxborough, D. n., George, K. P., Myers, J. n., Ashley, E. n., Haddad, F. n. 2019; 29 (3): 224–31

    Abstract

    There is limited data regarding ventricular remodeling in college female athletes, especially when appropriate scaling of cardiac dimensions to lean body mass (LBM) is considered. Moreover, it is not well established whether cardiac remodeling in female athletes is a balanced process with proportional increase in left ventricular (LV) mass and volume or the right and LV size.During the preparticipation competitive screening, 72 female college athletes volunteered to undergo dual energy x-ray absorptiometry scan for quantification of LBM and comprehensive 2D echocardiography including assessment of longitudinal myocardial strain. The athletes were divided in 2 groups according to the intensity of the dynamic and static components of their sport categories, ie, a higher intensity dynamic and resistive group (n = 37 participating in rowing, water polo and lacrosse) and a lower intensity group (n = 35, participating in short distance running, sailing, synchronized swimming, and softball). In addition, we recruited a group of 31 age-matched nonathlete controls.The mean age of the study population was 18.7 ± 1.0 years. When scaled to body surface area, the higher intensity group had 17.1 ± 3.6% (P < 0.001) greater LV mass when compared with the lower intensity group and 21.7 ± 4.0% (P < 0.001) greater LV mass than the control group. The differences persisted after scaling to LBM with 14.2 ± 3.2% (P < 0.001) greater LV mass in the higher intensity group. By contrast, there was no difference in any of the relative remodeling indices including the LV mass to volume ratio, right to LV area ratio, or left atrial to LV volume ratio (P > 0.50 for all). In addition, no significant difference was noted among the 3 groups in LV ejection fraction (P = 0.22), LV global longitudinal strain (P = 0.55), LV systolic strain rate (P = 0.62), or right ventricular global longitudinal strain (P = 0.61).Female collegiate athletes participating in higher intensity dynamic and resistive sports have higher indexed LV mass even when scaled to LBM. The remodeling process does however appear to be a balanced process not only at the intraventricular level but also at the interventricular and atrioventricular levels.

    View details for PubMedID 31033616

  • A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. Journal of genetic counseling Zastrow, D. B., Kohler, J. N., Bonner, D. n., Reuter, C. M., Fernandez, L. n., Grove, M. E., Fisk, D. G., Yang, Y. n., Eng, C. M., Ward, P. A., Bick, D. n., Worthey, E. A., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T. 2019; 28 (2): 213–28

    Abstract

    There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.

    View details for PubMedID 30964584

  • A Patient with Sjogren's Syndrome and Subsequent Diagnosis of Inclusion Body Myositis and Light-Chain Amyloidosis. Journal of general internal medicine Hom, J. n., Marwaha, S. n., Postolova, A. n., Kittle, J. n., Vasquez, R. n., Davidson, J. n., Kohler, J. n., Dries, A. n., Fernandez-Betancourt, L. n., Majcherska, M. n., Dearlove, J. n., Raghavan, S. n., Vogel, H. n., Bernstein, J. A., Fisher, P. n., Ashley, E. n., Sampson, J. n., Wheeler, M. n. 2019

    Abstract

    We discuss a challenging case of a 58-year-old Vietnamese-American woman who presented to her new primary care provider with an 8-year history of slowly progressive dysphagia, hoarseness, muscle weakness with associated frequent falls, and weight loss. She eventually reported dry eyes and dry mouth, and she was diagnosed with Sjogren's syndrome. Subsequently, she was additionally diagnosed with inclusion body myositis and gastric light-chain (AL) amyloidosis. Although inclusion body myositis has been previously associated with Sjogren's syndrome, inclusion body myositis is rare in non-Caucasians, and the trio of Sjogren's syndrome, inclusion body myositis, and AL amyloidosis has not been previously reported. Sjogren's syndrome is a systemic autoimmune condition characterized by ocular and oral dryness. It is one of the most common rheumatologic disorders in the USA and worldwide. Early diagnosis of Sjogren's is particularly important given the frequency and variety of associated autoimmune diseases and extraglandular manifestations. Furthermore, although inclusion body myositis has a low prevalence, it is the most common inflammatory myopathy in older adults and is unfortunately associated with long delays in diagnosis, so knowledge of this disorder is also crucial for practicing internists.

    View details for PubMedID 30887439

  • Defining genotype-phenotype relationships in patients with hypertrophic cardiomyopathy using cardiovascular magnetic resonance imaging. PloS one Miller, R. J., Heidary, S. n., Pavlovic, A. n., Schlachter, A. n., Dash, R. n., Fleischmann, D. n., Ashley, E. A., Wheeler, M. T., Yang, P. C. 2019; 14 (6): e0217612

    Abstract

    HCM is the most common inherited cardiomyopathy. Historically, there has been poor correlation between genotype and phenotype. However, CMR has the potential to more accurately assess disease phenotype. We characterized phenotype with CMR in a cohort of patients with confirmed HCM and high prevalence of genetic testing.Patients with a diagnosis of HCM, who had undergone contrast-enhanced CMR were identified. Left ventricular mass index (LVMI) and volumes were measured from steady-state free precession sequences. Late gadolinium enhancement (LGE) was quantified using the full width, half maximum method. All patients were prospectively followed for the development of septal reduction therapy, arrhythmia or death.We included 273 patients, mean age 51.2 ± 15.5, 62.9% male. Of those patients 202 (74.0%) underwent genetic testing with 90 pathogenic, likely pathogenic, or rare variants and 13 variants of uncertain significance identified. Median follow-up was 1138 days. Mean LVMI was 82.7 ± 30.6 and 145 patients had late gadolinium enhancement (LGE). Patients with beta-myosin heavy chain (MYH7) mutations had higher LV ejection fraction (68.8 vs 59.1, p<0.001) than those with cardiac myosin binding protein C (MYBPC3) mutations. Patients with MYBPC3 mutations were more likely to have LVEF < 55% (29.7% vs 4.9%, p = 0.005) or receive a defibrillator than those with MYH7 mutations (54.1% vs 26.8%, p = 0.020).We found that patients with MYBPC3 mutations were more likely to have impaired ventricular function and may be more prone to arrhythmic events. Larger studies using CMR phenotyping may be capable of identifying additional characteristics associated with less frequent genetic causes of HCM.

    View details for DOI 10.1371/journal.pone.0217612

    View details for PubMedID 31199839

  • Weakly supervised classification of rare aortic valve malformations using unlabeled cardiac MRI sequences Nature Communications Fries, J. A., Varma, P., Chen, V. S., Xiao, K., Tejeda, H., Saha, P., Dunnmon, J., Chubb, H., Maskatia, S., Fiterau, M., Delp, S., Ashley, E., Ré, C., Priest, J. R. 2019; 10
  • Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students. Journal of genetic counseling Grove, M. E., White, S. n., Fisk, D. G., Rego, S. n., Dagan-Rosenfeld, O. n., Kohler, J. N., Reuter, C. M., Bonner, D. n., Wheeler, M. T., Bernstein, J. A., Ormond, K. E., Hanson-Kahn, A. K. 2019

    Abstract

    With the wide adoption of next-generation sequencing (NGS)-based genetic tests, genetic counselors require increased familiarity with NGS technology, variant interpretation concepts, and variant assessment tools. The use of exome and genome sequencing in clinical care has expanded the reach and diversity of genetic testing. Regardless of the setting where genetic counselors are performing variant interpretation or reporting, most of them have learned these skills from colleagues, while on the job. Though traditional, lecture-based learning around these topics is important, there has been growing need for the inclusion of case-based, experiential training of genomics and variant interpretation for genetic counseling students, with the goal of creating a strong foundation in variant interpretation for new genetic counselors, regardless of what area of practice they enter. To address this need, we established a genomics and variant interpretation rotation for Stanford's genetic counseling training program. In response to changes in the genomics landscape, this has now evolved into three unique rotation experiences, each focused on variant interpretation in the context of various genomic settings, including clinical laboratory, research laboratory, and healthy genomic analysis studies. Here, we describe the goals and learning objectives that we have developed for these variant interpretation rotations, and illustrate how these concepts are applied in practice.

    View details for PubMedID 30706981

  • The Myheart Counts Cardiovascular Health Study: A Randomized Controlled Trial of Digital Health Coaching for Physical Activity Promotion Shcherbina, A., Hershman, S., King, A. C., Hekler, E., Pavlovic, A., Waggott, D., McConnell, M. V., Ashley, E. A., Harrington, R. A. LIPPINCOTT WILLIAMS & WILKINS. 2018: E767
  • Loss of function, missense, and intronic variants in NOTCH1 confer different risks for left ventricular outflow tract obstructive heart defects in two European cohorts. Genetic epidemiology Helle, E., Cordova-Palomera, A., Ojala, T., Saha, P., Potiny, P., Gustafsson, S., Ingelsson, E., Bamshad, M., Nickerson, D., Chong, J. X., University of Washington Center for Mendelian Genomics, Ashley, E., Priest, J. R. 2018

    Abstract

    Loss of function variants in NOTCH1 cause left ventricular outflow tract obstructive defects (LVOTO). However, the risk conferred by rare and noncoding variants in NOTCH1 for LVOTO remains largely uncharacterized. In a cohort of 49 families affected by hypoplastic left heart syndrome, a severe form of LVOTO, we discovered predicted loss of function NOTCH1 variants in 6% of individuals. Rare or low-frequency missense variants were found in 16% of families. To make a quantitative estimate of the genetic risk posed by variants in NOTCH1 for LVOTO, we studied associations of 400 coding and noncoding variants in NOTCH1 in 1,085 cases and 332,788 controls from the UK Biobank. Two rare intronic variants in strong linkage disequilibrium displayed significant association with risk for LVOTO amongst European-ancestry individuals. This result was replicated in an independent analysis of 210 cases and 68,762 controls of non-European and mixed ancestry. In conclusion, carrying rare predicted loss of function variants in NOTCH1 confer significant risk for LVOTO. In addition, the two intronic variants seem to be associated with an increased risk for these defects. Our approach demonstrates the utility of population-based data sets in quantifying the specific risk of individual variants for disease-related phenotypes.

    View details for PubMedID 30511478

  • Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease NEW ENGLAND JOURNAL OF MEDICINE Splinter, K., Adams, D. R., Bacino, C. A., Bellen, H. J., Bernstein, J. A., Cheatle-Jarvela, A. M., Eng, C. M., Esteves, C., Gahl, W. A., Hamid, R., Jacob, H. J., Kikani, B., Koeller, D. M., Kohane, I. S., Lee, B. H., Loscalzo, J., Luo, X., McCray, A. T., Metz, T. O., Mulvihill, J. J., Nelson, S. F., Palmer, C. S., Phillips, J. A., Pick, L., Postlethwait, J. H., Reuter, C., Shashi, V., Sweetser, D. A., Tifft, C. J., Walley, N. M., Wangler, M. F., Westerfield, M., Wheeler, M. T., Wise, A. L., Worthey, E. A., Yamamoto, S., Ashley, E. A., Undiagnosed Dis Network 2018; 379 (22): 2131–39
  • Precision Approach to Exercise Capacity and Outcome in Hypertrophic Cardiomyopathy, an International Multicenter Analysis Lee, S., Amar, D., Parikh, V., Myers, J., Wheeler, M., Jacoby, D., Colan, S., Pereira, A., Green, E., Olivotto, I., Day, S., Michels, M., Ho, C., Elliott, P., Ashley, E. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Regional Variation in RBM20 Causes a Highly Penetrant Arrhythmogenic Cardiomyopathy. Parikh, V. N., Caleshu, C., Reuter, C., Lazzeroni, L., Ingles, J., Kumar, S., Garcia, J., McCaleb, K., Adesiyun, T., Dedaghat-Hamedani, F., Graw, S., Gigli, M., Stolfo, D., Dal Ferro, M., Ing, A., Nussbaum, R., Funke, B., Wheeler, M. T., Hershberger, R. E., Cook, S., Steinmetz, L., Lakdawala, N. K., Taylor, M. R., Mestroni, L., Merlo, M., Sinagra, G., Semsarian, C., Meder, B., Judge, D. P., Ashley, E. A. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Reclassifying Hypertrophic Cardiomyopathy Variants of Unknown Significance Based on Structural Determinants Improves Risk Stratification. Garfinkel, A. C., Cirino, A. L., Day, S. M., Ashley, E. A., Michels, M., Colan, S. D., Jacoby, D., Olivotto, I., Toepfer, C. N., Pereira, A. C., Seidman, J. G., Ho, C. Y., Seidman, C. E. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Peak Oxygen Consumption is an Independent Predictor of Survival and Outcomes in Obstructive and Non-Obstructive Hypertrophic Cardiomyopathy (HCM) Patients: Results From the International Sarcomeric Human Cardiomyopathies Registry SHaRe) Vincent, T. D., Day, S. M., Jacoby, D. L., Colan, S. D., Olivotto, I., Ashley, E. A., Sehnert, A. J., Ho, C. Y., SHaRe Investigators LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Functional Clustering of Non-Truncating Mutations in Myosin Binding Protein C That Cause Hypertrophic Cardiomyopathy Thompson, A. D., Glazer, A., Hafeez, N., Rodriguez, J., Yob, J., Jacoby, D. L., Colan, S. D., Michels, M., Olivotto, I., Ashley, E. A., Ho, C. Y., Helms, A., Day, S. M., SHaRe Investigators LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Women With Hypertrophic Cardiomyopathy: Obstructed and Underdiagnosed? Results From the International SHaRe Registry Lakdawala, N. K., Olivotto, I., Day, S., Jacoby, D., Ashley, E., Michels, M., Pereira, A., Colan, S., Ho, C. Y. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Women With Hypertrophic Cardiomyopathy Experience Higher Rates of Heart Failure and Mortality Than Men - Results From the International Share Registry Lakdawala, N. K., Olivotto, I., Day, S., Ashley, E., Pereira, A., Michels, M., Colan, S., Jacoby, D., Ho, C. Y. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Impact of Race on Disease Expression and Clinical Outcomes in Hypertrophic Cardiomyopathy Eberly, L. A., Ho, C., Cirino, A., Day, S., Olivotto, I., Ashley, E. A., Michels, M., Colan, S., Jacoby, D., Pereira, A., Lakdawala, N. LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Obesity is a Major Driver of Obstruction and Heart Failure in Hypertrophic Cardiomyopathy: Results From the International Share Registry Fumagalli, C., Maurizi, N., Vincent-Tompkins, J., Ho, C. Y., Day, S. M., Ashley, E., Michels, M., Colan, S. D., Jacoby, D., Olivotto, I., The ShaRe Investigators LIPPINCOTT WILLIAMS & WILKINS. 2018
  • Large Q and S waves in lead III on the electrocardiogram distinguish patients with hypertrophic cardiomyopathy from athletes HEART Chen, A. S., Bent, R. E., Wheeler, M., Knowles, J. W., Haddad, F., Froelicher, V., Ashley, E., Perez, M. V. 2018; 104 (22): 1871–77
  • A Premature Termination Codon Mutation in MYBPC3 Causes Hypertrophic Cardiomyopathy via Chronic Activation of Nonsense-Mediated Decay. Circulation Seeger, T., Shrestha, R., Lam, C. K., Chen, C., McKeithan, W. L., Lau, E., Wnorowski, A., McMullen, G., Greenhaw, M., Lee, J., Oikonomopoulos, A., Lee, S., Yang, H., Mercola, M., Wheeler, M., Ashley, E. A., Yang, F., Karakikes, I., Wu, J. C. 2018

    Abstract

    BACKGROUND: Hypertrophic cardiomyopathy (HCM) is frequently caused by mutations in myosin binding protein C3 ( MYBPC3) resulting in a premature termination codon (PTC). The underlying mechanisms of how PTC mutations in MYBPC3 lead to the onset and progression of HCM are poorly understood. This study's aim was to investigate the molecular mechanisms underlying the pathogenesis of HCM associated with MYBPC3 PTC mutations by utilizing human isogenic induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs).METHODS: Isogenic iPSC lines were generated from patients harboring MYBPC3 PTC mutations (p.R943x; p.R1073P_Fsx4) using genome editing and then differentiated into cardiomyocytes. Comprehensive phenotypical and transcriptome analyses were performed.RESULTS: We observed aberrant calcium handling properties with prolonged decay kinetics and elevated diastolic calcium levels in HCM iPSC-CMs compared to isogenic controls without structural abnormalities or contractile dysfunction. The mRNA expression levels of MYBPC3 were significantly reduced in mutant iPSC-CMs, but the protein levels were comparable among isogenic iPSC-CMs, suggesting that haploinsufficiency of MYBPC3 does not contribute to the pathogenesis of HCM in vitro. Furthermore, truncated MYBPC3 peptides were not detected. At the molecular level, the nonsense-mediated decay (NMD) pathway was activated, and a set of genes involved in major cardiac signaling pathways was dysregulated in HCM iPSC-CMs, indicating an HCM gene signature in vitro. Specific inhibition of the NMD pathway in mutant iPSC-CMs resulted in reversal of the molecular phenotype and normalization of calcium handling abnormalities.CONCLUSIONS: iPSC-CMs carrying MYBPC3 PTC mutations displayed aberrant calcium signaling and molecular dysregulations in the absence of significant haploinsufficiency of MYBPC3 protein. Here we provided the first evidence of the direct connection between the chronically activated NMD pathway and HCM disease development.

    View details for PubMedID 30586709

  • Telomere shortening is a hallmark of genetic cardiomyopathies PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Chang, A. Y., Chang, A. H., Kirillova, A., Sasagawa, K., Su, W., Weber, G., Lin, J., Termglinchan, V., Karakikes, I., Seeger, T., Dainis, A. M., Hinson, J. T., Seidman, J., Seidman, C. E., Day, J. W., Ashley, E., Wu, J. C., Blau, H. M. 2018; 115 (37): 9276–81
  • Incident Atrial Fibrillation Is Associated With MYH7 Sarcomeric Gene Variation in Hypertrophic Cardiomyopathy. Circulation. Heart failure Lee, S., Ashley, E. A., Homburger, J., Caleshu, C., Green, E. M., Jacoby, D., Colan, S. D., Arteaga-Fernandez, E., Day, S. M., Girolami, F., Olivotto, I., Michels, M., Ho, C. Y., Perez, M. V., SHaRe Investigators 2018; 11 (9): e005191

    Abstract

    Background Although atrial fibrillation (AF) is common in hypertrophic cardiomyopathy (HCM) patients, the relationship between genetic variation and AF has been poorly defined. Characterizing genetic subtypes of HCM and their associations with AF may help to improve personalized medical care. We aimed to investigate the link between sarcomeric gene variation and incident AF in HCM patients. Methods and Results Patients from the multinational Sarcomeric Human Cardiomyopathy Registry were followed for incident AF. Those with likely pathogenic or pathogenic variants in sarcomeric genes were included. The AF incidence was ascertained by review of medical records and electrocardiograms at each investigative site. One thousand forty adult HCM patients, without baseline AF and with likely pathogenic or pathogenic variation in either MYH7 (n=296), MYBPC3 (n=659), or thin filament genes (n=85), were included. Compared with patients with variation in other sarcomeric genes, those with MYH7 variants were younger on first clinical encounter at the Sarcomeric Human Cardiomyopathy Registry site and more likely to be probands than the MYBPC3 variants. During an average follow-up of 7.2 years, 198 incident AF events occurred. Patients with likely pathogenic or pathogenic mutations in MYH7 had the highest incidence of AF after adjusting for age, sex, proband status, left atrial size, maximal wall thickness, and peak pressure gradient (hazard ratio, 1.7; 95% CI, 1.1-2.6; P=0.009). Conclusions During a mean follow-up of 7.2 years, new-onset AF developed in 19% of HCM patients with sarcomeric mutations. Compared with other sarcomeric genes, patients with likely pathogenic or pathogenic variation in MYH7 had a higher rate of incident AF independent of clinical and echocardiographic factors.

    View details for PubMedID 30354366

  • Incident Atrial Fibrillation Is Associated With MYH7 Sarcomeric Gene Variation in Hypertrophic Cardiomyopathy Results From the International Sarcomeric Human Cardiomyopathy Registry CIRCULATION-HEART FAILURE Lee, S., Ashley, E. A., Homburger, J., Caleshu, C., Green, E. M., Jacoby, D., Colan, S. D., Arteaga-Fernandez, E., Day, S. M., Girolami, F., Olivotto, I., Michels, M., Ho, C. Y., Perez, M. V., SHaRe Investigators 2018; 11 (9)
  • Telomere shortening is a hallmark of genetic cardiomyopathies. Proceedings of the National Academy of Sciences of the United States of America Chang, A. C., Chang, A. C., Kirillova, A., Sasagawa, K., Su, W., Weber, G., Lin, J., Termglinchan, V., Karakikes, I., Seeger, T., Dainis, A. M., Hinson, J. T., Seidman, J., Seidman, C. E., Day, J. W., Ashley, E., Wu, J. C., Blau, H. M. 2018

    Abstract

    This study demonstrates that significantly shortened telomeres are a hallmark of cardiomyocytes (CMs) from individuals with end-stage hypertrophic cardiomyopathy (HCM) or dilated cardiomyopathy (DCM) as a result of heritable defects in cardiac proteins critical to contractile function. Positioned at the ends of chromosomes, telomeres are DNA repeats that serve as protective caps that shorten with each cell division, a marker of aging. CMs are a known exception in which telomeres remain relatively stable throughout life in healthy individuals. We found that, relative to healthy controls, telomeres are significantly shorter in CMs of genetic HCM and DCM patient tissues harboring pathogenic mutations: TNNI3, MYBPC3, MYH7, DMD, TNNT2, and TTN Quantitative FISH (Q-FISH) of single cells revealed that telomeres were significantly reduced by 26% in HCM and 40% in DCM patient CMs in fixed tissue sections compared with CMs from age- and sex-matched healthy controls. In the cardiac tissues of the same patients, telomere shortening was not evident in vascular smooth muscle cells that do not express or require the contractile proteins, an important control. Telomere shortening was recapitulated in DCM and HCM CMs differentiated from patient-derived human-induced pluripotent stem cells (hiPSCs) measured by two independent assays. This study reveals telomere shortening as a hallmark of genetic HCM and DCM and demonstrates that this shortening can be modeled in vitro by using the hiPSC platform, enabling drug discovery.

    View details for PubMedID 30150400

  • Prevalence and Progression of Late Gadolinium Enhancement in Children and Adolescents With Hypertrophic Cardiomyopathy CIRCULATION Raja, A., Farhad, H., Valente, A., Couce, J., Jefferies, J., Bundgaard, H., Zahka, K., Lever, H., Murphy, A. M., Ashley, E., Day, S. M., Sherrid, M. V., Shi, L., Bluemke, D. A., Canter, C. E., Colan, S. D., Ho, C. Y. 2018; 138 (8): 782–92

    Abstract

    Background -Late gadolinium enhancement (LGE) on cardiac magnetic resonance imaging (CMR) is believed to represent dense replacement fibrosis. It is seen in ~60% of adult patients with hypertrophic cardiomyopathy (HCM). However, the prevalence of LGE in children and adolescents with HCM is not well established. Additionally, longitudinal studies describing the development and evolution of LGE in pediatric HCM are lacking. This study assesses the prevalence, progression, and clinical correlations of LGE in children and adolescents with, or genetically predisposed to, HCM. Methods -CMR scans from 195 HCM patients ≤21 years of age were analyzed in an observational, retrospective study, including 155 with overt HCM and 40 sarcomere mutation carriers without left ventricular (LV) hypertrophy. The extent of LGE was quantified by measuring regions with signal intensity >6 SD above nulled remote myocardium. Results -Patients were 14.3 ± 4.5 years old at baseline and 68% were male. LGE was present in 70 (46%) patients with overt HCM (median extent 3.3% [IQR 0.8 to 7.1]), but absent in mutation carriers without LVH. Thirty-one patients had more than one CMR (median interval between studies 2.4 years [IQR 1.5 to 3.2]). LGE was detected in 13 patients (42%) at baseline and 16 (52%) at follow-up CMR. The median extent of LGE increased by 2.4 g/year (range 0 to 13.2) from 2.9% (IQR 0.8 to 3.2) of LV mass to 4.3% (IQR 2.9 to 6.8) (p=0.02). In addition to LGE, LV mass and left atrial volume, indexed to body surface area, as well as z-score for LV mass increased significantly from first to most recent CMR. Conclusions -LGE was present in 46% of children and adolescents with overt HCM, in contrast to ~60% typically reported in adult HCM. In the subset of patients with serial imaging, statistically significant increases in LGE, left ventricular mass and left atrial size were detected over 2.5 years, indicating disease progression over time. Further prospective studies are required to confirm these findings and to better understand the clinical implications of LGE in pediatric HCM.

    View details for PubMedID 29622585

  • What's in a Name? Factors That Influence the Usage of Generic Versus Trade Names for Cardiac Medications Among Healthcare Providers CIRCULATION-CARDIOVASCULAR QUALITY AND OUTCOMES Ouyang, D., Tisdale, R., Cheng, P., Chi, J., Chen, J. H., Ashley, E. 2018; 11 (8)
  • Acetaminophen or Tylenol? A Retrospective Analysis of Medication Digital Communication Practices JOURNAL OF GENERAL INTERNAL MEDICINE Ouyang, D., Tisdale, R., Ashley, E., Chi, J., Chen, J. H. 2018; 33 (8): 1218–20
  • Apelin and APJ orchestrate complex tissue-specific control of cardiomyocyte hypertrophy and contractility in the hypertrophy-heart failure transition AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY Parikh, V. N., Liu, J., Shang, C., Woods, C., Chang, A. C., Zhao, M., Charo, D. N., Grunwald, Z., Huang, Y., Seo, K., Tsao, P. S., Bernstein, D., Ruiz-Lozano, P., Quertermous, T., Ashley, E. A. 2018; 315 (2): H348–H356
  • Serial echo-cardiopulmonary exercise test ramping for evaluation of patients with VAD Christle, J. W., Moneghetti, K., Haddad, F., Myers, J., Ashley, E. A., Wheeler, M., Banerjee, D. OXFORD UNIV PRESS. 2018: 386
  • What's in a Name? Factors That Influence the Usage of Generic Versus Trade Names for Cardiac Medications Among Healthcare Providers. Circulation. Cardiovascular quality and outcomes Ouyang, D., Tisdale, R., Cheng, P., Chi, J., Chen, J. H., Ashley, E. 2018; 11 (8): e004704

    View details for DOI 10.1161/CIRCOUTCOMES.118.004704

    View details for PubMedID 30354370

  • Time based versus strain based myocardial performance indices in hypertrophic cardiomyopathy, the merging role of left atrial strain. European heart journal cardiovascular Imaging Kobayashi, Y., Moneghetti, K. J., Bouajila, S., Stolfo, D., Finocchiaro, G., Kuznetsova, T., Liang, D., Schnittger, I., Ashley, E., Wheeler, M., Haddad, F. 2018

    Abstract

    Aims: The myocardial performance index (MPI) is a time-based index of global myocardial performance. In this study, we sought to compare the prognostic value of the MPI with other strain and remodelling indices in hypertrophic cardiomyopathy (HCM).Methods and results: We enrolled 126 patients with HCM and 50 age- and sex-matched controls. Along with traditional echocardiographic assessment, MPI, left ventricular global longitudinal strain (LVGLS), E/e' ratio, and total left atrial (LA) global strain (LAS) were also measured. Time-based MPI was calculated from flow or tissue-based pulse wave Doppler (PWD and TDI) as the (isovolumic-relaxation and contraction time)/systolic-time. We used hierarchical clustering and network analysis to better visualize the relationship between parameters. The primary endpoint was the composite of all-cause death, heart transplantation, left ventricular assist device implantation, and clinical worsening. Left ventricular outflow tract (LVOT) obstruction was present in 56% of patients. Compared with controls, patients with HCM had worse LVGLS (-14.0±3.4% vs. -19.6±1.5%), higher E/e' (12.9±7.2 vs. 6.1±1.5), LA volume index (LAVI) (36.4±13.8ml/m2 vs. 25.6±6.7ml/m2), and MPI (0.55±0.17 vs. 0.40±0.11 for PWD and 0.59±0.22 vs. 0.46±0.09 for TDI) (all P<0.001). During a median follow-up of 55months, 47 endpoints occurred. PWD or TDI-based MPI was not associated with outcome, while LAVI, LAS, LVGLS, and E/e' were (all P<0.01). On multivariable analysis, LVOT obstruction (P<0.001), LAS (P<0.001), and E/e' (P=0.02) were retained as independent associates. They were in different clusters suggesting complemental relationship between them.Conclusion: Time-based index is less predictive of outcome than strain or tissue Doppler indices. LAS may be a promising prognostic marker in HCM.

    View details for PubMedID 30060097

  • Genome Sequencing in HypertrophicCardiomyopathy. Journal of the American College of Cardiology Ashley, E. A., Reuter, C. M., Wheeler, M. T. 2018; 72 (4): 430–33

    View details for PubMedID 30025579

  • Genome Sequencing in Hypertrophic Cardiomyopathy JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Ashley, E. A., Reuter, C. M., Wheeler, M. T. 2018; 72 (4): 430-433
  • Applying current normative data to prognosis in heart failure: The Fitness Registry and the Importance of Exercise National Database (FRIEND) INTERNATIONAL JOURNAL OF CARDIOLOGY Moneghetti, K. J., Hock, J., Kaminsky, L., Arena, R., Lui, G. K., Haddad, F., Wheeler, M., Froelicher, V., Ashley, E., Myers, J., Christle, J. W. 2018; 263: 75–79

    Abstract

    Percent of predicted peak VO2 (ppVO2) is considered a standard measure for establishing disease severity, however, there are known limitations to traditional normative values. This study sought to compare ppVO2 from the newly derived "Fitness Registry and the Importance of Exercise: a National Database" (FRIEND) registry equation to conventional prediction equations in a clinical cohort of patients undergoing cardiopulmonary exercise testing (CPX).We selected 1094 patients referred for evaluation of heart failure (HF) symptoms who underwent CPX. ppVO2 was calculated using the FRIEND, Wasserman/Hansen and Jones equations. Participants were followed for a median of 4.5 years [Interquartile range 3.5-6.0] for the composite endpoint of death, advanced HF therapy, or acute decompensated HF requiring hospital admission. Mean age was 48 ± 15 years and 62% were female. The FRIEND registry equation predicted the lowest ppVO2 (measured/predicted; 71 ± 31%), compared to the Wasserman/Hansen (74 ± 29%) and Jones equations (83 ± 33%) (p < 0.001). All expressions of peak VO2 were significant as univariate predictors of outcome with no significant differences between equations on pairwise analysis of receiver operating characteristic curves. When compared at a similar threshold of ppVO2 the event rate was significantly lower in the FRIEND registry equation versus the currently used Wasserman and Jones equations.The use of the newly derived FRIEND registry equation predicts HF outcomes; however, it appears to predict a higher predicted VO2; the clinical implication being a lower threshold of percent predicted peak VO2 should be considered when risk stratifying patients with HF.

    View details for PubMedID 29525067

  • Mobile Health Advances in Physical Activity, Fitness, and Atrial Fibrillation Moving Hearts JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY McConnell, M. V., Turakhia, M. P., Harrington, R. A., King, A. C., Ashley, E. A. 2018; 71 (23): 2691–2701

    Abstract

    The growing recognition that "health" takes place outside of the hospital and clinic, plus recent advances in mobile and wearable devices, have propelled the field of mobile health (mHealth). Cardiovascular disease and prevention are major opportunities for mHealth, as mobile devices can monitor key physiological signals (e.g., physical activity, heart rate and rhythm) for promoting healthy behaviors, detecting disease, and aid in ongoing care. In this review, the authors provide an update on cardiovascular mHealth by highlighting recent progress and challenges with mobile and wearable devices for assessing and promoting physical activity and fitness, and for monitoring heart rate and rhythm for the detection and management of atrial fibrillation.

    View details for PubMedID 29880130

  • Apelin and APJ orchestrate complex tissue-specific control of cardiomyocyte hypertrophy and contractility in the hypertrophy-heart failure transition. American journal of physiology. Heart and circulatory physiology Parikh, V. N., Liu, J., Shang, C., Woods, C., Chang, A. C., Zhao, M., Charo, D. N., Grunwald, Z., Huang, Y., Seo, K., Tsao, P. S., Bernstein, D., Ruiz-Lozano, P., Quertermous, T., Ashley, E. A. 2018

    Abstract

    The G protein coupled receptor APJ is a promising therapeutic target for heart failure. Constitutive deletion of APJ in the mouse is protective against the hypertrophy-heart failure transition via elimination of ligand-independent, beta-arrestin dependent stretch transduction. However, the cellular origin of this stretch transduction and the details of its interaction with apelin signaling remain unknown. We generated mice with conditional elimination of APJ in the endothelium (APJendo-/-) and myocardium (APJmyo-/-). No baseline difference was observed in LV function in APJendo-/-, APJmyo-/- or controls (APJendo+/+, APJmyo+/+). After exposure to transaortic constriction (TAC), APJendo-/- animals developed left ventricular failure while APJmyo-/- were protected. At the cellular level, carbon fiber stretch of freshly isolated single cardiomyocytes demonstrated decreased contractile response to stretch in APJ-/- cardiomyocytes compared to APJ+/+ cardiomyocytes. Calcium transient did not change with stretch in either APJ-/- or APJ+/+ cardiomyocytes. Application of apelin to APJ+/+ cardiomyocytes resulted in decreased calcium transient. Further, hearts of mice treated with apelin exhibited decreased phosphorylation at Troponin I (cTnI) N-terminal residues (Ser 22,23), consistent with increased calcium sensitivity. These data establish that APJ stretch transduction is mediated specifically by myocardial APJ, that APJ is necessary for stretch-induced increases in contractility, and that apelin opposes APJ's stretch-mediated hypertrophy signaling by lowering calcium transient while maintaining contractility through myofilament calcium sensitization. These findings underscore apelin's unique potential as a therapeutic agent that can simultaneously support cardiac function and protect against the hypertrophy-heart failure transition.

    View details for PubMedID 29775410

  • Acetaminophen or Tylenol? A Retrospective Analysis of Medication Digital Communication Practices. Journal of general internal medicine Ouyang, D., Tisdale, R., Ashley, E., Chi, J., Chen, J. H. 2018

    View details for PubMedID 29717410

  • Right Ventricular Structure and Function in the Veteran Ultramarathon Runner: Is There Evidence for Chronic Maladaptation? JOURNAL OF THE AMERICAN SOCIETY OF ECHOCARDIOGRAPHY Rothwell, O., George, K., Somauroo, J., Lord, R., Stembridge, M., Shave, R., Hoffman, M. D., Wilson, M., Ashley, E., Haddad, F., Eijsvogels, T. H., Oxborough, D. 2018; 31 (5): 598-+

    Abstract

    It has been proposed that chronic exposure to prolonged strenuous exercise may result in maladaptation of the right ventricle (RV). The aim of this study was to establish RV structure and function, including septal insertion points, using conventional echocardiography and myocardial strain (ε) imaging in a veteran population of ultramarathon runners (UR) and age- and sex-matched controls.A retrospective study design provided 40 UR (>35 years old; mean ± SD training experience, 18 ± 12 years) and 24 sedentary controls who had previously undergone conventional two-dimensional, tissue Doppler and speckle-tracking echocardiography to measure RV size and function. Peak RV ε and strain rate (SR) were assessed from the base, mid, and apical lateral wall. SR were assessed during systole (SRs'), early diastole (SRe') and late diastole (SRa'). Regional assessment of RV insertion points was made at the basal inferoseptum and apical septum using left ventricular (LV) longitudinal ε and at the anteroseptum and inferoseptum using LV circumferential and radial ε.All structural indices of RV size were significantly larger in UR. RV regional and global peak ε were not different between groups, whereas basal RV SR was significantly lower in UR. UR had significantly higher peak LV circumferential ε (anteroseptum, -26% ± 8% vs -21% ± 6%; inferoseptum, -25% ± 6% vs -16% ± 9%) and higher peak LV longitudinal ε (apical septum, -28% ± 7% vs -22% ± 4%) compared with controls. There was regional heterogeneity in UR that was not observed in controls with significantly lower longitudinal ε at the basal inferoseptal insertion point when compared with the global ε (-19% ± 2% vs -22% ± 4%).Myocardial ε imaging highlights no overt maladaptation in this cohort of veteran UR, although lower insertion point ε, compared with global ε, in UR may warrant further investigation.

    View details for PubMedID 29305036

  • A reference equation for maximal aerobic power for treadmill and cycle ergometer exercise testing: Analysis from the FRIEND registry EUROPEAN JOURNAL OF PREVENTIVE CARDIOLOGY de Souza e Silva, C. G., Kaminsky, L. A., Arena, R., Christle, J. W., Araujo, C. S., Lima, R. M., Ashley, E. A., Myers, J. 2018; 25 (7): 742–50

    Abstract

    Background Maximal oxygen uptake (VO2max) is a powerful predictor of health outcomes. Valid and portable reference values are integral to interpreting measured VO2max; however, available reference standards lack validation and are specific to exercise mode. This study was undertaken to develop and validate a single equation for normal standards for VO2max for the treadmill or cycle ergometer in men and women. Methods Healthy individuals ( N = 10,881; 67.8% men, 20-85 years) who performed a maximal cardiopulmonary exercise test on either a treadmill or a cycle ergometer were studied. Of these, 7617 and 3264 individuals were randomly selected for development and validation of the equation, respectively. A Brazilian sample (1619 individuals) constituted a second validation cohort. The prediction equation was determined using multiple regression analysis, and comparisons were made with the widely-used Wasserman and European equations. Results Age, sex, weight, height and exercise mode were significant predictors of VO2max. The regression equation was: VO2max (ml kg-1 min-1) = 45.2 - 0.35*Age - 10.9*Sex (male = 1; female = 2) - 0.15*Weight (pounds) + 0.68*Height (inches) - 0.46*Exercise Mode (treadmill = 1; bike = 2) ( R = 0.79, R2 = 0.62, standard error of the estimate = 6.6 ml kg-1 min-1). Percentage predicted VO2max for the US and Brazilian validation cohorts were 102.8% and 95.8%, respectively. The new equation performed better than traditional equations, particularly among women and individuals ≥60 years old. Conclusion A combined equation was developed for normal standards for VO2max for different exercise modes derived from a US national registry. The equation provided a lower average error between measured and predicted VO2max than traditional equations even when applied to an independent cohort. Additional studies are needed to determine its portability.

    View details for PubMedID 29517365

  • Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank SCIENTIFIC REPORTS Tikkanen, E., Gustafsson, S., Amar, D., Shcherbina, A., Waggott, D., Ashley, E. A., Ingelsson, E. 2018; 8: 6451

    Abstract

    We performed a large genome-wide association study to discover genetic variation associated with muscular strength, and to evaluate shared genetic aetiology with and causal effects of muscular strength on several health indicators. In our discovery analysis of 223,315 individuals, we identified 101 loci associated with grip strength (P <5 × 10-8). Of these, 64 were associated (P < 0.01 and consistent direction) also in the replication dataset (N = 111,610). eQTL analyses highlighted several genes known to play a role in neuro-developmental disorders or brain function, and the results from meta-analysis showed a significant enrichment of gene expression of brain-related transcripts. Further, we observed inverse genetic correlations of grip strength with cardiometabolic traits, and positive correlation with parents' age of death and education. We also showed that grip strength had shared biological pathways with indicators of frailty, including cognitive performance scores. By use of Mendelian randomization, we provide evidence that higher grip strength is protective of both coronary heart disease (OR = 0.69, 95% CI 0.60-0.79, P < 0.0001) and atrial fibrillation (OR = 0.75, 95% CI 0.62-0.90, P = 0.003). In conclusion, our results show shared genetic aetiology between grip strength, and cardiometabolic and cognitive health; and suggest that maintaining muscular strength could prevent future cardiovascular events.

    View details for PubMedID 29691431

  • Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study NATURE COMMUNICATIONS DeBoever, C., Tanigawa, Y., Lindholm, M. E., McInnes, G., Lavertu, A., Ingelsson, E., Chang, C., Ashley, E. A., Bustamante, C. D., Daly, M. J., Rivas, M. A. 2018; 9: 1612

    Abstract

    Protein-truncating variants can have profound effects on gene function and are critical for clinical genome interpretation and generating therapeutic hypotheses, but their relevance to medical phenotypes has not been systematically assessed. Here, we characterize the effect of 18,228 protein-truncating variants across 135 phenotypes from the UK Biobank and find 27 associations between medical phenotypes and protein-truncating variants in genes outside the major histocompatibility complex. We perform phenome-wide analyses and directly measure the effect in homozygous carriers, commonly referred to as "human knockouts," across medical phenotypes for genes implicated as being protective against disease or associated with at least one phenotype in our study. We find several genes with strong pleiotropic or non-additive effects. Our results illustrate the importance of protein-truncating variants in a variety of diseases.

    View details for PubMedID 29691392

  • Large Q and S waves in lead III on the electrocardiogram distinguish patients with hypertrophic cardiomyopathy from athletes. Heart (British Cardiac Society) Chen, A. S., Bent, R. E., Wheeler, M., Knowles, J. W., Haddad, F., Froelicher, V., Ashley, E., Perez, M. V. 2018

    Abstract

    OBJECTIVE: To identify electrocardiographic findings, especially deep Q and S waves in lead III, that differentiate athletes from patients with hypertrophic cardiomyopathy (HCM).METHODS: Digital ECGs of athletes and patients with HCM followed at the Stanford Center for Inherited Cardiovascular Disease were studied retrospectively. All patients with HCM had an echocardiogram performed. A multivariable logistic regression model was used to calculate ORs for various demographic and ECG characteristics. Linear regression was used to correlate ECG characteristics with echocardiogram findings.RESULTS: We studied 1124 athletes and 240 patients with HCM. The average Q+Swave amplitude in lead III (IIIQ+S) was significantly higher in patients with HCM compared with athletes (0.71±0.69mV vs 0.21±0.17mV, p<0.001). In patients with HCM, IIIQ+S directly correlated with interventricular septal (IVS) thickness on echocardiography (rho=0.45, p<0.001). In a multivariable analysis adjusted for demographic and ECG characteristics, higher IIIQ+S values remained independently associated with HCM compared with athletes (OR=4.2 per 0.5mV, p<0.001). In subgroup analyses of young patients, African-American subjects and subjects without left axis deviation (LAD), IIIQ+S remained associated with HCM. The addition of IIIQ+S>1.0 mV as an abnormal finding to the International Criteria for athletic ECG interpretation improved sensitivity from 64.2% to 70.4%, with a minimal decrease in specificity.CONCLUSION: Large Q and S waves in lead III distinguished athletes from patients with HCM, independent of axis and well-known ECG markers associated with HCM. The correlation between IVS thickness in patients with HCM and IIIQ+S suggests a partial explanation for this association.

    View details for PubMedID 29680808

  • Cardiovascular Precision Medicine in the Genomics Era. JACC. Basic to translational science Dainis, A. M., Ashley, E. A. 2018; 3 (2): 313–26

    Abstract

    Precision medicine strives to delineate disease using multiple data sources-from genomics to digital health metrics-in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for eachindividual patient.

    View details for PubMedID 30062216

  • MEDICATION COMMUNICATION PRACTICES BETWEEN PROVIDERS IN CARDIOLOGY Tisdale, R., Ouyang, D., Cheng, P., Chi, J., Chen, J., Ashley, E. ELSEVIER SCIENCE INC. 2018: 2644
  • INTEGRATING CORRELATION BASED NETWORKS INTO RISK PROGNOSTICATION OF CARDIOMYOPATHY Moneghetti, K., Kim, J., Kobayashi, Y., Boralkar, K., Wheeler, M., Ashley, E., Haddad, F. ELSEVIER SCIENCE INC. 2018: 837
  • Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder AMERICAN JOURNAL OF HUMAN GENETICS Olahova, M., Yoon, W., Thompson, K., Jangam, S., Fernandez, L., Davidson, J. M., Kyle, J. E., Grove, M. E., Fisk, D. G., Kohler, J. N., Holmes, M., Dries, A. M., Huang, Y., Zhao, C., Contrepois, K., Zappala, Z., Fresard, L., Waggott, D., Zink, E. M., Kim, Y., Heyman, H. M., Stratton, K. G., Webb-Robertson, B. M., Snyder, M., Merker, J. D., Montgomery, S. B., Fisher, P. G., Feichtinger, R. G., Mayr, J. A., Hall, J., Barbosa, I. A., Simpson, M. A., Deshpande, C., Waters, K. M., Koeller, D. M., Metz, T. O., Morris, A. A., Schelley, S., Cowan, T., Friederich, M. W., McFarland, R., Van Hove, J. K., Enns, G. M., Yamamoto, S., Ashley, E. A., Wangler, M. F., Taylor, R. W., Bellen, H. J., Bernstein, J. A., Wheeler, M. T., Undiagnosed Diseases Network 2018; 102 (3): 494–504

    Abstract

    ATP synthase, H+ transporting, mitochondrial F1 complex, δ subunit (ATP5F1D; formerly ATP5D) is a subunit of mitochondrial ATP synthase and plays an important role in coupling proton translocation and ATP production. Here, we describe two individuals, each with homozygous missense variants in ATP5F1D, who presented with episodic lethargy, metabolic acidosis, 3-methylglutaconic aciduria, and hyperammonemia. Subject 1, homozygous for c.245C>T (p.Pro82Leu), presented with recurrent metabolic decompensation starting in the neonatal period, and subject 2, homozygous for c.317T>G (p.Val106Gly), presented with acute encephalopathy in childhood. Cultured skin fibroblasts from these individuals exhibited impaired assembly of F1FO ATP synthase and subsequent reduced complex V activity. Cells from subject 1 also exhibited a significant decrease in mitochondrial cristae. Knockdown of Drosophila ATPsynδ, the ATP5F1D homolog, in developing eyes and brains caused a near complete loss of the fly head, a phenotype that was fully rescued by wild-type human ATP5F1D. In contrast, expression of the ATP5F1D c.245C>T and c.317T>G variants rescued the head-size phenotype but recapitulated the eye and antennae defects seen in other genetic models of mitochondrial oxidative phosphorylation deficiency. Our data establish c.245C>T (p.Pro82Leu) and c.317T>G (p.Val106Gly) in ATP5F1D as pathogenic variants leading to a Mendelian mitochondrial disease featuring episodic metabolic decompensation.

    View details for PubMedID 29478781

  • Cardiovascular disease: The rise of the genetic risk score PLOS MEDICINE Knowles, J. W., Ashley, E. A. 2018; 15 (3): e1002546

    Abstract

    In a Perspective, Joshua Knowles and Euan Ashley discuss the potential for use of genetic risk scores in clinical practice.

    View details for PubMedID 29601582

  • Genetic Reduction in Left Ventricular Protein Kinase C-alpha and Adverse Ventricular Remodeling in Human Subjects CIRCULATION-CARDIOVASCULAR GENETICS Hu, R., Morley, M. P., Brandimarto, J., Tucker, N. R., Parsons, V. A., Zhao, S. D., Meder, B., Katus, H. A., Ruehle, F., Stoll, M., Villard, E., Cambien, F., Lin, H., Smith, N. L., Felix, J. F., Vasan, R. S., van der Harst, P., Newton-Cheh, C., Li, J., Kim, C. E., Hakonarson, H., Hannenhalli, S., Ashley, E. A., Moravec, C. S., Tang, W., Maillet, M., Molkentin, J. D., Ellinor, P. T., Margulies, K. B., Cappola, T. P. 2018; 11 (3): e001901

    Abstract

    Inhibition of PKC-α (protein kinase C-α) enhances contractility and cardioprotection in animal models, but effects in humans are unknown. Genotypes at rs9912468 strongly associate with PRKCA expression in the left ventricle, enabling genetic approaches to measure effects of reduced PKC-α in human populations.We analyzed the cis expression quantitative trait locus for PRKCA marked by rs9912468 using 313 left ventricular specimens from European Ancestry patients. The forward strand minor allele (G) at rs9912468 is associated with reduced PKC-α transcript abundance (1.7-fold reduction in minor allele homozygotes, P=1×10-41). This association was cardiac specific in expression quantitative trait locus data sets that span 16 human tissues. Cardiac epigenomic data revealed a predicted enhancer in complete (R2=1.0) linkage disequilibrium with rs9912468 within intron 2 of PRKCA. We cloned this region and used reporter constructs to verify cardiac-specific enhancer activity in vitro in cardiac and noncardiac cells and in vivo in zebrafish. The PRKCA enhancer contains 2 common genetic variants and 4 haplotypes; the haplotype correlated with the rs9912468 PKC-α-lowering allele (G) showed lowest activity. In contrast to previous reports in animal models, the PKC-α-lowering allele is associated with adverse left ventricular remodeling (higher mass, larger diastolic dimension), reduced fractional shortening, and higher risk of dilated cardiomyopathy in human populations.These findings support PKC-α as a regulator of the human heart but suggest that PKC-α inhibition may adversely affect the left ventricle depending on timing and duration. Pharmacological studies in human subjects are required to discern potential benefits and harms of PKC-α inhibitors as an approach to treat heart disease.

    View details for PubMedID 29540468

    View details for PubMedCentralID PMC5858599

  • Ring Finger Protein 207 Degrades T613M Kv11.1 Channel Ledford, H. A., Park, S., Sirish, P., Xu, W., Emigh, A. M., Timofeyev, V., Priest, J. R., Perez, M. V., Ashley, E. A., Yarov-Yarovoy, V., Zhang, X., Chiamvimonvat, N. CELL PRESS. 2018: 625A
  • A New Approach to Rare Diseases of Children: The Undiagnosed Diseases Network. The Journal of pediatrics Reuter, C. M., Brimble, E. n., DeFilippo, C. n., Dries, A. M., Enns, G. M., Ashley, E. A., Bernstein, J. A., Fisher, P. G., Wheeler, M. T. 2018

    View details for PubMedID 29331327

  • PHACOMATOSIS PIGMENTOVASCULARIS: A CASE WITH SOMATIC MUTATION IN GNAQ AND ATYPICAL PHENOTYPIC FEATURES Kumar, A., Zastrow, D., Prybol, C., Manning, M., Huang, Y., Fisher, P., Ashley, E., Teng, J., Wheeler, M., Bernstein, J. BMJ PUBLISHING GROUP. 2018: 202
  • Athletic Remodeling in Female College Athletes, the "Morganroth Hypothesis" Revisited. Clinical journal of sport medicine : official journal of the Canadian Academy of Sport Medicine Kooreman, Z. n., Giraldeau, G. n., Finocchiaro, G. n., Kobayashi, Y. n., Wheeler, M. n., Perez, M. n., Moneghetti, K. n., Oxborough, D. n., George, K. P., Myers, J. n., Ashley, E. n., Haddad, F. n. 2018

    Abstract

    There is limited data regarding ventricular remodeling in college female athletes, especially when appropriate scaling of cardiac dimensions to lean body mass (LBM) is considered. Moreover, it is not well established whether cardiac remodeling in female athletes is a balanced process with proportional increase in left ventricular (LV) mass and volume or the right and LV size.During the preparticipation competitive screening, 72 female college athletes volunteered to undergo dual energy x-ray absorptiometry scan for quantification of LBM and comprehensive 2D echocardiography including assessment of longitudinal myocardial strain. The athletes were divided in 2 groups according to the intensity of the dynamic and static components of their sport categories, ie, a higher intensity dynamic and resistive group (n = 37 participating in rowing, water polo and lacrosse) and a lower intensity group (n = 35, participating in short distance running, sailing, synchronized swimming, and softball). In addition, we recruited a group of 31 age-matched nonathlete controls.The mean age of the study population was 18.7 ± 1.0 years. When scaled to body surface area, the higher intensity group had 17.1 ± 3.6% (P < 0.001) greater LV mass when compared with the lower intensity group and 21.7 ± 4.0% (P < 0.001) greater LV mass than the control group. The differences persisted after scaling to LBM with 14.2 ± 3.2% (P < 0.001) greater LV mass in the higher intensity group. By contrast, there was no difference in any of the relative remodeling indices including the LV mass to volume ratio, right to LV area ratio, or left atrial to LV volume ratio (P > 0.50 for all). In addition, no significant difference was noted among the 3 groups in LV ejection fraction (P = 0.22), LV global longitudinal strain (P = 0.55), LV systolic strain rate (P = 0.62), or right ventricular global longitudinal strain (P = 0.61).Female collegiate athletes participating in higher intensity dynamic and resistive sports have higher indexed LV mass even when scaled to LBM. The remodeling process does however appear to be a balanced process not only at the intraventricular level but also at the interventricular and atrioventricular levels.

    View details for PubMedID 29369833

  • A method for determining exercise oscillatory ventilation in heart failure: Prognostic value and practical implications INTERNATIONAL JOURNAL OF CARDIOLOGY Vainshelboim, B., Amin, A., Christle, J. W., Hebbal, S., Ashley, E. A., Myers, J. 2017; 249: 287–91

    Abstract

    Exercise oscillatory ventilation (EOV) has been shown to be a powerful prognostic marker in chronic heart failure (CHF). However, EOV is poorly defined, its measurement lacks standardization and it is underutilized in clinical practice. The purpose of this pilot study was to investigate the prognostic value of a modified definition of EOV in patients with CHF.Eighty-nine CHF patients (56.5±8.4years) (64% NYHA class III-IV) underwent cardiopulmonary exercise testing. EOV was defined as meeting all the following criteria: (1) ≥3 consecutive cyclic fluctuations of ventilation during exercise; (2) average amplitude over 3 ventilatory oscillations ≥5L; and (3) an average length of three oscillatory cycles 40s to 140s. Adverse cardiac events were tracked during 28±19months follow up. Cox proportional hazard analysis was used to determine the association between cardiac events and EOV.Forty-eight patients (54%) met all three criteria and were determined to have EOV. These patients exhibited significantly increased risk for adverse cardiac events [hazard ratio=2.2, 95% CI (1.2 to 4.1), p=0.011] compared to patients without EOV. After adjusting for age and established prognostic covariates (peak VO2 and VE/VCO2 slope), the modified EOV definition was the only significant variable in the multivariate model [hazard ratio=2.0, 95% CI (1.1 to 3.7), p=0.035].The proposed method for determining EOV was independently associated with increased risk for adverse cardiac events in CHF patients. While larger prospective studies are needed, this definition provides a relatively simple and more objective characterization of EOV, suggesting its potential application in clinical practice.

    View details for PubMedID 28918895

  • Impact of Demographic Features, Lifestyle, and Comorbidities on the Clinical Expression of Hypertrophic Cardiomyopathy. Journal of the American Heart Association Finocchiaro, G., Magavern, E., Sinagra, G., Ashley, E., Papadakis, M., Tome-Esteban, M., Sharma, S., Olivotto, I. 2017; 6 (12)

    View details for DOI 10.1161/JAHA.117.007161

    View details for PubMedID 29237589

    View details for PubMedCentralID PMC5779031

  • Impact of Demographic Features, Lifestyle, and Comorbidities on the Clinical Expression of Hypertrophic Cardiomyopathy JOURNAL OF THE AMERICAN HEART ASSOCIATION Finocchiaro, G., Magavem, E., Sinagra, G., Ashley, E., Papadakis, M., Tome-Esteban, M., Sharma, S., Olivotto, I. 2017; 6 (12)
  • Load-dependent effects of apelin on murine cardiomyocytes PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY Peyronnet, R., Bollensdorff, C., Capel, R. A., Rog-Zielinska, E. A., Woods, C. E., Charo, D. N., Lookin, O., Fajardo, G., Ho, M., Quertermous, T., Ashley, E. A., Kohl, P. 2017; 130: 333–43

    Abstract

    The apelin peptide is described as one of the most potent inotropic agents, produced endogenously in a wide range of cells, including cardiomyocytes. Despite positive effects on cardiac contractility in multicellular preparations, as well as indications of cardio-protective actions in several diseases, its effects and mechanisms of action at the cellular level are incompletely understood. Here, we report apelin effects on dynamic mechanical characteristics of single ventricular cardiomyocytes, isolated from mouse models (control, apelin-deficient [Apelin-KO], apelin-receptor KO mouse [APJ-KO]), and rat. Dynamic changes in maximal velocity of cell shortening and relaxation were monitored. In addition, more traditional indicators of inotropic effects, such as maximum shortening (in mechanically unloaded cells) or peak force development (in auxotonic contracting cells, preloaded using the carbon fibre technique) were studied. The key finding is that, using Apelin-KO cardiomyocytes exposed to different preloads with the 2-carbon fibre technique, we observe a lowering of the slope of the end-diastolic stress-length relation in response to 10 nM apelin, an effect that is preload-dependent. This suggests a positive lusitropic effect of apelin, which could explain earlier counter-intuitive findings on an apelin-induced increase in contractility occurring without matching rise in oxygen consumption.

    View details for PubMedID 28935153

  • Mind the Gap: Current Challenges and Future State of Heart Failure Care CANADIAN JOURNAL OF CARDIOLOGY McDonald, M. A., Ashley, E. A., Fedak, P. M., Hawkins, N., Januzzi, J. L., McMurray, J. V., Parikh, V. N., Rao, V., Svystonyuk, D., Teerlink, J. R., Virani, S. 2017; 33 (11): 1434–49

    Abstract

    The past decade has seen many advances in the management of heart failure (HF) that have improved survival and quality of life for patients living with this condition. A number of gaps remain in our understanding of the pathophysiology of HF, and the application of emerging treatment strategies is an exciting but daunting challenge. It is possible that advances in genetic evaluation of cardiomyopathy will provide a more refined approach to characterizing HF syndromes, whereas large-scale clinical trials on the horizon should further clarify the role of novel pharmacologic agents and invasive therapies. Cardiac repair and regeneration hold great promise, but a number of pragmatic issues will limit clinical application in the near term. Replacing cardiac function with ventricular assist devices represents significant progress in the management of advanced disease; however, unacceptable rates of complications and costs need to be addressed before broader use in the general HF population is feasible. The ability to personalize care is limited, and the optimal model of disease management in the Canadian context remains uncertain. The emergence of biomarker-guided management and remote monitoring technologies might facilitate a more personalized approach to care in an effort to maintain health and stability and to prevent worsening HF. Ultimately, a greater understanding of how and when to intervene in the setting of acute HF should translate into improved outcomes for the highest-risk subgroup of patients. This review highlights key challenges in the management of HF and highlights the progress toward an ideal future state.

    View details for PubMedID 29111107

  • Human Genome Sequencing at the Population Scale: A Primer on High-Throughput DNA Sequencing and Analysis AMERICAN JOURNAL OF EPIDEMIOLOGY Goldfeder, R. L., Wall, D. P., Khoury, M. J., Ioannidis, J. A., Ashley, E. A. 2017; 186 (8): 1000–1009

    Abstract

    Most human diseases have underlying genetic causes. To better understand the impact of genes on disease and its implications for medicine and public health, researchers have pursued methods for determining the sequences of individual genes, then all genes, and now complete human genomes. Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequencing continues to decline, more and more individuals are having their genomes sequenced. This may facilitate better population-level disease subtyping and characterization, as well as individual-level diagnosis and personalized treatment and prevention plans. In this review, we describe several massively parallel high-throughput DNA sequencing technologies and their associated strengths, limitations, and error modes, with a focus on applications in epidemiologic research and precision medicine. We detail the methods used to computationally process and interpret sequence data to inform medical or preventative action.

    View details for DOI 10.1093/aje/kww224

    View details for Web of Science ID 000412798300013

    View details for PubMedID 29040395

  • Care in Specialized Centers and Data Sharing Increase Agreement in Hypertrophic Cardiomyopathy Genetic Test Interpretation CIRCULATION-CARDIOVASCULAR GENETICS Furqan, A., Arscott, P., Girolami, F., Cirino, A. L., Michels, M., Day, S. M., Olivotto, I., Ho, C. Y., Ashley, E., Green, E. M., Caleshu, C., SHaRe Consortium 2017; 10 (5)

    Abstract

    Clinically impactful differences in the interpretation of genetic test results occur between laboratories and clinicians. To improve the classification of variants, a better understanding of why discrepancies occur and how they can be reduced is needed.We examined the frequency, causes, and resolution of discordant variant classifications in the Sarcomeric Human Cardiomyopathy Registry (SHaRe), a consortium of international centers with expertise in the clinical management and genetic architecture of hypertrophic cardiomyopathy. Of the 112 variants present in patients at >1 center, 23 had discordant classifications among centers (20.5%; Fleiss κ, 0.54). Discordance was more than twice as frequent among clinical laboratories in ClinVar, a public archive of variant classifications (315/695 variants; 45.2%; Fleiss κ, 0.30; P<0.001). Discordance in SHaRe most frequently occurred because hypertrophic cardiomyopathy centers had access to different privately held data when making their classifications (75.0%). Centers reassessed their classifications based on a comprehensive and current data summary, leading to reclassifications that reduced the discordance rate from 20.5% to 10.7%. Different interpretations of rarity and co-occurrence with pathogenic variants contributed to residual discordance.Discordance in variant classification among hypertrophic cardiomyopathy centers is largely attributable to privately held data. Some discrepancies are caused by differences in expert assessment of conflicting data. Discordance was markedly lower among centers specialized in hypertrophic cardiomyopathy than among clinical laboratories, suggesting that optimal genetic test interpretation occurs in the context of clinical care delivered by specialized centers with both clinical and genetics expertise.

    View details for PubMedID 28986452

  • Report from the Annual Conference of the British Society of Echocardiography, November 2016, Queen Elizabeth II Conference Centre, London. Echo research and practice Steeds, R. P., Cowie, M. R., Rana, B. S., Chambers, J. B., Ray, S., Srinivasan, J., Schwarz, K., Neil, C. J., Scally, C., Horowitz, J. D., Frenneaux, M. P., Pislaru, C., Dawson, D. K., Rothwell, O. J., George, K., Somauroo, J. D., Lord, R., Stembridge, M., Shave, R., Hoffman, M., Ashley, E. A., Haddad, F., Eijsvogels, T. M., Oxborough, D., Hampson, R., Kinsey, C. D., Gurunathan, S., Vamvakidou, A., Karogiannis, N., Senior, R., Ahmadvazir, S., Shah, B. N., Zacharias, K., Bowen, D., Robinson, S., Ihekwaba, U., Parker, K., Boyd, J., Densem, C. G., Atkinson, C., Hinton, J., Gaisie, E. B., Rakhit, D. J., Yue, A. M., Roberts, P. R., Thomas, D., Phen, P., Sibley, J., Fergey, S., Russhard, P. 2017; 4 (3): M1

    View details for DOI 10.1530/ERP-17-0046

    View details for PubMedID 30390608

  • Report from the Annual Conference of the British Society of Echocardiography, November 2016, Queen Elizabeth II Conference Centre, London ECHO RESEARCH AND PRACTICE Steeds, R. P., Cowie, M. R., Rana, B. S., Chambers, J. B., Ray, S., Srinivasan, J., Schwarz, K., Neil, C. J., Scally, C., Horowitz, J. D., Frenneaux, M. P., Pislaru, C., Dawson, D. K., Rothwell, O. J., George, K., Somauroo, J. D., Lord, R., Stembridge, M., Shave, R., Hoffman, M., Ashley, E. A., Haddad, F., Eijsvogels, T. H., Oxborough, D., Hampson, R., Kinsey, C. D., Gurunathan, S., Vamvakidou, A., Karogiannis, N., Senior, R., Ahmadvazir, S., Shah, B. N., Zacharias, K., Bowen, D., Robinson, S., Ihekwaba, U., Parker, K., Boyd, J., Densem, C. G., Atkinson, C., Hinton, J., Gaisie, E. B., Rakhit, D. J., Yue, A. M., Roberts, P. R., Thomas, D., Phen, P., Sibley, J., Fergey, S., Russhard, P. 2017; 4 (3): M1–M16
  • Navigating Genetic and Phenotypic Uncertainty in Left Ventricular Noncompaction CIRCULATION-CARDIOVASCULAR GENETICS Rhee, J., Grove, M. E., Ashley, E. A. 2017; 10 (4)
  • Navigating Genetic and Phenotypic Uncertainty in Left Ventricular Noncompaction. Circulation. Cardiovascular genetics Rhee, J. W., Grove, M. E., Ashley, E. A. 2017; 10 (4)

    View details for DOI 10.1161/CIRCGENETICS.117.001857

    View details for PubMedID 28798026

  • Incremental value of right heart metrics and exercise performance to well-validated risk scores in dilated cardiomyopathy. European heart journal cardiovascular Imaging Moneghetti, K. J., Giraldeau, G., Wheeler, M. T., Kobayashi, Y., Vrtovec, B., Boulate, D., Kuznetsova, T., Schnittger, I., Wu, J. C., Myers, J., Ashley, E., Haddad, F. 2017

    Abstract

    Risk stratification in heart failure (HF) relies on several established clinical risk scores, however, myocardial deformation, right heart metrics, and exercise performance have not usually been considered. This study sought to assess the incremental value of advanced echocardiographic and cardiopulmonary exercise testing (CPX) parameters to validated risk scores in HF.The Meta-Analysis Global Group in Chronic Heart Failure (MAGGIC) and Metabolic Exercise Test Data Combined with Cardiac and Kidney Indexes (MECKI) scores were applied to 208 ambulatory patients with dilated cardiomyopathy (DCM) who completed echocardiography in conjunction with CPX as part of the Stanford Exercise Testing registry. Patients were followed for the composite end point of death, heart transplant, left ventricular device implantation, and hospitalization for acute HF. Mean age, left ventricular ejection fraction (LVEF), and left ventricular global longitudinal strain (LVGLS) were 47 ± 13 years, 33 ± 13%, and -10.6 ± 4.4%, respectively, while right ventricular free-wall longitudinal strain was -18.8 ± 5.5%. Partial correlation mapping identified strong correlations between LVEF, LVGLS, and LV systolic strain rate, with a moderate correlation between these metrics and peak VO2. Over a median follow up of 5.3 years, the composite end point occurred in 60 patients. Cox proportional hazards identified MAGGIC score [hazard ratio (HR) (2.04 [1.39-3.01], P < 0.01], peak VO2 HR (0.52 [0.28-0.97], P = 0.04), and right atrial volume indexed (RAVI) HR (1.31 [1.07-1.61], P < 0.01) as independent correlates of outcome. RAVI remained an independent correlate when combined with the MECKI score (2.21 [1.59-3.07]), P < 0.01, RAVI, 1.33 [1.06-1.67], P = 0.01).Our study demonstrates that RAVI is complementary to well-validated HF risk scores and highlights the importance of exercise performance in DCM.

    View details for DOI 10.1093/ehjci/jex187

    View details for PubMedID 28977353

  • A comparison of methods for determining the ventilatory threshold: implications for surgical risk stratification CANADIAN JOURNAL OF ANESTHESIA-JOURNAL CANADIEN D ANESTHESIE Vainshelboim, B., Rao, S., Chan, K., Lima, R. M., Ashley, E. A., Myers, J. 2017; 64 (6): 634-642

    Abstract

    The ventilatory threshold (VT) is an objective physiological marker of the capacity of aerobic endurance that has good prognostic applications in preoperative settings. Nevertheless, determining the VT can be challenging due to physiological and methodological issues, especially in evaluating surgical risk. The purpose of the current study was to compare different methods of determining VT and to highlight the implications for assessing perioperative risk.Our study entailed analysis of 445 treadmill cardiopulmonary exercise tests from 140 presurgical candidates with an aortic abdominal aneurysm (≥3.0 to ≤5.0 cm) and a mean (standard deviation [SD]) age of 72 (8) yr. We used three methods to determine the VT in 328 comparable tests, namely, self-detected metabolic system (MS), experts' visual (V) readings, and software using a log-log transformation (LLT) of ventilation vs oxygen uptake. Differences and agreement between the three methods were assessed using analysis of variance (ANOVA), coefficient of variation (CV), typical error limits of agreement (LoA), and interclass correlation coefficients (ICC).Overall, ANOVA revealed significant differences between the methods [MS = 14.1 (4.3) mLO2·kg(-1)·min(-1); V = 14.6 (4.4) mLO2·kg(-1)·min(-1); and LLT = 12.3 (3.3) mLO2·kg(-1)·min(-1); P < 0.001]. The assessment of agreement between methods provided the following results: ICC = 0.85; 95% confidence interval (CI), 0.82 to 0.87; P < 0.001; typical error, 2.1-2.8 mLO2·kg(-1)·min(-1); and, 95% LoA and CV ranged from 43 to 55% and 15.9 to 19.6%, respectively.The results show clinically significant variations between the methods and underscore the challenges of determining VT for perioperative risk stratification. The findings highlight the importance of meticulous evaluation of VT for predicting surgical outcomes. Future studies should address the prognostic perioperative utility of computed mathematical models combined with an expert's review. This trial was registered at ClinicalTrials.gov, identifier: NCT00349947.

    View details for DOI 10.1007/s12630-017-0862-8

    View details for Web of Science ID 000401518100009

    View details for PubMedID 28382529

  • Accuracy in Wrist-Worn, Sensor-Based Measurements of Heart Rate and Energy Expenditure in a Diverse Cohort JOURNAL OF PERSONALIZED MEDICINE Shcherbina, A., Mattsson, C., Waggott, D., Salisbury, H., Christle, J. W., Hastie, T., Wheeler, M. T., Ashley, E. A. 2017; 7 (2)

    View details for DOI 10.3390/jpm7020003

    View details for Web of Science ID 000457946800001

  • Delivering Clinical Grade Sequencing and Genetic Test Interpretation for Cardiovascular Medicine. Circulation. Cardiovascular genetics Harper, A. R., Parikh, V. N., Goldfeder, R. L., Caleshu, C., Ashley, E. A. 2017; 10 (2)

    View details for DOI 10.1161/CIRCGENETICS.116.001221

    View details for PubMedID 28411191

  • Left atrial function and phenotypes in asymmetric hypertrophic cardiomyopathy. Echocardiography (Mount Kisco, N.Y.) Kobayashi, Y., Wheeler, M., Finocchiaro, G., Ariyama, M., Kobayashi, Y., Perez, M. V., Liang, D., Kuznetsova, T., Schnittger, I., Ashley, E., Haddad, F. 2017

    Abstract

    Few studies have analyzed changes in left atrial (LA) function associated with different phenotypes of asymmetric hypertrophic cardiomyopathy (HCM). We sought to demonstrate the association of impairments in LA function with disease phenotype in patients with obstructive and nonobstructive HCM.From Stanford Cardiomyopathy Registry, we randomly selected 50 age-/sex-matched healthy controls, 35 patients with nonobstructive HCM (HCM 1), 35 patients with obstructive HCM (HCM 2), and 35 patients with obstructive HCM requiring septal reduction therapy (HCM 3). Echocardiography was performed to evaluate left ventricular (LV) strain as well as LA function including LA emptying fraction and LA strain.The mean age was 51±14 years and 57% were male. LA volume index differed among all four predefined groups (25.6±6.7 mL/m(2) in controls, 32.2±13.3 mL/m(2) in HCM 1, 42.0±12.9 mL/m(2) in HCM 2, 52.4±15.2 mL/m(2) for HCM 3, and P<.05 all between groups). All measurement of LA function was impaired in patients with HCM than controls. Total and passive LA function was further impaired in HCM 2 or 3 compared with HCM 1, while active LA function was not different among the three groups. Among LV strains, only septal longitudinal strain differed among all groups (-18.5±1.9% in controls, -14.5±1.9% in HCM 1, -13.3±1.8% in HCM 2, -11.6±2.3% in HCM 3, and P<.05 all between groups).LA function was impaired in patients with HCM even in minimally symptomatic nonobstructive phenotype. Total and passive LA function was further impaired in patients with obstructive HCM.

    View details for DOI 10.1111/echo.13533

    View details for PubMedID 28370331

  • Max: Analysis from the Fitness Registry and the Importance of Exercise National Database (FRIEND Registry). Progress in cardiovascular diseases Myers, J., Kaminsky, L. A., Lima, R., Christle, J., Ashley, E., Arena, R. 2017

    Abstract

    Existing normal standards for maximal oxygen uptake (VO2 max) are problematic because they tend to be population specific, lack normal distribution and portability, and are poorly represented by women. The objective of the current study was to apply the Fitness Registry and the Importance of Exercise: A National Data Base (FRIEND) Registry to improve upon previous regression formulas for normal standards for VO2 max using treadmill testing. Maximal treadmill tests were performed in 7783 healthy men and women (20-79years; maximal RER >1.0) from the FRIEND registry and a separate validation cohort of 1287 subjects. A regression equation for VO2 max was derived from the FRIEND registry and compared to the validation cohort and two commonly used equations (Wasserman and European). Age, gender, and body weight were the only significant predictors of VO2 max (multiple R=0.79, R(2)=0.62, p<0.001). The equation for predicting VO2 max was: [Formula: see text] Marked differences were observed in percentage predicted VO2 max achieved between commonly used reference equations, particularly among women, overweight and obese subjects. In the validation sample, the FRIEND equation closely paralleled measured VO2 max, with the validation group yielding a percent predicted VO2 max of 100.4% based on the FRIEND equation. An equation for age-predicted VO2 max derived from the FRIEND registry provided a lower average error between measured and predicted VO2 max than traditional equations, and thus may provide a more suitable normal standard relative to traditional equations.

    View details for DOI 10.1016/j.pcad.2017.03.002

    View details for PubMedID 28377168

  • INTERDISCIPLINARY PERIPARTUM CARE OF THE PATIENT WITH DIASTOLIC HEART FAILURE IN NON-OBSTRUCTIVE HYPERTROPHIC CARDIOMYOPATHY Beutner, K., Ashley, E., Wheeler, M., Parikh, V., Wheeler, L., Hoover, V., Platt, J., Salisbury, H., Johnson-Furlan, C., Nancy, R. ELSEVIER SCIENCE INC. 2017: 2118
  • ADDRESSING REFERENCE ECHOCARDIOGRAPHIC PARAMETERS IN ATHLETIC SCREENING: A COLLEGE FOOTBALL-BASED STUDY FOCUSING ON THE IMPLICATIONS OF RACE AND CORRECTION FOR BODY COMPOSITION Moneghetti, K., Singh, T., Kooreman, Z., Christle, J., Froelicher, V., Wheeler, M., Ashley, E., Haddad, F. ELSEVIER SCIENCE INC. 2017: 1453
  • SYSTOLIC DYSFUNCTION WITHOUT LV DILATATION IN A COHORT OF PATIENTS WITH LAMIN A/C CARDIOMYOPATHY Parikh, V., Amsallem, M., Haddad, F., Ashley, E., Wheeler, M. ELSEVIER SCIENCE INC. 2017: 846
  • INTEGRATING MYOCARDIAL STRAIN AND EXERCISE PERFORMANCE INTO PROGNOSTICATION OF HYPERTROPHIC CARDIOMYOPATHY Moneghetti, K., Stolfo, D., Christle, J., Kobayashi, Y., Finocchiaro, G., Sinagra, G., Myers, J., Ashley, E., Haddad, F., Wheeler, M. ELSEVIER SCIENCE INC. 2017: 833
  • IDENTIFYING THE OPTIMAL ECHOCARDIOGRAPHIC VARIABLES TO PREDICT OUTCOME THROUGH CORRELATION MAPPING IN PATIENTS WITH DILATED CARDIOMYOPATHY Moneghetti, K., Kim, J., Giraldeau, G., Kobayashi, Y., Boralkar, K., Schnittger, I., Ashley, E., Wheeler, M., Haddad, F. ELSEVIER SCIENCE INC. 2017: 1535
  • Effect of lossy compression of quality scores on variant calling. Briefings in bioinformatics Ochoa, I., Hernaez, M., Goldfeder, R., Weissman, T., Ashley, E. 2017; 18 (2): 183-194

    Abstract

    Recent advancements in sequencing technology have led to a drastic reduction in genome sequencing costs. This development has generated an unprecedented amount of data that must be stored, processed, and communicated. To facilitate this effort, compression of genomic files has been proposed. Specifically, lossy compression of quality scores is emerging as a natural candidate for reducing the growing costs of storage. A main goal of performing DNA sequencing in population studies and clinical settings is to identify genetic variation. Though the field agrees that smaller files are advantageous, the cost of lossy compression, in terms of variant discovery, is unclear.Bioinformatic algorithms to identify SNPs and INDELs use base quality score information; here, we evaluate the effect of lossy compression of quality scores on SNP and INDEL detection. Specifically, we investigate how the output of the variant caller when using the original data differs from that obtained when quality scores are replaced by those generated by a lossy compressor. Using gold standard genomic datasets and simulated data, we are able to analyze how accurate the output of the variant calling is, both for the original data and that previously lossily compressed. We show that lossy compression can significantly alleviate the storage while maintaining variant calling performance comparable to that with the original data. Further, in some cases lossy compression can lead to variant calling performance that is superior to that using the original file. We envisage our findings and framework serving as a benchmark in future development and analyses of lossy genomic data compressors.

    View details for DOI 10.1093/bib/bbw011

    View details for PubMedID 26966283

  • HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction From Long Single-Molecule Reads IEEE TRANSACTIONS ON NANOBIOSCIENCE Mangul, S., Yang, T. (., Hormozdiari, F., Dainis, A. M., Tseng, E., Ashley, E. A., Zelikovsky, A., Eskin, E. 2017; 16 (2): 108-115

    Abstract

    Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts, allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms. In this paper, we present Haplotype-specific Isoform reconstruction (HapIso), a method able to tolerate the relatively high error rate of the single-molecule platform and partition the isoform reads into the parental alleles. Phasing the reads according to the allele of origin allows our method to efficiently distinguish between the read errors and the true biological mutations. HapIso uses a k -means clustering algorithm aiming to group the reads into two meaningful clusters maximizing the similarity of the reads within the cluster and minimizing the similarity of the reads from different clusters. Each cluster corresponds to a parental haplotype. We used the family pedigree information to evaluate our approach. Experimental validation suggests that HapIso is able to tolerate the relatively high error rate and accurately partition the reads into the parental alleles of the isoform transcripts. We also applied HapIso to novel clinical single-molecule RNA-Seq data to estimate allele-specific expression of genes of interest. Our method was able to correct reads and determine Glu1883Lys point mutation of clinical significance validated by GeneDx HCM panel. Furthermore, our method is the first method able to reconstruct the haplotype-specific isoforms from long single-molecule reads.

    View details for DOI 10.1109/TNB.2017.2675981

    View details for Web of Science ID 000399943600005

    View details for PubMedID 28328508

  • Effect of lossy compression of quality scores on variant calling BRIEFINGS IN BIOINFORMATICS Ochoa, I., Hernaez, M., Goldfeder, R., Weissman, T., Ashley, E. 2017; 18 (2): 183-194

    Abstract

    Recent advancements in sequencing technology have led to a drastic reduction in genome sequencing costs. This development has generated an unprecedented amount of data that must be stored, processed, and communicated. To facilitate this effort, compression of genomic files has been proposed. Specifically, lossy compression of quality scores is emerging as a natural candidate for reducing the growing costs of storage. A main goal of performing DNA sequencing in population studies and clinical settings is to identify genetic variation. Though the field agrees that smaller files are advantageous, the cost of lossy compression, in terms of variant discovery, is unclear.Bioinformatic algorithms to identify SNPs and INDELs use base quality score information; here, we evaluate the effect of lossy compression of quality scores on SNP and INDEL detection. Specifically, we investigate how the output of the variant caller when using the original data differs from that obtained when quality scores are replaced by those generated by a lossy compressor. Using gold standard genomic datasets and simulated data, we are able to analyze how accurate the output of the variant calling is, both for the original data and that previously lossily compressed. We show that lossy compression can significantly alleviate the storage while maintaining variant calling performance comparable to that with the original data. Further, in some cases lossy compression can lead to variant calling performance that is superior to that using the original file. We envisage our findings and framework serving as a benchmark in future development and analyses of lossy genomic data compressors.

    View details for DOI 10.1093/bib/bbw011

    View details for Web of Science ID 000397060200002

  • Orexin: a Missing Link Between Sleep Disorders and Heart Failure? Current heart failure reports Pan, S., Cabral, C. S., Ashley, E. A., Perez, M. V. 2017

    Abstract

    Sleep disorders represent a significant comorbidity in the heart failure population, and there is mounting evidence that treatment of sleep disorders such as obstructive sleep apnea can significantly improve cardiac function. However, the link between these two disorders is still not entirely clear.Recently, a novel neurohormonal pathway has been elucidated involving signaling molecules now collectively known as the orexins, which have been implicated in regulating autonomic function during sleep/wake cycles. Further evidence has mounted that orexin signaling is deeply perturbed in the setting of sleep disorders, and furthermore that abnormal orexin signaling may be implicated in the pathology of heart failure. The orexin signaling pathway represents an enticing novel target for both the treatment of sleep disorders as well as heart failure, and may represent one facet of the "missing link" between these two prevalent and often comorbid diseases.

    View details for DOI 10.1007/s11897-017-0322-3

    View details for PubMedID 28215031

  • The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease AMERICAN JOURNAL OF HUMAN GENETICS Ramoni, R. B., Mulvihill, J. J., Adams, D. R., Allard, P., Ashley, E. A., Bernstein, J. A., Gahl, W. A., Hamid, R., Loscalzo, J., McCray, A. T., Shashi, V., Tifft, C. J., Wise, A. L. 2017; 100 (2): 185-192

    Abstract

    Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.

    View details for DOI 10.1016/j.athg.2017.01.006

    View details for PubMedID 28157539

  • Next-Generation Sequencing in Cardiovascular Disease Present Clinical Applications and the Horizon of Precision Medicine CIRCULATION Parikh, V. N., Ashley, E. A. 2017; 135 (5): 406–9

    View details for PubMedID 28137961

    View details for PubMedCentralID PMC5310819

  • in a patient with a complex connective tissue phenotype. Cold Spring Harbor molecular case studies Zastrow, D. B., Zornio, P. A., Dries, A., Kohler, J., Fernandez, L., Waggott, D., Walkiewicz, M., Eng, C. M., Manning, M. A., Farrelly, E., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T. 2017; 3 (1)

    Abstract

    Here we describe a patient who presented with a history of congenital diaphragmatic hernia, inguinal hernia, and recurrent umbilical hernia. She also has joint laxity, hypotonia, and dysmorphic features. A unifying diagnosis was not identified based on her clinical phenotype. As part of her evaluation through the Undiagnosed Diseases Network, trio whole-exome sequencing was performed. Pathogenic variants in FBN1 and TRPS1 were identified as causing two distinct autosomal dominant conditions, each with de novo inheritance. Fibrillin 1 (FBN1) mutations are associated with Marfan syndrome and a spectrum of similar phenotypes. TRPS1 mutations are associated with trichorhinophalangeal syndrome types I and III. Features of both conditions are evident in the patient reported here. Discrepant features of the conditions (e.g., stature) and the young age of the patient may have made a clinical diagnosis more difficult in the absence of exome-wide genetic testing.

    View details for DOI 10.1101/mcs.a001388

    View details for PubMedID 28050602

  • Exome sequencing identifies de novo pathogenic variants in FBN1 and TRPS1 in a patient with a complex connective tissue phenotype COLD SPRING HARBOR MOLECULAR CASE STUDIES Zastrow, D. B., Zornio, P. A., Dries, A., Kohler, J., Fernandez, L., Waggott, D., Walkiewicz, M., Eng, C. M., Manning, M. A., Farrelly, E., Fisher, P. G., Ashley, E. A., Bernstein, J. A., Wheeler, M. T., Undiagnosed Dis Network 2017; 3 (1)
  • Impact of a Genetic Risk Score for Coronary Artery Disease on Reducing Cardiovascular Risk: A Pilot Randomized Controlled Study. Frontiers in cardiovascular medicine Knowles, J. W., Zarafshar, S. n., Pavlovic, A. n., Goldstein, B. A., Tsai, S. n., Li, J. n., McConnell, M. V., Absher, D. n., Ashley, E. A., Kiernan, M. n., Ioannidis, J. P., Assimes, T. L. 2017; 4: 53

    Abstract

    We tested whether providing a genetic risk score (GRS) for coronary artery disease (CAD) would serve as a motivator to improve adherence to risk-reducing strategies.We randomized 94 participants with at least moderate risk of CAD to receive standard-of-care with (N = 49) or without (N = 45) their GRS at a subsequent 3-month follow-up visit. Our primary outcome was change in low density lipoprotein cholesterol (LDL-C) between the 3- and 6-month follow-up visits (ΔLDL-C). Secondary outcomes included other CAD risk factors, weight loss, diet, physical activity, risk perceptions, and psychological outcomes. In pre-specified analyses, we examined whether there was a greater motivational effect in participants with a higher GRS.Sixty-five participants completed the protocol including 30 participants in the GRS arm. We found no change in the primary outcome between participants receiving their GRS and standard-of-care participants (ΔLDL-C: -13 vs. -9 mg/dl). Among participants with a higher GRS, we observed modest effects on weight loss and physical activity. All other secondary outcomes were not significantly different, including anxiety and worry.Adding GRS to standard-of-care did not change lipids, adherence, or psychological outcomes. Potential modest benefits in weight loss and physical activity for participants with high GRS need to be validated in larger trials.

    View details for PubMedID 28856136

  • Value of Strain Imaging and Maximal Oxygen Consumption in Patients With Hypertrophic Cardiomyopathy. The American journal of cardiology Moneghetti, K. J., Stolfo, D. n., Christle, J. W., Kobayashi, Y. n., Finocchiaro, G. n., Sinagra, G. n., Myers, J. n., Ashley, E. A., Haddad, F. n., Wheeler, M. T. 2017; 120 (7): 1203–8

    Abstract

    Longitudinal strain (LS) has been shown to be predictive of outcome in hypertrophic cardiomyopathy (HC). Percent predicted peak oxygen uptake (ppVO2), among other cardiopulmonary exercise testing (CPX) metrics, is a strong predictor of prognosis in HC. However, there has been limited investigation into the combination of LS and CPX metrics. This study sought to determine how LS and parameters of exercise performance contribute to prognosis in HC. One hundred and thirty-one consecutive patients with HC who underwent CPX and stress echocardiography were included. Global, septal, and lateral LS were assessed at rest and stress. Eighty matched individuals were used as controls. Patients were followed for the composite end point of death and worsening heart failure. All absolute LS components were lower in patients with HC than in controls (global 14.3 ± 4.0% vs 18.8 ± 2.2%, p <0.001; septal 11.9 ± 4.9% vs 17.9 ± 2.7%, p <0.001; lateral 16.0 ± 4.7% vs 19.4 ± 3.1%, p = 0.001). Global strain reserve was also reduced in patients with HC (13 ± 5% vs 19 ± 8%, p = 0.002). Over a median follow-up of 56 months (interquartile range 14 to 69), the composite end point occurred in 53 patients. Global LS was predictive of outcome on univariate analysis (0.55 [0.41 to 0.74], p <0.001). When combined with CPX metrics, lateral LS was the only strain variable predictive of outcome along with indexed left atrial volume (LAVI) and ppVO2. The worst outcomes were observed for patients with lateral LS <16.1%, LAVI >52 ml/m2, and ppVO2 <80%. The combination of lateral LS, LAVI, and ppVO2 presents a simple model for outcome prediction.

    View details for PubMedID 28802509

  • A non-exercise based V02max prediction using FRIEND dataset with a Neural Network Henriques, J., Carvalho, P., Rocha, T., Paredes, S., Cabiddu, R., Trimer, R., Mendes, R., Borghi-Silva, A., Kaminsky, L., Ashley, E., Arena, R., Myers, J., IEEE IEEE. 2017: 4203–6

    Abstract

    The main goal of this work is the development of models, based on computational intelligence techniques, in particular neural networks, to predict the maximum oxygen consumption value. While the maximum oxygen consumption is a direct mark of the cardiorespiratory fitness, several studies have also confirmed it also as a powerful predictor of risk for adverse outcomes, such as hypertension, obesity, and diabetes. Therefore, the existence of simpler and accurate models, establishing an alternative to standard cardiopulmonary exercise tests, with the potential to be employed in the stratification of the general population in daily clinical practice, would be of major importance. In the current study, different models were implemented and compared: 1) the traditional Wasserman/Hansen equation; 2) linear regression and; 3) non-linear neural networks. Their performance was evaluated based on the "FRIEND - Fitness Registry and the Importance of Exercise: The National Data Base" [1] being, in the present study, a subset of 12262 individuals employed. The accuracy of the models was performed through the computation of sensitivity and specificity values. The results show the superiority of neural networks in the prediction of maximum oxygen consumption.

    View details for Web of Science ID 000427085304159

    View details for PubMedID 29060824

  • Incremental value of right heart metrics and exercise performance to well-validated risk scores in dilated cardiomyopathy European Heart Journal - Cardiovascular Imaging Moneghetti , K. J., Giraldeau, G., Wheeler, M. T., Kobayashi , Y., Vrtovec, B., Boulate, D., Kuznetsova, T., Schnittger, I., Wu, J. C., Myers, J., Ashely, E., Haddad , F. 2017

    View details for DOI 10.1093/ehjci/jex187

  • Contractile reserve and cardiopulmonary exercise parameters in patients with dilated cardiomyopathy, the two dimensions of exercise testing. Echocardiography (Mount Kisco, N.Y.) Moneghetti, K. J., Kobayashi, Y. n., Christle, J. W., Ariyama, M. n., Vrtovec, B. n., Kouznetsova, T. n., Wilson, A. n., Ashley, E. n., Wheeler, M. T., Myers, J. n., Haddad, F. n. 2017

    Abstract

    Left ventricular (LV) contractile reserve assessed using imaging and cardiopulmonary exercise testing (CPX) has been shown to predict outcome in patients with dilated cardiomyopathy (DCM). Few clinical studies have, however, analyzed the relationship between them.A cohort of 75 ambulatory patients with DCM underwent stress treadmill echocardiography with CPX. LV contractile reserve was calculated as absolute change (ΔLVEF=LVEFpeak -LVEFrest ) and percent change (%LVEF=[(LVEFpeak -LVEFrest )/LVEFpeak) ]×100) in LVEF, circumferential and longitudinal strain (LS). Exercise capacity was measured as peak oxygen uptake (peak VO2 ) and ventilatory efficiency as the slope of minute ventilation to CO2 production (VE/VCO2 slope). Values of contractile reserve were compared to matched controls. We also explored which metric of ventricular response (absolute or percent change) was less dependent on baseline LV function.Patients with DCM had a mean age, rest and peak LVEF of 44±10 years, 42±10% and 50±12%, respectively. Among parameters of contractile reserve, peak cardiac output was the strongest parameter associated with peak VO2 (r=.63, P<.001). Along with age, sex, and BMI, it explained more than 70% of the variance in peak VO2 . In contrast, LVEF and LS were only weakly related to peak VO2 . With regard to ventilatory efficiency, the strongest parameter that emerged was right atrial volume index (r=.36, P<.001). Percent change in LVEF was more independent of baseline function than absolute change.Echocardiographic contractile reserve and CPX provide complementary information. Percent change in contractile reserve was most independent of baseline function, therefore may be preferred when analyzing the ventricular response to exercise.

    View details for PubMedID 28681553

  • Informed Consent. New England journal of medicine Grady, C., Cummings, S. R., Rowbotham, M. C., McConnell, M. V., Ashley, E. A., Kang, G. 2017; 376 (9): 856-867

    View details for DOI 10.1056/NEJMra1603773

    View details for PubMedID 28249147

  • Functional assessment and transplantation of the donor heart after circulatory death JOURNAL OF HEART AND LUNG TRANSPLANTATION Messer, S. J., Axell, R. G., Colah, S., White, P. A., Ryan, M., Page, A. A., Parizkova, B., Valchanov, K., White, C. W., Freed, D. H., Ashley, E., Dunning, J., Goddard, M., Parameshwar, J., Watson, C. J., Krieg, T., Ali, A., Tsui, S., Large, S. R. 2016; 35 (12): 1443-1452

    Abstract

    After a severe shortage of brain-dead donors, the demand for heart transplantation has never been greater. In an attempt to increase organ supply, abdominal and lung transplant programs have turned to the donation after circulatory-determined death (DCD) donor. However, because heart function cannot be assessed after circulatory death, DCD heart transplantation was deemed high risk and never adopted routinely. We report a novel method of functional assessment of the DCD heart resulting in a successful clinical program.Normothermic regional perfusion (NRP) was used to restore function to the arrested DCD heart within the donor after exclusion of the cerebral circulation. After weaning from support, DCD hearts underwent functional assessment with cardiac-output studies, echocardiography, and pressure-volume loops. In the feasibility phase, hearts were transported perfused before evaluation of function in modified working mode extracorporeally. After the establishment of a reliable assessment technique, hearts with demonstrable good function were then selected for clinical transplantation.NRP was instituted in 13 adult DCD donors, median age of 33 years (interquartile range [IQR], 28-38 years), after a median ischemic time from withdrawal to perfusion of 24 minutes (IQR, 21-29; range, 17-146 minutes). Two of 4 hearts in the feasibility phase were unsuitable for transplantation after functional assessment. Nine DCD hearts were transplanted in the clinical phase, with 100% survival. The median intensive care duration was 5 days (IQR, 4-5 days), with 2 patients requiring mechanical support. There were no episodes of rejection (total, 1,436 patient-days; range, 48-297). During the same period, we performed 20 standard heart transplants using brain-dead donors.NRP allows rapid reperfusion and functional assessment of the DCD donor heart, ensuring only viable hearts are selected for transplantation. This technique minimizes the risk of primary graft dysfunction and maximizes confidence in DCD heart transplantation, realizing a 45% increase in our heart transplant activity.

    View details for DOI 10.1016/j.healun.2016.07.004

    View details for PubMedID 27916176

  • Exploratory insights from the right-sided electrocardiogram following prolonged endurance exercise. European journal of sport science Lord, R., George, K., Somauroo, J., Jain, N., Reese, K., Hoffman, M. D., Haddad, F., Ashley, E., Jones, H., Oxborough, D. 2016; 16 (8): 1014-1022

    Abstract

    Prolonged strenuous exercise has a profound effect on cardiac function. The right heart may be more susceptible to this imposition; yet, right-sided chest leads have not been utilised in this setting.Thirty highly trained athletes at the 2014 Western States 100-mile Endurance Run from Squaw Valley to Auburn, California (body mass 68 ± 12 kg, age 45 ± 10 years, 57 ± 15 miles per week) were recruited for the study. Pre- and post-race, a right-sided 12-lead ECG was obtained and data were extracted for P, R and S waves, J point, ST segment and T wave amplitude. Data were compared using Students T-test and statistical significance set as P < .05.There was a significant increase in P wave amplitude (29%) and QTc interval (4%) pre- to post-race from standard 12-lead ECG. From the right-sided12-lead ECG, a 23% (P = .01) and 38% (P = .03) increase in J point amplitude in V1R and V2R and a 22% (P = .05) increase in ST segment integral in V2R and V3R were evident. T wave inversion was evident in leads V2R-V6R in 50-90% of athletes, respectively. Close examination revealed marked heterogeneity in individual ECGs.Completion of a 100-mile ultra-marathon resulted in significant changes in the right-sided ECG alongside more marked responses in specific individuals. P wave, ST segment and T wave changes post-race are indicative of acute exercise-induced right heart electrical adaptation.

    View details for DOI 10.1080/17461391.2016.1165292

    View details for PubMedID 27027796

  • Interdisciplinary psychosocial care for families with inherited cardiovascular diseases. Trends in cardiovascular medicine Caleshu, C., Kasparian, N. A., Edwards, K. S., Yeates, L., Semsarian, C., Perez, M., Ashley, E., Turner, C. J., Knowles, J. W., Ingles, J. 2016; 26 (7): 647-653

    Abstract

    Inherited cardiovascular diseases pose unique and complex psychosocial challenges for families, including coming to terms with life-long cardiac disease, risk of sudden death, grief related to the sudden death of a loved one, activity restrictions, and inheritance risk to other family members. Psychosocial factors impact not only mental health but also physical health and cooperation with clinical recommendations. We describe an interdisciplinary approach to the care of families with inherited cardiovascular disease, in which psychological care provided by specialized cardiac genetic counselors, nurses, and psychologists is embedded within the cardiovascular care team. We report illustrative cases and the supporting literature to demonstrate common scenarios, as well as practical guidance for clinicians working in the inherited cardiovascular disease setting.

    View details for DOI 10.1016/j.tcm.2016.04.010

    View details for PubMedID 27256036

  • Alterations in Cardiac Mechanics Following Ultra-Endurance Exercise: Insights from Left and Right Ventricular Area-Deformation Loops. Journal of the American Society of Echocardiography Lord, R., George, K., Somauroo, J., Stembridge, M., Jain, N., Hoffman, M. D., Shave, R., Haddad, F., Ashley, E., Jones, H., Oxborough, D. 2016; 29 (9): 879-887 e1

    Abstract

    The aim of this study was to use novel area-deformation (ε) loops to interrogate the interaction between the right ventricular (RV) and left ventricular (LV) mechanics following a 100-mile endurance run.Fifteen participants (mean body mass, 70.1 ± 8.8 kg; mean age, 40 ± 8 years) were recruited for the study. Echocardiography was performed before the race, after the race, and 6 hours into recovery. RV and LV area and longitudinal ε were assessed using standard and speckle-tracking echocardiography. Following cubic spline interpolation, these variables were obtained across the same cardiac cycle and used to derive area-ε loops.The RV area-ε loop demonstrated a rightward shift after the race, with increased RV area (from 26.0 to 27.1 cm(2)) and reduced peak RV ε (from -28.6% to -25.8%). The recovery RV area-ε loop was similar to the postrace loop. A leftward shift was observed in the LV area-ε loop after the race, secondary to reduced LV area (from 35.8 to 32.5 cm(2)) and reduced peak ε (from -18.3% to -16.6%). In recovery, LV ε values returned toward baseline.A 100-mile ultramarathon resulted in a rightward shift in the RV area-ε loop as a result of RV dilatation. There was a concomitant leftward shift in the LV area-ε loop as a result of underfilling of the left ventricle. At 6 hours after exercise, there was a partial recovery of the left ventricle, while RV function remained depressed. It appears that changes in RV function do not have a serial impact on the left ventricle during recovery from ultra-endurance activity.

    View details for DOI 10.1016/j.echo.2016.05.004

    View details for PubMedID 27373587

  • Whole exome sequencing of a Finnish HLHS cohort reveals new variants in known LVOTO related genes and identifies new candidate genes Helle, E., Ojala, T., Ashley, E., Priest, J. R. OXFORD UNIV PRESS. 2016: 1036
  • Phase 2 study of A797, an oral, selective p38 mitogen-activated protein kinase inhibitor, in patients with lamin A/C-related dilated cardiomyopathy MacRae, C., Taylor, M. G., Mestroni, L., Moses, J. R., Ashley, E. A., Wheeler, M. T., Lakdawala, N. K., Hershberger, R. E., Ptaszynski, M., Sandor, V., Saunders, M. E., Oliver, C., Lee, P. A., Judge, D. P. OXFORD UNIV PRESS. 2016: 1011
  • Taming the genome: towards better genetic test interpretation GENOME MEDICINE Caleshu, C., Ashley, E. A. 2016; 8

    Abstract

    Advances in sequencing technology have taught us much about the human genome, including how difficult it is to interpret rare variation. Improvements in genetic test interpretation are likely to come through data sharing, international collaborative efforts to develop disease-gene specific guidelines, and computational analyses using big data.

    View details for DOI 10.1186/s13073-016-0325-9

    View details for Web of Science ID 000378592700002

    View details for PubMedID 27324065

    View details for PubMedCentralID PMC4915179

  • The Undiagnosed Diseases Program Reply JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Gahl, W. A., Wise, A. L., Ashley, E. A. 2016; 315 (17): 1904

    View details for PubMedID 27139070

  • Hypertrophic Cardiomyopathy as a Cause of Sudden Cardiac Death in the Young: A Meta-Analysis AMERICAN JOURNAL OF MEDICINE Ullal, A. J., Abdelfattah, R. S., Ashley, E. A., Froelicher, V. F. 2016; 129 (5): 486-?

    Abstract

    Sudden cardiac death is often linked with hypertrophic cardiomyopathy in young athletes, but with a divergence of study results. We performed a meta-analysis to compare the prevalence of sudden cardiac deaths associated with hypertrophic cardiomyopathy vs sudden cardiac deaths associated with structurally normal hearts.A structured search of MEDLINE was conducted for studies published from 1990 through 2014. Retrospective cohort studies, patient registries, and autopsy series examining sudden cardiac death etiology in young individuals (age ≤35 years) were included. A random-effects model was applied to generate pooled summary estimates of the percentage of sudden cardiac deaths with structurally normal hearts at postmortem vs those caused by hypertrophic cardiomyopathy. Heterogeneity was assessed using I(2). Subgroup analyses were conducted based on study location, patient age groups, and population types.Thirty-four studies were included, representing a combined sample of 4605 subjects. The overall pooled percentage of sudden cardiac deaths caused by hypertrophic cardiomyopathy was 10.3% (95% confidence interval [CI], 8.0%-12.6%; I(2) = 87.2%), while sudden cardiac deaths with structurally normal hearts at death were more common (P <.001) at 26.7% (95% CI, 21.0%-32.3%; I(2) = 95.3%). In nonathlete subjects, the pooled percentage of sudden cardiac deaths associated with structurally normal hearts (30.7%; 95% CI, 23.0%-38.4%; I(2) = 96.3%) were significantly more common (P <.001) than sudden cardiac death caused by hypertrophic cardiomyopathy (7.8%; 95% CI, 5.8%-9.9%; I(2) = 80.1%). Among athletes, there was no significant difference between summary estimates of hypertrophic cardiomyopathy and structurally normal hearts (P = .57), except in Europe where structurally normal hearts were more common (P = .01).Hypertrophic cardiomyopathy is not a more common finding at death than structurally normal hearts in young subjects with sudden cardiac death. Increased attention should be directed toward identifying causes of death associated with a structurally normal heart in subjects with sudden cardiac death.

    View details for DOI 10.1016/j.amjmed.2015.12.027

    View details for PubMedID 26800575

  • Impact of Septal Reduction on Left Atrial Size and Diastole in Hypertrophic Cardiomyopathy ECHOCARDIOGRAPHY-A JOURNAL OF CARDIOVASCULAR ULTRASOUND AND ALLIED TECHNIQUES Finocchiaro, G., Haddad, F., Kobayashi, Y., Lee, D., Pavlovic, A., Schnittger, I., Sinagra, G., Magavern, E., Myers, J., Froelicher, V., Knowles, J. W., Ashley, E. 2016; 33 (5): 686-694

    Abstract

    Both myectomy and alcohol septal ablation (ASA) can substantially reduce left ventricular (LV) outflow obstruction, relieve symptoms, and improve outcomes in hypertrophic cardiomyopathy (HCM). It is unclear whether septal reduction decreases left atrial (LA) size and improves diastolic function. The aim of this study was to analyze the consequences of septal reduction on LA size and diastolic function in a cohort of patients with HCM.Forty patients (mean age: 50 ± 14, male sex 64%) with HCM who underwent septal reduction (myectomy or alcohol septal ablation) were studied. Retrospective analyses of echocardiograms preprocedure, postprocedure, and at 1 year of follow-up were performed.Thirty-one patients had septal myectomy and 9 ASA. The degree of reduction in rest peak LV outflow tract gradient was significant (57 ± 32 vs. 23 ± 20 mmHg at 1 year, P < 0.001). Maximal interventricular septal thickness decreased from 22 ± 6 mm preprocedure to 19 ± 4 mm postprocedure (P < 0.001); moderate-to-severe mitral regurgitation (MR) was initially present in 34% of the sample and only 2% after the procedure. Average LA volume index (LAVI) decreased from 63 ± 20 to 55 ± 20 mL/m(2) at the 1-year follow-up (P < 0.001). We did not observe a significant improvement in diastolic function at Doppler (E/A 1.2 ± 0.4 vs. 1.1 ± 0.5, P = 0.07; E' 7.6 ± 3.6 vs. 6.9 ± 3.0, P = 0.4) pre- and postprocedure, respectively). At 1 year, only 5% of the patients were severely symptomatic (NYHA III). On multivariate analysis, a significant change in the LVOT gradient during stress (Δ gradient ≥30 mmHg) was the only variable independently associated with LAVI reverse remodeling >10 mL/m(2) [OR = 6.4 (CI 95% 1.12-36.44), P = 0.04].Septal reduction is effective in the relief of LV obstruction and symptoms in patients with HCM. The hemodynamic changes result in a significant LA reverse remodeling, but not in an improvement of diastolic function in these patients.

    View details for DOI 10.1111/echo.13158

    View details for PubMedID 26926154

  • A research roadmap for next-generation sequencing informatics SCIENCE TRANSLATIONAL MEDICINE Altman, R. B., Prabhu, S., Sidow, A., Zook, J. M., Goldfeder, R., Litwack, D., Ashley, E., Asimenos, G., Bustamante, C. D., Donigan, K., Giacomini, K. M., Johansen, E., Khuri, N., Lee, E., Liang, X. S., Salit, M., Serang, O., Tezak, Z., Wall, D. P., Mansfield, E., Kass-Hout, T. 2016; 8 (335)

    Abstract

    Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic.

    View details for DOI 10.1126/scitranslmed.aaf7314

    View details for PubMedID 27099173

  • De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS genetics Priest, J. R., Osoegawa, K., Mohammed, N., Nanda, V., Kundu, R., Schultz, K., Lammer, E. J., Girirajan, S., Scheetz, T., Waggott, D., Haddad, F., Reddy, S., Bernstein, D., Burns, T., Steimle, J. D., Yang, X. H., Moskowitz, I. P., Hurles, M., Lifton, R. P., Nickerson, D., Bamshad, M., Eichler, E. E., Mital, S., Sheffield, V., Quertermous, T., Gelb, B. D., Portman, M., Ashley, E. A. 2016; 12 (4)

    Abstract

    Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.

    View details for DOI 10.1371/journal.pgen.1005963

    View details for PubMedID 27058611

  • Athlome Project Consortium: a concerted effort to discover genomic and other "omic" markers of athletic performance. Physiological genomics Pitsiladis, Y. P., Tanaka, M., Eynon, N., Bouchard, C., North, K. N., Williams, A. G., Collins, M., Moran, C. N., Britton, S. L., Fuku, N., Ashley, E. A., Klissouras, V., Lucia, A., Ahmetov, I. I., de Geus, E., Alsayrafi, M. 2016; 48 (3): 183-190

    Abstract

    Despite numerous attempts to discover genetic variants associated with elite athletic performance, injury predisposition, and elite/world-class athletic status, there has been limited progress to date. Past reliance on candidate gene studies predominantly focusing on genotyping a limited number of single nucleotide polymorphisms or the insertion/deletion variants in small, often heterogeneous cohorts (i.e., made up of athletes of quite different sport specialties) have not generated the kind of results that could offer solid opportunities to bridge the gap between basic research in exercise sciences and deliverables in biomedicine. A retrospective view of genetic association studies with complex disease traits indicates that transition to hypothesis-free genome-wide approaches will be more fruitful. In studies of complex disease, it is well recognized that the magnitude of genetic association is often smaller than initially anticipated, and, as such, large sample sizes are required to identify the gene effects robustly. A symposium was held in Athens and on the Greek island of Santorini from 14-17 May 2015 to review the main findings in exercise genetics and genomics and to explore promising trends and possibilities. The symposium also offered a forum for the development of a position stand (the Santorini Declaration). Among the participants, many were involved in ongoing collaborative studies (e.g., ELITE, GAMES, Gene SMART, GENESIS, and POWERGENE). A consensus emerged among participants that it would be advantageous to bring together all current studies and those recently launched into one new large collaborative initiative, which was subsequently named the Athlome Project Consortium.

    View details for DOI 10.1152/physiolgenomics.00105.2015

    View details for PubMedID 26715623

    View details for PubMedCentralID PMC4773890

  • Comparison of left ventricular manual versus automated derived longitudinal strain: implications for clinical practice and research INTERNATIONAL JOURNAL OF CARDIOVASCULAR IMAGING Kobayashi, Y., Ariyama, M., Kobayashi, Y., Giraldeau, G., Fleischman, D., Kozelj, M., Vrtovec, B., Ashley, E., Kuznetsova, T., Schnittger, I., Liang, D., Haddad, F. 2016; 32 (3): 429-437

    Abstract

    Systolic global longitudinal strain (GLS) is emerging as a useful metric of ventricular function in heart failure and usually assessed using post-processing software. The purpose of this study was to investigate whether longitudinal strain (LS) derived using manual-tracings of ventricular lengths (manual-LS) can be reliable and time efficient when compared to LS obtained by post-processing software (software-LS). Apical 4-chamber view images were retrospectively examined in 50 healthy controls, 100 patients with dilated cardiomyopathy (DCM), and 100 with hypertrophic cardiomyopathy (HCM). We measured endocardial and mid-wall manual-LS and software-LS, using peak of average regional curve [software-LS(a)] and global ventricular lengths [software-LS(l)] according to definition of Lagragian strain. We compared manual-LS and software-LS by using Bland-Altman plot and coefficient of variation (COV). In addition, test-retest was also performed for further assessment of variability in measurements. While manual-LS was obtained in all subjects, software-LS could be obtained in 238 subjects (95 %). The time spent for obtaining manual-LS was significantly shorter than for the software-LS (94 ± 39 s vs. 141 ± 79 s, P < 0.001). Overall, manual-LS had an excellent correlation with both software-LS (a) (R(2) = 0.93, P < 0.001) and software-LS(l) (R(2) = 0.84, P < 0.001). The bias (95 %CI) between endocardial manual-LS and software-LS(a) was 0.4 % [-2.8, 3.6 %] in absolute and 3.5 % [-17.0, 24.0 %] in relative difference while it was 0.4 % [-2.5, 3.3 %] and 3.4 % [-16.2, 23.1 %], respectively with software-LS(l). Mid-wall manual-LS and mid-wall software-LS(a) also had good agreement [a bias (95 % CI) for absolute value of 0.1 % [-2.1, 2.5 %] in HCM, and 0.2 % [-2.2, 2.6 %] in controls]. The COV for manual and software derived LS were below 6 %. Test-retest showed good variability for both methods (COVs were 5.8 and 4.7 for endocardial and mid-wall manual-LS, and 4.6 and 4.9 for endocardial and mid-wall software-LS(a), respectively. Manual-LS appears to be as reproducible as software-LS; this may be of value especially when global strain is the metric of interest.

    View details for DOI 10.1007/s10554-015-0804-x

    View details for Web of Science ID 000370166100008

    View details for PubMedID 26578468

  • Sports genetics moving forward: lessons learned from medical research. Physiological genomics Mattsson, C. M., Wheeler, M. T., Waggott, D., Caleshu, C., Ashley, E. A. 2016; 48 (3): 175-182

    Abstract

    Sports genetics can take advantage of lessons learned from human disease genetics. By righting past mistakes and increasing scientific rigor, we can magnify the breadth and depth of knowledge in the field. We present an outline of challenges facing sports genetics in the light of experiences from medical research. Sports performance is complex, resulting from a combination of a wide variety of different traits and attributes. Improving sports genetics will foremost require analyses based on detailed phenotyping. To find widely valid, reproducible common variants associated with athletic phenotypes, study sample sizes must be dramatically increased. One paradox is that in order to confirm relevance, replications in specific populations must be undertaken. Family studies of athletes may facilitate the discovery of rare variants with large effects on athletic phenotypes. The complexity of the human genome, combined with the complexity of athletic phenotypes, will require additional metadata and biological validation to identify a comprehensive set of genes involved. Analysis of personal genetic and multiomic profiles contribute to our conceptualization of precision medicine; the same will be the case in precision sports science. In the refinement of sports genetics it is essential to evaluate similarities and differences between sexes and among ethnicities. Sports genetics to date have been hampered by small sample sizes and biased methodology, which can lead to erroneous associations and overestimation of effect sizes. Consequently, currently available genetic tests based on these inherently limited data cannot predict athletic performance with any accuracy.

    View details for DOI 10.1152/physiolgenomics.00109.2015

    View details for PubMedID 26757801

  • Somatic Mosaicism of Novel SCN5A Mutation in Purkinje System (PS) may Underlie 2: 1 Block in an Infant with Long QT Syndrome (LQTS) Yu, J. K., Boyle, P. M., O'Hara, T., Priest, J. R., Ashley, E., Trayanova, N. A. CELL PRESS. 2016: 527A
  • Medical implications of technical accuracy in genome sequencing. Genome medicine Goldfeder, R. L., Priest, J. R., Zook, J. M., Grove, M. E., Waggott, D., Wheeler, M. T., Salit, M., Ashley, E. A. 2016; 8 (1): 24-?

    Abstract

    As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome.We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation.We observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6% of the exonic bases in ClinVar and OMIM genes and 82.1% of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50% of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2.Together, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting.

    View details for DOI 10.1186/s13073-016-0269-0

    View details for PubMedID 26932475

    View details for PubMedCentralID PMC4774017

  • Redox regulation of vascular remodeling. Cellular and molecular life sciences : CMLS Karimi Galougahi, K., Ashley, E. A., Ali, Z. A. 2016; 73 (2): 349-63

    Abstract

    Vascular remodeling is a dynamic process of structural and functional changes in response to biochemical and biomechanical signals in a complex in vivo milieu. While inherently adaptive, dysregulation leads to maladaptive remodeling. Reactive oxygen species participate in homeostatic cell signaling in tightly regulated- and compartmentalized cellular circuits. It is well established that perturbations in oxidation-reduction (redox) homeostasis can lead to a state of oxidative-, and more recently, reductive stress. We provide an overview of the redox signaling in the vasculature and review the role of oxidative- and reductive stress in maladaptive vascular remodeling. Particular emphasis has been placed on essential processes that determine phenotype modulation, migration and fate of the main cell types in the vessel wall. Recent advances in systems biology and the translational opportunities they may provide to specifically target the redox pathways driving pathological vascular remodeling are discussed.

    View details for DOI 10.1007/s00018-015-2068-y

    View details for PubMedID 26483132

  • Denoising of Quality Scores for Boosted Inference and Reduced Storage Ochoa, I., Hernaez, M., Goldfeder, R., Weissman, T., Ashley, E., Bilgin, A., Marcellin, M. W., SerraSagrista, J., Storer, J. A. IEEE. 2016: 251–60

    Abstract

    Massive amounts of sequencing data are being generated thanks to advances in sequencing technology and a dramatic drop in the sequencing cost. Much of the raw data are comprised of nucleotides and the corresponding quality scores that indicate their reliability. The latter are more difficult to compress and are themselves noisy. Lossless and lossy compression of the quality scores has recently been proposed to alleviate the storage costs, but reducing the noise in the quality scores has remained largely unexplored. This raw data is processed in order to identify variants; these genetic variants are used in important applications, such as medical decision making. Thus improving the performance of the variant calling by reducing the noise contained in the quality scores is important. We propose a denoising scheme that reduces the noise of the quality scores and we demonstrate improved inference with this denoised data. Specifically, we show that replacing the quality scores with those generated by the proposed denoiser results in more accurate variant calling in general. Moreover, a consequence of the denoising is that the entropy of the produced quality scores is smaller, and thus significant compression can be achieved with respect to lossless compression of the original quality scores. We expect our results to provide a baseline for future research in denoising of quality scores. The code used in this work as well as a Supplement with all the results are available at http://web.stanford.edu/~iochoa/DCCdenoiser_CodeAndSupplement.zip.

    View details for PubMedID 29098178

  • Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments. Van Valen, D., Kudo, T., Lane, K., Macklin, D., Quach, N., DeFelice, M., Maayan, I., Tanouchi, Y., Ashley, E., Covert, M. W. AMER SOC CELL BIOLOGY. 2016
  • Redox regulation of vascular remodeling CELLULAR AND MOLECULAR LIFE SCIENCES Galougahi, K. K., Ashley, E. A., Ali, Z. A. 2016; 73 (2): 349-363

    Abstract

    Vascular remodeling is a dynamic process of structural and functional changes in response to biochemical and biomechanical signals in a complex in vivo milieu. While inherently adaptive, dysregulation leads to maladaptive remodeling. Reactive oxygen species participate in homeostatic cell signaling in tightly regulated- and compartmentalized cellular circuits. It is well established that perturbations in oxidation-reduction (redox) homeostasis can lead to a state of oxidative-, and more recently, reductive stress. We provide an overview of the redox signaling in the vasculature and review the role of oxidative- and reductive stress in maladaptive vascular remodeling. Particular emphasis has been placed on essential processes that determine phenotype modulation, migration and fate of the main cell types in the vessel wall. Recent advances in systems biology and the translational opportunities they may provide to specifically target the redox pathways driving pathological vascular remodeling are discussed.

    View details for DOI 10.1007/s00018-015-2068-y

    View details for Web of Science ID 000368077900007

  • The Future of Genomic Research in Athletic Performance and Adaptation to Training. Medicine and sport science Wang, G., Tanaka, M., Eynon, N., North, K. N., Williams, A. G., Collins, M., Moran, C. N., Britton, S. L., Fuku, N., Ashley, E. A., Klissouras, V., Lucia, A., Ahmetov, I. I., de Geus, E., Alsayrafi, M., Pitsiladis, Y. P. 2016; 61: 55-67

    Abstract

    Despite numerous attempts to discover genetic variants associated with elite athletic performance, an individual's trainability and injury predisposition, there has been limited progress to date. Past reliance on candidate gene studies focusing predominantly on genotyping a limited number of genetic variants in small, often heterogeneous cohorts has not generated results of practical significance. Hypothesis-free genome-wide approaches will in the future provide more comprehensive coverage and in-depth understanding of the biology underlying sports-related traits and related genetic mechanisms. Large, collaborative projects with sound experimental designs (e.g. clearly defined phenotypes, considerations and controls for sources of variability, and necessary replications) are required to produce meaningful results, especially when a hypothesis-free approach is used. It remains to be determined whether the novel approaches under current implementation will result in findings with real practical significance. This review will briefly summarize current and future directions in exercise genetics and genomics.

    View details for DOI 10.1159/000445241

    View details for PubMedID 27287077

  • Examining Prevailing Genotype-Phenotype Correlations in Hypertrophic Cardiomyopathy: Findings From The Sarcomeric Human Cardiomyopathy Registry (SHaRe) Ho, C. Y., Day, S. M., Ashley, E. A., Michels, M., Pereira, A., Fox, J., Caleshu, C., Cirino, A. L., Colan, S., Wrolstad, D., Green, E. M., Olivotto, I., SHaRe Investigators LIPPINCOTT WILLIAMS & WILKINS. 2015: 2277
  • Direct-to-consumer genetic testing for predicting sports performance and talent identification: Consensus statement BRITISH JOURNAL OF SPORTS MEDICINE Webborn, N., Williams, A., McNamee, M., Bouchard, C., Pitsiladis, Y., Ahmetov, I., Ashley, E., Byrne, N., Camporesi, S., Collins, M., Dijkstra, P., Eynon, N., Fuku, N., Garton, F. C., Hoppe, N., Holm, S., Kaye, J., Klissouras, V., Lucia, A., Maase, K., Moran, C., North, K. N., Pigozzi, F., Wang, G. 2015; 49 (23): 1486-1491

    Abstract

    The general consensus among sport and exercise genetics researchers is that genetic tests have no role to play in talent identification or the individualised prescription of training to maximise performance. Despite the lack of evidence, recent years have witnessed the rise of an emerging market of direct-to-consumer marketing (DTC) tests that claim to be able to identify children's athletic talents. Targeted consumers include mainly coaches and parents. There is concern among the scientific community that the current level of knowledge is being misrepresented for commercial purposes. There remains a lack of universally accepted guidelines and legislation for DTC testing in relation to all forms of genetic testing and not just for talent identification. There is concern over the lack of clarity of information over which specific genes or variants are being tested and the almost universal lack of appropriate genetic counselling for the interpretation of the genetic data to consumers. Furthermore independent studies have identified issues relating to quality control by DTC laboratories with different results being reported from samples from the same individual. Consequently, in the current state of knowledge, no child or young athlete should be exposed to DTC genetic testing to define or alter training or for talent identification aimed at selecting gifted children or adolescents. Large scale collaborative projects, may help to develop a stronger scientific foundation on these issues in the future.

    View details for DOI 10.1136/bjsports-2015-095343

    View details for PubMedID 26582191

  • Gender Differences in Ventricular Remodeling and Function in College Athletes, Insights from Lean Body Mass Scaling and Deformation Imaging AMERICAN JOURNAL OF CARDIOLOGY Giraldeau, G., Kobayashi, Y., Finocchiaro, G., Wheeler, M., Perez, M., Kuznetsova, T., Lord, R., George, K. P., Oxborough, D., Schnittger, T., Froelicher, V., Liang, D., Ashley, E., Haddad, F. 2015; 116 (10): 1610-1616

    Abstract

    Several studies suggest gender differences in ventricular dimensions in athletes. Few studies have, however, made comparisons of data indexed for lean body mass (LBM) using allometry. Ninety Caucasian college athletes (mixed sports) who were matched for age, ethnicity, and sport total cardiovascular demands underwent dual-energy x-ray absorptiometry scan for quantification of LBM. Athletes underwent comprehensive assessment of left and right ventricular and atrial structure and function using 2-dimensional echocardiography and deformation imaging using the TomTec analysis system. The mean age of the study population was 18.9 ± 1.9 years. Female athletes (n = 45) had a greater fat free percentage (19.4 ± 3.7%) compared to male athletes (11.5 ± 3.7%). When scaled to body surface area, male had on average 19 ± 3% (p <0.001) greater left ventricular (LV) mass; in contrast, when scaled to LBM, there was no significant difference in indexed LV mass -1.4 ± 3.0% (p = 0.63). Similarly, when allometrically scaled to LBM, there was no significant gender-based difference in LV or left atrial volumes. Although female athletes had mildly higher LV ejection fraction and LV global longitudinal strain in absolute value, systolic strain rate and allometrically indexed stroke volume were not different between genders (1.5 ± 3.6% [p = 0.63] and 0.0 ± 3.7% [p = 0.93], respectively). There were no differences in any of the functional atrial indexes including strain or strain rate parameters. In conclusion, gender-related differences in ventricular dimensions or function (stroke volume) appear less marked, if not absent, when indexing using LBM allometrically.

    View details for DOI 10.1016/j.amjcard.2015.08.026

    View details for PubMedID 26456207

  • Limitations of Current AHA Guidelines and Proposal of New Guidelines for the Preparticipation Examination of Athletes CLINICAL JOURNAL OF SPORT MEDICINE Dunn, T. P., Pickham, D., Aggarwal, S., Saini, D., Kumar, N., Wheeler, M. T., Perez, M., Ashley, E., Froelicher, V. F. 2015; 25 (6): 472-477

    Abstract

    To examine the prevalence of athletes who screen positive with the preparticipation examination guidelines from the American Heart Association, the AHA 12-elements, in combination with 3 screening electrocardiogram (ECG) criteria.Observational cross-sectional study.Stanford University Sports Medicine Clinic.Total of 1596 participants, including 297 (167 male; mean age, 16.2 years) high school athletes, 1016 (541 male; mean age, 18.8 years) collegiate athletes, and 283 (mean age, 26.3 years) male professional athletes.Athletes were screened using the 8 personal and family history questions from the AHA 12-elements. Electrocardiograms were obtained for all participants and interpreted using Seattle criteria, Stanford criteria, and European Society of Cardiology (ESC) recommendations.Approximately one-quarter of all athletes (23.8%) had at least 1 positive response to the AHA personal and family history elements. High school and college athletes had similar rates of having at least 1 positive response (25.9% vs 27.4%), whereas professional athletes had a significantly lower rate of having at least 1 positive response (8.8%, P < 0.05). Females reported more episodes of unexplained syncope (11.4% vs 7.5%, P = 0.017) and excessive exertional dyspnea with exercise (11.1% vs 6.1%, P = 0.001) than males. High school athletes had more positive responses to the family history elements when compared with college athletes (P < 0.05). The percentage of athletes who had an abnormal ECG varied between Seattle criteria (6.0%), Stanford criteria (8.8%), and ESC recommendations (26.8%).Many athletes screen positive under current screening recommendations, and ECG results vary widely by interpretation criteria.In a patient population without any adverse cardiovascular events, the currently recommended AHA 12-elements have an unacceptably high rate of false positives. Newer screening guidelines are needed, with fewer false positives and evidence-based updates.

    View details for Web of Science ID 000364310700003

    View details for PubMedID 25915146

  • Promise of Precision Medicine Reply JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Ashley, E. A. 2015; 314 (16): 1752–53

    View details for PubMedID 26505606

  • Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data PLOS GENETICS Dewey, F. E., Grove, M. E., Priest, J. R., Waggott, D., Batra, P., Miller, C. L., Wheeler, M., Zia, A., Pan, C., Karzcewski, K. J., Miyake, C., Whirl-Carrillo, M., Klein, T. E., Datta, S., Altman, R. B., Snyder, M., Quertermous, T., Ashley, E. A. 2015; 11 (10)

    Abstract

    High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing, prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies. There are significant barriers to realizing this goal that are related to the difficult task of interpreting personal genetic variation. A comprehensive, widely accessible application for interpretation of whole genome sequence data is needed. Here, we present a series of methods for identification of genetic variants and genotypes with clinical associations, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios. We demonstrate application of these methods for disease and drug response prognostication in whole genome sequence data from twelve unrelated adults, and for disease gene discovery in one father-mother-child trio with apparently simplex congenital ventricular arrhythmia. In doing so we identify clinically actionable inherited disease risk and drug response genotypes in pre-symptomatic individuals. We also nominate a new candidate gene in congenital arrhythmia, ATP2B4, and provide experimental evidence of a regulatory role for variants discovered using this framework.

    View details for DOI 10.1371/journal.pgen.1005496

    View details for Web of Science ID 000364401600008

    View details for PubMedID 26448358

    View details for PubMedCentralID PMC4598191

  • A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. Circulation research Wilson, K. D., Shen, P., Fung, E., Karakikes, I., Zhang, A., Inanloorahatloo, K., Odegaard, J., Sallam, K., Davis, R. W., Lui, G. K., Ashley, E. A., Scharfe, C., Wu, J. C. 2015; 117 (7): 603-611

    Abstract

    Thousands of mutations across >50 genes have been implicated in inherited cardiomyopathies. However, options for sequencing this rapidly evolving gene set are limited because many sequencing services and off-the-shelf kits suffer from slow turnaround, inefficient capture of genomic DNA, and high cost. Furthermore, customization of these assays to cover emerging targets that suit individual needs is often expensive and time consuming.We sought to develop a custom high throughput, clinical-grade next-generation sequencing assay for detecting cardiac disease gene mutations with improved accuracy, flexibility, turnaround, and cost.We used double-stranded probes (complementary long padlock probes), an inexpensive and customizable capture technology, to efficiently capture and amplify the entire coding region and flanking intronic and regulatory sequences of 88 genes and 40 microRNAs associated with inherited cardiomyopathies, congenital heart disease, and cardiac development. Multiplexing 11 samples per sequencing run resulted in a mean base pair coverage of 420, of which 97% had >20× coverage and >99% were concordant with known heterozygous single nucleotide polymorphisms. The assay correctly detected germline variants in 24 individuals and revealed several polymorphic regions in miR-499. Total run time was 3 days at an approximate cost of $100 per sample.Accurate, high-throughput detection of mutations across numerous cardiac genes is achievable with complementary long padlock probe technology. Moreover, this format allows facile insertion of additional probes as more cardiomyopathy and congenital heart disease genes are discovered, giving researchers a powerful new tool for DNA mutation detection and discovery.

    View details for DOI 10.1161/CIRCRESAHA.115.306723

    View details for PubMedID 26265630

  • The impact of chronic endurance and resistance training upon the right ventricular phenotype in male athletes. European journal of applied physiology Utomi, V., Oxborough, D., Ashley, E., Lord, R., Fletcher, S., Stembridge, M., Shave, R., Hoffman, M. D., Whyte, G., Somauroo, J., Sharma, S., George, K. 2015; 115 (8): 1673-1682

    Abstract

    The traditional view of differential left ventricular adaptation to training type has been questioned. Right ventricular (RV) data in athletes are emerging but whether training type mediates this is not clear. The primary aim of this study was to evaluate the RV phenotype in endurance- vs. resistance-trained male athletes. Secondary aims included comparison of RV function in all groups using myocardial speckle tracking, and the impact of allometric scaling on RV data interpretation.A prospective cross-sectional design assessed RV structure and function in 19 endurance-trained (ET), 21 resistance-trained (RT) and 21 sedentary control subjects (CT). Standard 2D tissue Doppler imaging and speckle tracking echocardiography assessed RV structure and function. Indexing of RV structural parameters to body surface area (BSA) was undertaken using allometric scaling.A higher absolute RV diastolic area was observed in ET (mean ± SD: 27 ± 4 cm(2)) compared to CT (22 ± 4 cm(2); P < 0.05) that was maintained after scaling. Whilst absolute RV longitudinal dimension was greater in ET (88 ± 9 mm) than CT (81 ± 10 mm; P < 0.05), this difference was removed after scaling. Wall thickness was not different between ET and RT and there were no between group differences in global or regional RV function.We present some evidence of RV adaptation to chronic ET in male athletes but limited structural characteristics of an athletic heart were observed in RT. Global and regional RV functions were comparable between groups. Allometric scaling altered data interpretation in some variables.

    View details for DOI 10.1007/s00421-015-3147-3

    View details for PubMedID 25779702

  • Bayesian Selection of Modifier Genes in Hypertrophic Cardiomyopathy Through Whole Genome Sequencing Wheeler, M., Waggott, D., Grove, M., Dewey, F., Pan, C., Pavlovic, A., Goldfeder, R., Puckelwartz, M., Day, S., McNally, E., Dorn, G. W., Ashley, E. LIPPINCOTT WILLIAMS & WILKINS. 2015
  • Achieving high-sensitivity for clinical applications using augmented exome sequencing GENOME MEDICINE Patwardhan, A., Harris, J., Leng, N., Bartha, G., Church, D. M., Luo, S., Haudenschild, C., Pratt, M., Zook, J., Salit, M., Tirch, J., Morra, M., Chervitz, S., Li, M., Clark, M., Garcia, S., Chandratillake, G., Kirk, S., Ashley, E., Snyder, M., Altman, R., Bustamante, C., Butte, A. J., West, J., Chen, R. 2015; 7

    Abstract

    Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide coverage that is inadequate for clinical assessment.Using sequence data obtained from the NA12878 reference sample and pre-defined lists of medically-relevant protein-coding and noncoding sequences, we compared the breadth and depth of coverage obtained among four commercial exome capture platforms and whole genome sequencing. In addition, we evaluated the performance of an augmented exome strategy, ACE, that extends coverage in medically relevant regions and enhances coverage in areas that are challenging to sequence. Leveraging reference call-sets, we also examined the effects of improved coverage on variant detection sensitivity.We observed coverage shortfalls with each of the conventional exome-capture and whole-genome platforms across several medically interpretable genes. These gaps included areas of the genome required for reporting recently established secondary findings (ACMG) and known disease-associated loci. The augmented exome strategy recovered many of these gaps, resulting in improved coverage in these areas. At clinically-relevant coverage levels (100 % bases covered at ≥20×), ACE improved coverage among genes in the medically interpretable genome (>90 % covered relative to 10-78 % with other platforms), the set of ACMG secondary finding genes (91 % covered relative to 4-75 % with other platforms) and a subset of variants known to be associated with human disease (99 % covered relative to 52-95 % with other platforms). Improved coverage translated into improvements in sensitivity, with ACE variant detection sensitivities (>97.5 % SNVs, >92.5 % InDels) exceeding that observed with conventional whole-exome and whole-genome platforms.Clinicians should consider analytical performance when making clinical assessments, given that even a few missed variants can lead to reporting false negative results. An augmented exome strategy provides a level of coverage not achievable with other platforms, thus addressing concerns regarding the lack of sensitivity in clinically important regions. In clinical applications where comprehensive coverage of medically interpretable areas of the genome requires higher localized sequencing depth, an augmented exome approach offers both cost and performance advantages over other sequencing-based tests.

    View details for DOI 10.1186/s13073-015-0197-4

    View details for Web of Science ID 000359428300001

    View details for PubMedID 26269718

    View details for PubMedCentralID PMC4534066

  • Long-term outcomes of septal reduction for obstructive hypertrophic cardiomyopathy. Journal of cardiology Sedehi, D., Finocchiaro, G., Tibayan, Y., Chi, J., Pavlovic, A., Kim, Y. M., Tibayan, F. A., Reitz, B. A., Robbins, R. C., Woo, J., Ha, R., Lee, D. P., Ashley, E. A. 2015; 66 (1): 57-62

    Abstract

    Surgical myectomy and alcohol septal ablation (ASA) aim to decrease left ventricular outflow tract (LVOT) gradient in hypertrophic cardiomyopathy (HCM). Outcome of myectomy beyond 10 years has rarely been described. We describe 20 years of follow-up of surgical myectomy and 5 years of follow-up for ASA performed for obstructive HCM.We studied 171 patients who underwent myectomy for symptomatic LVOT obstruction between 1972 and 2006. In addition, we studied 52 patients who underwent ASA for the same indication and who declined surgery. Follow-up of New York Heart Association (NYHA) functional class, echocardiographic data, and vital status were obtained from patient records. Mortality rates were compared with expected mortality rates of age- and sex-matched populations.Surgical myectomy improved NYHA class (2.74±0.65 to 1.54±0.74, p<0.001), reduced resting gradient (67.4±43.4mmHg to 11.2±16.4mmHg, p<0.001), and inducible LVOT gradient (98.1±34.7mmHg to 33.6±34.9mmHg, p<0.001). Similarly, ASA improved functional class (2.99±0.35 to 1.5±0.74, p<0.001), resting gradient (67.1±26.9mmHg to 23.9±29.4mmHg, p<0.001) and provoked gradient (104.4±34.9mmHg to 35.5±38.6mmHg, p<0.001). Survival after myectomy at 5, 10, 15, and 20 years of follow-up was 92.9%, 81.1%, 68.9%, and 47.5%, respectively. Of note, long-term survival after myectomy was lower than for the general population [standardized mortality ratio (SMR)=1.40, p<0.005], but still compared favorably with historical data from non-operated HCM patients. Survival after ASA at 2 and 5 years was 97.8% and 94.7%, respectively. Short-term (5 year) survival after ASA (SMR=0.61, p=0.48) was comparable to that of the general population.Long-term follow-up of septal reduction strategies in obstructive HCM reveals that surgical myectomy and ASA are effective for symptom relief and LVOT gradient reduction and are associated with favorable survival. While overall prognosis for the community HCM population is similar to the general population, the need for surgical myectomy may identify a sub-group with poorer long-term prognosis. We await long-term outcomes of more extensive myectomy approaches adopted in the past 10 years at major institutions.

    View details for DOI 10.1016/j.jjcc.2014.08.010

    View details for PubMedID 25238885

  • Long-term outcomes of septal reduction for obstructive hypertrophic cardiomyopathy JOURNAL OF CARDIOLOGY Sedehi, D., Finocchiaro, G., Tibayan, Y., Chi, J., Pavlovic, A., Kim, Y. M., Tibayan, F. A., Reitz, B. A., Robbins, R. C., Woo, J., Ha, R., Lee, D. P., Ashley, E. A. 2015; 66 (1-2): 57-62

    Abstract

    Surgical myectomy and alcohol septal ablation (ASA) aim to decrease left ventricular outflow tract (LVOT) gradient in hypertrophic cardiomyopathy (HCM). Outcome of myectomy beyond 10 years has rarely been described. We describe 20 years of follow-up of surgical myectomy and 5 years of follow-up for ASA performed for obstructive HCM.We studied 171 patients who underwent myectomy for symptomatic LVOT obstruction between 1972 and 2006. In addition, we studied 52 patients who underwent ASA for the same indication and who declined surgery. Follow-up of New York Heart Association (NYHA) functional class, echocardiographic data, and vital status were obtained from patient records. Mortality rates were compared with expected mortality rates of age- and sex-matched populations.Surgical myectomy improved NYHA class (2.74±0.65 to 1.54±0.74, p<0.001), reduced resting gradient (67.4±43.4mmHg to 11.2±16.4mmHg, p<0.001), and inducible LVOT gradient (98.1±34.7mmHg to 33.6±34.9mmHg, p<0.001). Similarly, ASA improved functional class (2.99±0.35 to 1.5±0.74, p<0.001), resting gradient (67.1±26.9mmHg to 23.9±29.4mmHg, p<0.001) and provoked gradient (104.4±34.9mmHg to 35.5±38.6mmHg, p<0.001). Survival after myectomy at 5, 10, 15, and 20 years of follow-up was 92.9%, 81.1%, 68.9%, and 47.5%, respectively. Of note, long-term survival after myectomy was lower than for the general population [standardized mortality ratio (SMR)=1.40, p<0.005], but still compared favorably with historical data from non-operated HCM patients. Survival after ASA at 2 and 5 years was 97.8% and 94.7%, respectively. Short-term (5 year) survival after ASA (SMR=0.61, p=0.48) was comparable to that of the general population.Long-term follow-up of septal reduction strategies in obstructive HCM reveals that surgical myectomy and ASA are effective for symptom relief and LVOT gradient reduction and are associated with favorable survival. While overall prognosis for the community HCM population is similar to the general population, the need for surgical myectomy may identify a sub-group with poorer long-term prognosis. We await long-term outcomes of more extensive myectomy approaches adopted in the past 10 years at major institutions.

    View details for DOI 10.1016/j.jjcc.2014.08.010

    View details for Web of Science ID 000359684600010

  • Systematic Comparison of Digital Electrocardiograms From Healthy Athletes and Patients With Hypertrophic Cardiomyopathy. Journal of the American College of Cardiology Bent, R. E., Wheeler, M. T., Hadley, D., Knowles, J. W., Pavlovic, A., Finocchiaro, G., Haddad, F., Salisbury, H., Race, S., Shmargad, Y., Matheson, G. O., Kumar, N., Saini, D., Froelicher, V., Ashley, E., Perez, M. V. 2015; 65 (22): 2462-2463

    View details for DOI 10.1016/j.jacc.2015.03.559

    View details for PubMedID 26046742

  • Arrhythmogenic Right Ventricular Cardiomyopathy Toward a Modern Clinical and Genomic Understanding CIRCULATION-CARDIOVASCULAR GENETICS Dunn, K. E., Ashley, E. A. 2015; 8 (3): 421–24

    View details for PubMedID 26082552

  • Prevalence and Prognostic Role of Right Ventricular Involvement in Stress-Induced Cardiomyopathy JOURNAL OF CARDIAC FAILURE Finocchiaro, G., Kobayashi, Y., Magavern, E., Zhou, J. Q., Ashley, E., Sinagra, G., Schnittger, I., Knowles, J. W., Fearon, W. F., Haddad, F., Tremmel, J. A. 2015; 21 (5): 419-425

    Abstract

    Stress-induced cardiomyopathy (SCM) is a reversible cardiomyopathy observed in patients without significant coronary disease. The aim of this study was to assess the incidence and clinical significance of right ventricular (RV) involvement in SCM.We retrospectively analyzed echocardiograms from 40 consecutive patients who presented with SCM at Stanford University Medical Center from September 2000 to November 2010. The primary end point was overall mortality. RV involvement was observed in 20 patients (50%; global RV hypokinesia in 15 patients and focal RV apical akinesia in 5 patients). The independent correlates of RV involvement were older age (odds ratio [OR] 1.09, 95% confidence interval [CI] 1.02-1.7two, P = .01) and LVEF (per 10% decrease: OR 3.60, CI 1.77-7.32; P = .02). At a mean follow-up of 44 ± 32 months, 12 patients (30%) died (in-hospital death in 3 patients). At multivariate analysis, the presence of an RV fractional area change <35% emerged as an independent predictor of death (OR 3.6, CI 1.06-12.41; P = .04).RV involvement is a common finding in SCM, and may present as either global or focal RV apical involvement. Both older age and lower LVEF are associated with a higher risk of RV involvement, which appears to be a major predictor of death.

    View details for DOI 10.1016/j.cardfail.2015.02.001

    View details for PubMedID 25704104

  • Computerized Q wave dimensions in athletes and hypertrophic cardiomyopathy patients JOURNAL OF ELECTROCARDIOLOGY Bent, R. E., Wheeler, M. T., Hadley, D., Froelicher, V., Ashley, E., Perez, M. V. 2015; 48 (3): 362-367

    Abstract

    There is controversy regarding Q wave criteria for assessing risk for hypertrophic cardiomyopathy (HCM) in young athletes.The 12-lead ECGs from Preparticipation screening in healthy athletes and patients with HCM were studied retrospectively. All 12 leads were measured using the same automated ECG analysis program.There were a total of 225 HCM patients and 1124 athletes with 12-lead electrocardiograms available for analysis. Athletes were on average 20 years of age, 65% were male and 24% were African-American. Patients with HCM were on average 51 years of age, 56% were male and 5.8% were African-American. Q waves by either amplitude, duration or area criteria were more prevalent in males than females, in lateral leads than inferior and in HCM patients than athletes. The most striking difference in Q waves between the groups was in Limb lead I and in the females. Tall, skinny Q waves were rare in athletes and had the highest prevalence of only 3.7% in male HCM patients.Q waves are more common in males compared to females and in patients with HCM compared to athletes. Q waves of 30 ms or more in limb lead I appear to offer the greatest discriminatory value for separating patients with HCM from athletes.

    View details for DOI 10.1016/j.jelectrocard.2015.01.009

    View details for PubMedID 25732098

  • Cardiopulmonary responses and prognosis in hypertrophic cardiomyopathy: a potential role for comprehensive noninvasive hemodynamic assessment. JACC. Heart failure Finocchiaro, G., Haddad, F., Knowles, J. W., Caleshu, C., Pavlovic, A., Homburger, J., Shmargad, Y., Sinagra, G., Magavern, E., Wong, M., Perez, M., Schnittger, I., Myers, J., Froelicher, V., Ashley, E. A. 2015; 3 (5): 408-418

    Abstract

    This study sought to discover the key determinants of exercise capacity, maximal oxygen consumption (oxygen uptake [Vo2]), and ventilatory efficiency (ventilation/carbon dioxide output [VE/Vco2] slope) and assess the prognostic potential of metabolic exercise testing in hypertrophic cardiomyopathy (HCM).The intrinsic mechanisms leading to reduced functional tolerance in HCM are unclear.The study sample included 156 HCM patients consecutively enrolled from January 1, 2007 to January 1, 2012 with a complete clinical assessment, including rest and stress echocardiography and cardiopulmonary exercise test (CPET) with impedance cardiography. Patients were also followed for the composite outcome of cardiac-related death, heart transplant, and functional deterioration leading to septal reduction therapy (myectomy or septal alcohol ablation).Abnormalities in CPET responses were frequent, with 39% (n = 61) of the sample showing a reduced exercise tolerance (Vo2 max <80% of predicted) and 19% (n = 30) characterized by impaired ventilatory efficiency (VE/Vco2 slope >34). The variables most strongly associated with exercise capacity (expressed in metabolic equivalents), were peak cardiac index (r = 0.51, p < 0.001), age (r = -0.25, p < 0.01), male sex (r = 0.24, p = 0.02), and indexed right ventricular end-diastolic area (r = 0.31, p = 0.002), resulting in an R(2) of 0.51, p < 0.001. Peak cardiac index was the main predictor of peak Vo2 (r = 0.61, p < 0.001). The variables most strongly related to VE/VCO2 slope were E/E' (r = 0.23, p = 0.021) and indexed left atrial volume index (LAVI) (r = 0.34, p = 0.005) (model R(2) = 0.15). The composite endpoint occurred in 21 (13%) patients. In an exploratory analysis, 3 variables were independently associated with the composite outcome (mean follow-up 27 ± 11 months): peak Vo2 <80% of predicted (hazard ratio: 4.11; 95% confidence interval [CI]: 1.46 to 11.59; p = 0.008), VE/Vco2 slope >34 (hazard ratio: 3.14; 95% CI: 1.26 to 7.87; p = 0.014), and LAVI >40 ml/m(2) (hazard ratio: 3.32; 95% CI: 1.08 to 10.16; p = 0.036).In HCM, peak cardiac index is the main determinant of exercise capacity, but it is not significantly related to ventilatory efficiency. Peak Vo2, ventilatory inefficiency, and LAVI are associated with an increased risk of major events in the short-term follow-up.

    View details for DOI 10.1016/j.jchf.2014.11.011

    View details for PubMedID 25863972

  • The Independent Predictive Value of Peak Oxygen Consumption, Left ventricular Strain and Atrial Remodelling in Patients With Dilated Cardiomyopathy Boulate, D., Banerjee, D., Ariyama, M., Wheeler, M., Knowles, J. W., Kobayashi, Y., Perez, M., Wu, J., Schnittger, I., Kouznetsova, T., Myers, J., Haddad, F., Ashley, E. A. ELSEVIER SCIENCE INC. 2015: S186
  • Hypertrophic cardiomyopathy: can the horse be put back in the barn? Journal of the American College of Cardiology Wheeler, M. T., Ashley, E. A. 2015; 65 (6): 570-572

    View details for DOI 10.1016/j.jacc.2014.12.004

    View details for PubMedID 25677316

  • RNA-Seq identifies novel myocardial gene expression signatures of heart failure GENOMICS Liu, Y., Morley, M., Brandimarto, J., Hannenhalli, S., Hu, Y., Ashley, E. A., Tang, W. H., Moravec, C. S., Margulies, K. B., Cappola, T. P., Li, M., Consortium, M. 2015; 105 (2): 83-89

    Abstract

    Heart failure is a complex clinical syndrome and has become the most common reason for adult hospitalization in developed countries. Two subtypes of heart failure, ischemic heart disease (ISCH) and dilated cardiomyopathy (DCM), have been studied using microarray platforms. However, microarray has limited resolution. Here we applied RNA sequencing (RNA-Seq) to identify gene signatures for heart failure from six individuals, including three controls, one ISCH and two DCM patients. Using genes identified from this small RNA-Seq dataset, we were able to accurately classify heart failure status in a much larger set of 313 individuals. The identified genes significantly overlapped with genes identified via genome-wide association studies for cardiometabolic traits and the promoters of those genes were enriched for binding sites for transcriptions factors. Our results indicate that it is possible to use RNA-Seq to classify disease status for complex diseases such as heart failure using an extremely small training dataset.

    View details for DOI 10.1016/j.ygeno.2014.12.002

    View details for Web of Science ID 000348840200003

    View details for PubMedID 25528681

  • Using "big data" to dissect clinical heterogeneity. Circulation Altman, R. B., Ashley, E. A. 2015; 131 (3): 232-233

    View details for DOI 10.1161/CIRCULATIONAHA.114.014106

    View details for PubMedID 25601948

  • Additive prognostic value of a cardiopulmonary exercise test score in patients with heart failure and intermediate risk INTERNATIONAL JOURNAL OF CARDIOLOGY Ritt, L. E., Myers, J., Stein, R., Arena, R., Guazzi, M., Chase, P., Bensimhon, D., Ashley, E., Cahalin, L. P., Forman, D. E. 2015; 178: 262–64

    View details for PubMedID 25464266

  • Personalized preventive medicine: genetics and the response to regular exercise in preventive interventions. Progress in cardiovascular diseases Bouchard, C., Antunes-Correa, L. M., Ashley, E. A., Franklin, N., Hwang, P. M., Mattsson, C. M., Negrao, C. E., Phillips, S. A., Sarzynski, M. A., Wang, P., Wheeler, M. T. 2015; 57 (4): 337-346

    Abstract

    Regular exercise and a physically active lifestyle have favorable effects on health. Several issues related to this theme are addressed in this report. A comment on the requirements of personalized exercise medicine and in-depth biological profiling along with the opportunities that they offer is presented. This is followed by a brief overview of the evidence for the contributions of genetic differences to the ability to benefit from regular exercise. Subsequently, studies showing that mutations in TP53 influence exercise capacity in mice and humans are succinctly described. The evidence for effects of exercise on endothelial function in health and disease also is covered. Finally, changes in cardiac and skeletal muscle in response to exercise and their implications for patients with cardiac disease are summarized. Innovative research strategies are needed to define the molecular mechanisms involved in adaptation to exercise and to translate them into useful clinical and public health applications.

    View details for DOI 10.1016/j.pcad.2014.08.005

    View details for PubMedID 25559061

  • Establishing disease causality for a novel gene variant in familial dilated cardiomyopathy using a functional in-vitro assay of regulated thin filaments and human cardiac myosin. BMC medical genetics Pan, S., Sommese, R. F., Sallam, K. I., Nag, S., Sutton, S., Miller, S. M., Spudich, J. A., Ruppel, K. M., Ashley, E. A. 2015; 16 (1): 97-?

    Abstract

    As next generation sequencing for the genetic diagnosis of cardiovascular disorders becomes more widely used, establishing causality for putative disease causing variants becomes increasingly relevant. Diseases of the cardiac sarcomere provide a particular challenge in this regard because of the complexity of assaying the effect of genetic variants in human cardiac contractile proteins.In this study we identified a novel variant R205Q in the cardiac troponin T gene (TNNT2). Carriers of the variant allele exhibited increased chamber volumes associated with decreased left ventricular ejection fraction. To clarify the causal role of this variant, we generated recombinant variant human protein and examined its calcium kinetics as well as the maximally activated ADP release of human β-cardiac myosin with regulated thin filaments containing the mutant troponin T. We found that the R205Q mutation significantly decreased the calcium sensitivity of the thin filament by altering the effective calcium dissociation kinetics.The development of moderate throughput post-genomic assays is an essential step in the realization of the potential of next generation sequencing. Although technically challenging, biochemical and functional assays of human cardiac contractile proteins of the thin filament can be achieved and provide an orthogonal source of information to inform the question of causality for individual variants.

    View details for DOI 10.1186/s12881-015-0243-5

    View details for PubMedID 26498512

    View details for PubMedCentralID PMC4620603

  • Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome medicine Patwardhan, A., Harris, J., Leng, N., Bartha, G., Church, D. M., Luo, S., Haudenschild, C., Pratt, M., Zook, J., Salit, M., Tirch, J., Morra, M., Chervitz, S., Li, M., Clark, M., Garcia, S., Chandratillake, G., Kirk, S., Ashley, E., Snyder, M., Altman, R., Bustamante, C., Butte, A. J., West, J., Chen, R. 2015; 7 (1): 71-?

    Abstract

    Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide coverage that is inadequate for clinical assessment.Using sequence data obtained from the NA12878 reference sample and pre-defined lists of medically-relevant protein-coding and noncoding sequences, we compared the breadth and depth of coverage obtained among four commercial exome capture platforms and whole genome sequencing. In addition, we evaluated the performance of an augmented exome strategy, ACE, that extends coverage in medically relevant regions and enhances coverage in areas that are challenging to sequence. Leveraging reference call-sets, we also examined the effects of improved coverage on variant detection sensitivity.We observed coverage shortfalls with each of the conventional exome-capture and whole-genome platforms across several medically interpretable genes. These gaps included areas of the genome required for reporting recently established secondary findings (ACMG) and known disease-associated loci. The augmented exome strategy recovered many of these gaps, resulting in improved coverage in these areas. At clinically-relevant coverage levels (100 % bases covered at ≥20×), ACE improved coverage among genes in the medically interpretable genome (>90 % covered relative to 10-78 % with other platforms), the set of ACMG secondary finding genes (91 % covered relative to 4-75 % with other platforms) and a subset of variants known to be associated with human disease (99 % covered relative to 52-95 % with other platforms). Improved coverage translated into improvements in sensitivity, with ACE variant detection sensitivities (>97.5 % SNVs, >92.5 % InDels) exceeding that observed with conventional whole-exome and whole-genome platforms.Clinicians should consider analytical performance when making clinical assessments, given that even a few missed variants can lead to reporting false negative results. An augmented exome strategy provides a level of coverage not achievable with other platforms, thus addressing concerns regarding the lack of sensitivity in clinically important regions. In clinical applications where comprehensive coverage of medically interpretable areas of the genome requires higher localized sequencing depth, an augmented exome approach offers both cost and performance advantages over other sequencing-based tests.

    View details for DOI 10.1186/s13073-015-0197-4

    View details for PubMedID 26269718

  • The right ventricle following ultra-endurance exercise: insights from novel echocardiography and 12-lead electrocardiography EUROPEAN JOURNAL OF APPLIED PHYSIOLOGY Lord, R., Somauroo, J., Stembridge, M., Jain, N., Hoffman, M. D., George, K., Jones, H., Shave, R., Haddad, F., Ashley, E., Oxborough, D. 2015; 115 (1): 71-80

    Abstract

    There is contradictory evidence related to the impact of ultra-marathon running on right ventricular (RV) structure and function. Consequently, the aims of this study were to: (1) comprehensively assess RV structure and function before and immediately following a 100-mile ultra-marathon in highly trained runners, (2) determine the nature of RV recovery 6 h post-race, and (3) document 12-lead electrocardiogram (ECG) changes post-exercise.Echocardiography and 12-lead ECG were assessed in 15 competitors in a repeated measures design before and immediately after completion of the 2013 Western States Endurance Race. A subset of nine was reassessed 6 h into recovery. Standard echocardiography was used to determine RV size, function and wall stress. Myocardial speckle tracking (MST) provided peak, time to peak and temporal indices for RV longitudinal strain and strain rates (ε and SR).RV size was increased post-race (inflow tract 14 %, outflow tract 11 %, P = 0.004 and 0.002). RV wall stress was elevated by 11 % post-race. Peak RV ε was reduced by 10 % (P = 0.007) and significantly delayed post-race (P = 0.008). Most changes in RV function persisted at the 6-h assessment. Post-race there was an increase in the prevalence of right-sided ECG changes.Completion of a 100-mile ultra-marathon resulted in acute changes in RV structure and function that persisted 6 h into recovery and are consistent with sustained exposure to an elevated RV wall stress. These findings were supported by right-sided changes to the 12-lead ECG.

    View details for DOI 10.1007/s00421-014-2995-6

    View details for Web of Science ID 000347293500004

    View details for PubMedID 25204280

  • INHERIT (INHibition of the renin angiotensin system in hypertrophic cardiomyopathy and the Effect on hypertrophy-a Randomised Intervention Trial with losartan). Global cardiology science & practice Olivotto, I., Ashley, E. A. 2015; 2015: 7-?

    Abstract

    Early pharmacological interventions on transgenic models of hypertrophic cardiomyopathy (HCM) using angiotensin receptor blockers (ARBs) may be effective in preventing development of clinical phenotype or causing phenotype regression in early stages of disease. In the clinical setting, however, the effects of ARBs on HCM phenotype have been less consistent. INHERIT (INHibition of the renin angiotensin system in hypertrophic cardiomyopathy and the Effect on hypertrophy-a Randomised Intervention Trial with losartan) was designed to assess the effect of 100 mg of losartan in promoting the regression of LV hypertrophy in HCM. The primary end-point of the study was the reduction in LV mass assessed by MRI or computed tomography. After 12 months, no reduction in LV mass was observed in the losartan arm, and there was no difference in LV mass change with the placebo arm. The same was true for all secondary endpoints. The implications of these findings are discussed in the light of further, ongoing study targeting the HCM phenotype.

    View details for DOI 10.5339/gcsp.2015.7

    View details for PubMedID 25830151

    View details for PubMedCentralID PMC4374100

  • Assessing the Impact of False Positive and False Negative Variant Calls on Clinical Genome Interpretation Zook, J. M., Goldfeder, R., Priest, J., Grove, M., Wheeler, M., Ashley, E., Salit, M. ELSEVIER SCIENCE INC. 2014: 711
  • Genomics in clinical practice HEART Priest, J. R., Ashley, E. A. 2014; 100 (20): 1569–70

    View details for DOI 10.1136/heartjnl-2014-306111

    View details for Web of Science ID 000343232400004

    View details for PubMedID 25063760

    View details for PubMedCentralID PMC5603306

  • Stable, Covalent Attachment of Laminin to Microposts Improves the Contractility of Mouse Neonatal Cardiomyocytes ACS APPLIED MATERIALS & INTERFACES Ribeiro, A. J., Zaleta-Rivera, K., Ashley, E. A., Pruitt, B. L. 2014; 6 (17): 15516-15526

    Abstract

    The mechanical output of contracting cardiomyocytes, the muscle cells of the heart, relates to healthy and disease states of the heart. Culturing cardiomyocytes on arrays of elastomeric microposts can enable inexpensive and high-throughput studies of heart disease at the single-cell level. However, cardiomyocytes weakly adhere to these microposts, which limits the possibility of using biomechanical assays of single cardiomyocytes to study heart disease. We hypothesized that a stable covalent attachment of laminin to the surface of microposts improves cardiomyocyte contractility. We cultured cells on polydimethylsiloxane microposts with laminin covalently bonded with the organosilanes 3-glycidoxypropyltrimethoxysilane and 3-aminopropyltriethoxysilane with glutaraldehyde. We measured displacement of microposts induced by the contractility of mouse neonatal cardiomyocytes, which attach better than mature cardiomyocytes to substrates. We observed time-dependent changes in contractile parameters such as micropost deformation, contractility rates, contraction and relaxation speeds, and the times of contractions. These parameters were affected by the density of laminin on microposts and by the stability of laminin binding to micropost surfaces. Organosilane-mediated binding resulted in higher laminin surface density and laminin binding stability. 3-glycidoxypropyltrimethoxysilane provided the highest laminin density but did not provide stable protein binding with time. Higher surface protein binding stability and strength were observed with 3-aminopropyltriethoxysilane with glutaraldehyde. In cultured cardiomyocytes, contractility rate, contraction speeds, and contraction time increased with higher laminin stability. Given these variations in contractile function, we conclude that binding of laminin to microposts via 3-aminopropyltriethoxysilane with glutaraldehyde improves contractility observed by an increase in beating rate and contraction speed as it occurs during the postnatal maturation of cardiomyocytes. This approach is promising for future studies to mimic in vivo tissue environments.

    View details for Web of Science ID 000341544200092

    View details for PubMedCentralID PMC4160263

  • Stable, covalent attachment of laminin to microposts improves the contractility of mouse neonatal cardiomyocytes. ACS applied materials & interfaces Ribeiro, A. J., Zaleta-Rivera, K., Ashley, E. A., Pruitt, B. L. 2014; 6 (17): 15516-15526

    Abstract

    The mechanical output of contracting cardiomyocytes, the muscle cells of the heart, relates to healthy and disease states of the heart. Culturing cardiomyocytes on arrays of elastomeric microposts can enable inexpensive and high-throughput studies of heart disease at the single-cell level. However, cardiomyocytes weakly adhere to these microposts, which limits the possibility of using biomechanical assays of single cardiomyocytes to study heart disease. We hypothesized that a stable covalent attachment of laminin to the surface of microposts improves cardiomyocyte contractility. We cultured cells on polydimethylsiloxane microposts with laminin covalently bonded with the organosilanes 3-glycidoxypropyltrimethoxysilane and 3-aminopropyltriethoxysilane with glutaraldehyde. We measured displacement of microposts induced by the contractility of mouse neonatal cardiomyocytes, which attach better than mature cardiomyocytes to substrates. We observed time-dependent changes in contractile parameters such as micropost deformation, contractility rates, contraction and relaxation speeds, and the times of contractions. These parameters were affected by the density of laminin on microposts and by the stability of laminin binding to micropost surfaces. Organosilane-mediated binding resulted in higher laminin surface density and laminin binding stability. 3-glycidoxypropyltrimethoxysilane provided the highest laminin density but did not provide stable protein binding with time. Higher surface protein binding stability and strength were observed with 3-aminopropyltriethoxysilane with glutaraldehyde. In cultured cardiomyocytes, contractility rate, contraction speeds, and contraction time increased with higher laminin stability. Given these variations in contractile function, we conclude that binding of laminin to microposts via 3-aminopropyltriethoxysilane with glutaraldehyde improves contractility observed by an increase in beating rate and contraction speed as it occurs during the postnatal maturation of cardiomyocytes. This approach is promising for future studies to mimic in vivo tissue environments.

    View details for DOI 10.1021/am5042324

    View details for PubMedID 25133578

  • RV remodeling in college athletes engaged in mixed strength and endurance training: do the current echocardiographic reference values apply? Finocchiaro, G., Knowles, J. W., Perez, M., Schnittger, I., Magavern, E., Puryear, J., Sinagra, G., Froelicher, V., Ashley, E., Haddad, F. OXFORD UNIV PRESS. 2014: 729–30
  • Impact of latent obstruction on exercise tolerance in hypertrophic cardiomyopathy Finocchiaro, G., Haddad, F., Knowles, J. W., Pavlovic, A., Sinagra, G., Magavern, E., Wong, M., Myers, J., Froelicher, V., Ashley, E. A. OXFORD UNIV PRESS. 2014: 927
  • Predominance of normal left ventricular geometry in the male 'athlete's heart' HEART Utomi, V., Oxborough, D., Ashley, E., Lord, R., Fletcher, S., Stembridge, M., Shave, R., Hoffman, M. D., Whyte, G., Somauroo, J., Sharma, S., George, K. 2014; 100 (16): 1264-?

    Abstract

    This study evaluated (a) global LV adaption to endurance versus resistance training in male athletes, (b) LV assessment using by modern imaging technologies and (c) the impact of scaling for body size on LV structural data.A prospective cross-sectional design assessed the LV in 18 elite endurance-trained (ET), 19 elite resistance-trained (RT) and 17 sedentary control (CT) participants. Standard 2D, tissue Doppler and speckle tracking echocardiography assessed LV structure and function. Indexing of LV structures to body surface area (BSA) was undertaken using ratio and allometric scaling.Absolute and scaled LV end-diastolic volume (ET: 43.7±6.8; RT: 34.2±7.4; CT 32.5±8.9 mL/m(1.5); p<0.05) and LV mass (ET: 29.8±6.6; RT: 25.4±8.7; CT 25.9±6.4 g/m(2.7); p < 0.05) were significantly higher in ET compared with RT and CT. LV wall thickness were not different between ET and RT. 65% of ET and 95% of RT had normal geometry. Stroke volume was higher in ET compared with both RT and CT (p<0.05). Whilst regional tissue velocity data were not different between groups, longitudinal and basal circumferential strain (ε) was reduced in RT compared with ET.In this comprehensive evaluation of the male athlete's heart (AH), normal LV geometry was predominant in both athlete groups. In the ET, 30% demonstrated an eccentric hypertrophy with no concentric hypertrophy in RT. Cardiac ε data in RT require further evaluation, and any interpretation of LV size should appropriately index for differences in body size.

    View details for DOI 10.1136/heartjnl-2014-305904

    View details for PubMedID 24916049

  • Interpreting whole-genome sequencing--reply. JAMA Dewey, F., Ashley, E., Quertermous, T. 2014; 312 (3): 296-297

    View details for DOI 10.1001/jama.2014.6605

    View details for PubMedID 25027152

  • Whole-Exome Sequencing Reveals TopBP1 as a Novel Gene in Idiopathic Pulmonary Arterial Hypertension AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE Perez, V. A., Yuan, K., Lyuksyutova, M. A., Dewey, F., Orcholski, M. E., Shuffle, E. M., Mathur, M., Yancy, L., Rojas, V., Li, C. G., Cao, A., Alastalo, T., Khazeni, N., Cimprich, K. A., Butte, A. J., Ashley, E., Zamanian, R. T. 2014; 189 (10): 1260-1272

    Abstract

    Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening disorder characterized by progressive loss of pulmonary microvessels. Although mutations in the bone morphogenetic receptor 2 (BMPR2) are found in 80% of heritable and ∼15% of patients with IPAH, their low penetrance (∼20%) suggests that other unidentified genetic modifiers are required for manifestation of the disease phenotype. Use of whole-exome sequencing (WES) has recently led to the discovery of novel susceptibility genes in heritable PAH, but whether WES can also accelerate gene discovery in IPAH remains unknown.To determine whether WES can help identify novel gene modifiers in patients with IPAH.Exome capture and sequencing was performed on genomic DNA isolated from 12 unrelated patients with IPAH lacking BMPR2 mutations. Observed genetic variants were prioritized according to their pathogenic potential using ANNOVAR.A total of nine genes were identified as high-priority candidates. Our top hit was topoisomerase DNA binding II binding protein 1 (TopBP1), a gene involved in the response to DNA damage and replication stress. We found that TopBP1 expression was reduced in vascular lesions and pulmonary endothelial cells isolated from patients with IPAH. Although TopBP1 deficiency made endothelial cells susceptible to DNA damage and apoptosis in response to hydroxyurea, its restoration resulted in less DNA damage and improved cell survival.WES led to the discovery of TopBP1, a gene whose deficiency may increase susceptibility to small vessel loss in IPAH. We predict that use of WES will help identify gene modifiers that influence an individual's risk of developing IPAH.

    View details for DOI 10.1164/rccm.201310-17490C

    View details for Web of Science ID 000336017200018

    View details for PubMedID 24702692

    View details for PubMedCentralID PMC4225850

  • Latent obstruction and left atrial size are predictors of clinical deterioration leading to septal reduction in hypertrophic cardiomyopathy. Journal of cardiac failure Finocchiaro, G., Haddad, F., Pavlovic, A., Sinagra, G., Schnittger, I., Knowles, J. W., Perez, M., Magavern, E., Myers, J., Ashley, E. 2014; 20 (4): 236-243

    Abstract

    Exercise echocardiography is a reliable tool to assess left ventricular (LV) dynamic obstruction in hypertrophic cardiomyopathy (HCM). The aim of this study was to determine the role of exercise echocardiography in the evaluation of latent obstruction and in predicting clinical deterioration in HCM patients.We considered 283 HCM patients studied with exercise echocardiography. The end point was clinical deterioration leading to septal reduction (myectomy or alcohol septal ablation). LV latent obstruction was present at enrollment in 67 patients (24%). During a mean follow-up of 42 ± 31 months, 42 patients had clinical deterioration leading to septal reduction therapy: in 12/67 (22%) patients with a latent obstruction at enrollment, in 28/84 (33%) patients with obstruction at rest, and in 2/132 (1.5%) with obstruction neither at rest or during stress. Multivariate analysis identified the following variables as independently associated with the end point: LV gradient >30 mm Hg at rest (hazard ratio [HR] 2.56, 95% CI 1.27-5.14; P = .009), LV gradient >30 mm Hg during stress (HR 4.96, 95% CI 1.81-13.61; P = .002), and indexed left atrial volume (LAVi ) >40 mL/m(2) (HR 2.86, 95% CI 1.47-5.55; P = .002). In patients with a latent obstruction, the strongest independent predictor of outcome was LAVi >40 mL/m(2) (HR 3.75, 95% CI 1.12-12.51; P = .032).Assessment of LV gradient during stress with exercise echocardiography is an important tool for the evaluation of latent obstruction in HCM and may have a role in risk stratification of these patients.

    View details for DOI 10.1016/j.cardfail.2014.01.014

    View details for PubMedID 24486928

  • Exercise capacity and paroxysmal atrial fibrillation in patients with hypertrophic cardiomyopathy. Heart Azarbal, F., Singh, M., Finocchiaro, G., Le, V., Schnittger, I., Wang, P., Myers, J., Ashley, E., Perez, M. 2014; 100 (8): 624-630

    Abstract

    Atrial fibrillation (AF) is the most common arrhythmia among patients with hypertrophic cardiomyopathy (HCM). The relationship between paroxysmal AF and exercise capacity in this population is incompletely understood.Patients with HCM underwent symptom-limited cardiopulmonary testing with expired gas analysis at Stanford Hospital between October 2006 and October 2012. Baseline demographics, medical histories and resting echocardiograms were obtained for all subjects. Diagnosis of AF was established by review of medical records and baseline ECG. Those with paroxysmal AF were in sinus rhythm at the time of cardiopulmonary testing with expired gas analysis. Exercise intolerance was defined as peak VO2<20 mL/kg/min. We used multivariate logistic regression to evaluate the association between exercise intolerance and paroxysmal AF.Among the 265 patients recruited, 55 had AF (28 paroxysmal and 27 permanent). Compared with those without AF, subjects with paroxysmal AF were older, more likely to use antiarrhythmic and anticoagulant medications, and had larger left atria. Patients with paroxysmal AF achieved lower peak VO2 (21.9±9.2 mL/kg/min vs 26.9±10.8 mL/kg/min, p=0.02) and were more likely to have exercise intolerance (61% vs 28%, p<0.001) compared with those without AF. After adjustment for age, sex and body mass index (BMI) exercise intolerance remained significantly associated with paroxysmal AF (OR 4.65, 95% CI 1.83 to 11.83, p=0.001).Patients with HCM and paroxysmal AF demonstrate exercise intolerance despite being in sinus rhythm at the time of exercise testing.

    View details for DOI 10.1136/heartjnl-2013-304908

    View details for PubMedID 24326897

  • Unexplained double-chambered left ventricle associated with contracting right ventricular aneurysm and right atrial enlargement. Echocardiography (Mount Kisco, N.Y.) Finocchiaro, G., Murphy, D., Pavlovic, A., Haddad, F., Shiran, H., Sinagra, G., Ashley, E. A., Knowles, J. W. 2014; 31 (3): E80-4

    Abstract

    In this article, we describe a double-chambered left ventricle (LV) associated with a functional right ventricular (RV) aneurysm and right atrial (RA) enlargement in an asymptomatic 24-year-old woman with a family history of sudden cardiac death. We will discuss the differential diagnosis, genetic testing and possible prognostic implications.

    View details for DOI 10.1111/echo.12467

    View details for PubMedID 24299065

  • Unexplained double-chambered left ventricle associated with contracting right ventricular aneurysm and right atrial enlargement. Echocardiography (Mount Kisco, N.Y.) Finocchiaro, G., Murphy, D., Pavlovic, A., Haddad, F., Shiran, H., Sinagra, G., Ashley, E. A., Knowles, J. W. 2014; 31 (3): E80-4

    View details for DOI 10.1111/echo.12467

    View details for PubMedID 24299065

  • A neural network approach to predicting outcomes in heart failure using cardiopulmonary exercise testing INTERNATIONAL JOURNAL OF CARDIOLOGY Myers, J., de Souza, C. R., Borghi-Silva, A., Guazzi, M., Chase, P., Bensimhon, D., Peberdy, M. A., Ashley, E., West, E., Cahalin, L. P., Forman, D., Arena, R. 2014; 171 (2): 265-269

    Abstract

    To determine the utility of an artificial neural network (ANN) in predicting cardiovascular (CV) death in patients with heart failure (HF).ANNs use weighted inputs in multiple layers of mathematical connections in order to predict outcomes from multiple risk markers. This approach has not been applied in the context of cardiopulmonary exercise testing (CPX) to predict risk in patients with HF.2635 patients with HF underwent CPX and were followed for a mean of 29±30months. The sample was divided randomly into ANN training and testing sets to predict CV mortality. Peak VO2, VE/VCO2 slope, heart rate recovery, oxygen uptake efficiency slope, and end-tidal CO2 pressure were included in the model. The predictive accuracy of the ANN was compared to logistic regression (LR) and a Cox proportional hazards (PH) score. A multi-layer feed-forward ANN was used and was tested with a single hidden layer containing a varying number of hidden neurons.There were 291 CV deaths during the follow-up. An abnormal VE/VCO2 slope was the strongest predictor of CV mortality using conventional PH analysis (hazard ratio 3.04; 95% CI 2.2-4.2, p<0.001). After training, the ANN was more accurate in predicting CV mortality compared to LR and PH; ROC areas for the ANN, LR, and PH models were 0.72, 0.70, and 0.69, respectively. Age and BMI-adjusted odds ratios were 4.2, 2.6, and 2.9, for ANN, LR, and PH, respectively.An ANN model slightly improves upon conventional methods for estimating CV mortality risk using established CPX responses.

    View details for DOI 10.1016/j.ijcard.2013.12.031

    View details for Web of Science ID 000329982200047

    View details for PubMedID 24387896

  • Patterns and prognosis of all components of the J-wave pattern in multiethnic athletes and ambulatory patients. American heart journal Muramoto, D., Yong, C. M., Singh, N., Aggarwal, S., Perez, M., Ashley, E., Hadley, D., Froelicher, V. 2014; 167 (2): 259-266

    Abstract

    Despite recent concern about the significance of the J-wave pattern (also often referred to as early repolarization) and the importance of screening in athletes, there are limited rigorous prognostic data characterizing the 3 components of the J-wave pattern (ST elevation, J waves, and QRS slurs). We aim to assess the prevalence, patterns, and prognosis of the J-wave pattern among both stable clinical and athlete populations.We retrospectively studied 4,041 electrocardiograms from a multiethnic clinical population from 1997 to 1999 at the Veterans Affairs Palo Alto Health Care System. We also examined preparticipation electrocardiograms of 1,114 Stanford University varsity athletes from 2007 to 2008. Strictly defined criteria for components of the J-wave pattern were examined. In clinical subjects, prognosis was assessed using the end point of cardiovascular death after 7 years of follow-up.Components of the J-wave pattern were most prevalent in males; African Americans; and, particularly, athletes, with the greatest variations demonstrated in the lateral leads. ST elevation was the most common. Inferior J waves and slurs, previously linked to cardiovascular risk, were observed in 9.6% of clinical subjects and 12.3% of athletes. J waves, slurs, or ST elevation was not associated with time to cardiovascular death in clinical subjects, and ST-segment slope abnormalities were not prevalent enough in conjunction with them to reach significance.J waves, slurs, or ST elevation was not associated with increased hazard of cardiovascular death in our large multiethnic, ambulatory population. Even subsets of J-wave patterns, recently proposed to pose a risk of arrhythmic death, occurred at such a high prevalence as to negate their utility in screening.

    View details for DOI 10.1016/j.ahj.2013.10.027

    View details for PubMedID 24439988

  • Contractility of Neonatal Cardiomyocytes is Altered with Different Densities of Laminin Covalently Attached to Microposts Ribeiro, A. S., Zaleta-Rivera, K., Ashley, E. A., Pruitt, B. L. CELL PRESS. 2014: 211A
  • Prevalence and clinical correlates of right ventricular dysfunction in patients with hypertrophic cardiomyopathy. American journal of cardiology Finocchiaro, G., Knowles, J. W., Pavlovic, A., Perez, M., Magavern, E., Sinagra, G., Haddad, F., Ashley, E. A. 2014; 113 (2): 361-367

    Abstract

    Hypertrophic cardiomyopathy (HC) is a disease that mainly affects the left ventricle (LV), however recent studies have suggested that it can also be associated with right ventricular (RV) dysfunction. The objective of this study was to determine the prevalence of RV dysfunction in patients with HC and its relation with LV function and outcome. A total of 324 consecutive patients with HC who received care at Stanford Hospital from 1999 to 2012 were included in the study. A group of 99 prospectively recruited age- and gender-matched healthy volunteers were used as controls. RV function was quantified using the RV fractional area change, tricuspid annular plane systolic excursion (TAPSE), and RV myocardial performance index (RVMPI). Compared with the controls, the patients with HC had a higher RVMPI (0.51 ± 0.18 vs 0.25 ± 0.06, p <0.001) and lower TAPSE (20 ± 3 vs 24 ± 4, p <0.001). RV dysfunction based on an RVMPI >0.4 and TAPSE <16 mm was found in 71% and 11% of the HC and control groups, respectively. Worst LV function and greater pulmonary pressures were independent correlates of RV dysfunction. At an average follow-up of 3.7 ± 2.3 years, 17 patients had died and 4 had undergone heart transplantation. LV ejection fraction <50% and TAPSE <16 mm were independent correlates of outcome (hazard ratio 3.98, 95% confidence interval 1.22 to 13.04, p = 0.02; and hazard ratio 3.66, 95% confidence interval 1.38 to 9.69, p = 0.009, respectively). In conclusion, RV dysfunction based on the RVMPI is common in patients with HC and more frequently observed in patients with LV dysfunction and pulmonary hypertension. RV dysfunction based on the TAPSE was independently associated with an increased likelihood of death or transplantation.

    View details for DOI 10.1016/j.amjcard.2013.09.045

    View details for PubMedID 24230980

  • Rat model of veno-arterial extracorporeal membrane oxygenation. Journal of translational medicine Ali, A. A., Downey, P., Singh, G., Qi, W., George, I., Takayama, H., Kirtane, A., Krishnan, P., Zalewski, A., Freed, D., Large, S. R., Ashley, E. A., Leon, M. B., Bacchetta, M., Ali, Z. A. 2014; 12: 37-?

    Abstract

    We aim to develop a rat model of veno-arterial extracorporeal membrane oxygenation (VA-ECMO).VA-ECMO was established in twelve Male Sprague-Dawley rats (250-350 g) through cannulation of the right jugular vein for venous drainage and the right femoral artery for arterial reinfusion. Arterial blood pressure was measured using a conductance catheter through cannulation of the left carotid artery. Heart rate was monitored by electrocardiography and arterial blood gas parameters with a blood gas analyzer. The VA-ECMO circuit was tested by subjecting the rats to hypoxic cardiac arrest with resuscitation using VA-ECMO. Both load-dependent and load-independent measures of myocardial contractility were measured using pressure-volume loop analysis to confirm restoration of myocardial function post-resuscitation.Following hypoxic cardiac arrest VA-ECMO provided sufficient oxygenation to support the circulation. The haemodynamic and blood gas parameters were maintained at transition and during ECMO. All animals were resuscitated, regained cardiac function and were able to be weaned off ECMO post-resuscitation.We have established a safe, high-throughput, economical, functioning rat model of VA-ECMO.

    View details for DOI 10.1186/1479-5876-12-37

    View details for PubMedID 24507588

    View details for PubMedCentralID PMC3925959

  • Loss Of Carboxylesterase 1 Activity Is Associated With Reduced Bone Morphogenetic Protein Receptor 2 Activity And Membrane Localization In Pulmonary Endothelial Cells Aurora, R., Orcholski, M., Khurshudyan, A., Dewey, F., Ashley, E., Morriseau, C., Hammock, B., Zamanian, R. T., Perez, V. AMER THORACIC SOC. 2014
  • Carboxylesterase 1, A Novel Candidate Gene In Pulmonary Arterial Hypertension, Protects The Pulmonary Endothelium Against Methamphetamine-Mediated Injury Orcholski, M., Khurshudyan, A., Morriseau, C., Dewey, F., Ashley, E., Hammock, B., Zamanian, R. T., Perez, V. AMER THORACIC SOC. 2014
  • Identification of a New Target of miR-16, Vacuolar Protein Sorting 4a. PloS one Adhikari, N., Guan, W., Capaldo, B., Mackey, A. J., Carlson, M., Ramakrishnan, S., Walek, D., Gupta, M., Mitchell, A., Eckman, P., John, R., Ashley, E., Barton, P. J., Hall, J. L. 2014; 9 (7)

    View details for DOI 10.1371/journal.pone.0101509

    View details for PubMedID 25033200

  • How does morphology impact on diastolic function in hypertrophic cardiomyopathy? A single centre experience. BMJ open Finocchiaro, G., Haddad, F., Pavlovic, A., Magavern, E., Sinagra, G., Knowles, J. W., Myers, J., Ashley, E. A. 2014; 4 (6)

    View details for DOI 10.1136/bmjopen-2014-004814

    View details for PubMedID 24928584

  • A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care. Genes Boyd, S. D., Galli, S. J., Schrijver, I., Zehnder, J. L., Ashley, E. A., Merker, J. D. 2014; 5 (3): 748-766

    Abstract

    The tremendous increase in DNA sequencing capacity arising from the commercialization of "next generation" instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of "omics" testing into clinical care.

    View details for DOI 10.3390/genes5030748

    View details for PubMedID 25257203

  • How does morphology impact on diastolic function in hypertrophic cardiomyopathy? A single centre experience. BMJ open Finocchiaro, G., Haddad, F., Pavlovic, A., Magavern, E., Sinagra, G., Knowles, J. W., Myers, J., Ashley, E. A. 2014; 4 (6)

    Abstract

    It is unclear if morphology impacts on diastole in hypertrophic cardiomyopathy (HCM). We sought to determine the relationship between various parameters of diastolic function and morphology in a large HCM cohort.Tertiary referral centre from Stanford, California, USA.383 patients with HCM and normal systolic function between 1999 and 2011. A group of 100 prospectively recruited age-matched and sex-matched healthy participants were used as controls.Echocardiograms were assessed by two blinded board-certified cardiologists. HCM morphology was classified as described in the literature (reverse, sigmoid, symmetric, apical and undefined).Reverse curvature morphology was most commonly observed (218 (57%). Lateral mitral annular E'<12 cm/s was present in 86% of reverse, 88% of sigmoid, 79% of symmetric, 86% of apical and 81% of undefined morphology, p=0.65. E/E' was similarly elevated (E/E': 12.3±7.9 in reverse curvature, 12.1±6.1 in sigmoid, 12.7±9.5 in symmetric, 9.4±4.0 in apical, 12.7±7.9 in undefined morphology, p=0.71) and indexed left atrial volume (LAVi)>40 mL/m(2) was present in 47% in reverse curvature, 33% in sigmoid, 32% in symmetric, 37% in apical and 32% in undefined, p=0.09. Each morphology showed altered parameters of diastolic function when compared with the control population. Left ventricular (LV) obstruction was independently associated with all three diastolic parameters considered, in particular with LAVi>40 mL/m(2) (OR 2.04 (95% CI 1.23 to 3.39), p=0.005), E/E'>15 (OR 4.66 (95% CI 2.51 to 8.64), p<0.001) and E'<8 (OR 2.55 (95% CI 1.42 to 4.53), p=0.001). Other correlates of diastolic dysfunction were age, LV wall thickness and moderate-to-severe mitral regurgitation.In HCM, diastolic dysfunction is present to similar degrees independently from the morphological pattern. The main correlates of diastolic dysfunction are LV obstruction, age, degree of hypertrophy and degree of mitral regurgitation.

    View details for DOI 10.1136/bmjopen-2014-004814

    View details for PubMedID 24928584

    View details for PubMedCentralID PMC4067898

  • Identification of a new target of miR-16, Vacuolar Protein Sorting 4a. PloS one Adhikari, N., Guan, W., Capaldo, B., Mackey, A. J., Carlson, M., Ramakrishnan, S., Walek, D., Gupta, M., Mitchell, A., Eckman, P., John, R., Ashley, E., Barton, P. J., Hall, J. L. 2014; 9 (7)

    Abstract

    The rationale was to utilize a bioinformatics approach to identify miRNA binding sites in genes with single nucleotide mutations (SNPs) to discover pathways in heart failure (HF).The objective was to focus on the genes containing miRNA binding sites with miRNAs that were significantly altered in end-stage HF and in response to a left ventricular assist device (LVAD).BEDTools v2.14.3 was used to discriminate SNPs within predicted 3'UTR miRNA binding sites. A member of the miR-15/107 family, miR-16, was decreased in the circulation of end-stage HF patients and increased in response to a LVAD (p<0.001). MiR-16 decreased Vacuolar Protein Sorting 4a (VPS4a) expression in HEK 293T cells (p<0.01). The SNP rs16958754 was identified in the miR-15/107 family binding site of VPS4a which abolished direct binding of miR-16 to the 3'UTR of VPS4a (p<0.05). VPS4a was increased in the circulation of end-stage HF patients (p<0.001), and led to a decrease in the number of HEK 293T cells in vitro (p<0.001).We provide evidence that miR-16 decreases in the circulation of end-stage HF patients and increases with a LVAD. Modeling studies suggest that miR-16 binds to and decreases expression of VPS4a. Overexpression of VPS4a decreases cell number. Together, these experiments suggest that miR-16 and VPS4a expression are altered in end-stage HF and in response to unloading with a LVAD. This signaling pathway may lead to reduced circulating cell number in HF.

    View details for DOI 10.1371/journal.pone.0101509

    View details for PubMedID 25033200

  • Rare Variation in Sarcomeric Genes Accompanies MYH7 Hypertrophic Cardiomyopathy Caliri, S. J., Dewey, F. E., Grove, M. E., Priest, J., Shringarpure, S., Pan, C., Datta, S., Puckelwartz, M. J., Golbus, J. R., Snyder, M., Bustamante, C. D., Day, S., McNally, E., Cappola, T., Dorn, G., Ashley, E. A. LIPPINCOTT WILLIAMS & WILKINS. 2013: E161–E162
  • Exome Sequencing of Atrioventricular Septal Defects Reveals Rare and de novo Variants in Genes Related to Congenital Heart Disease and Cardiac Development Priest, J. R., Girirajan, S., Dewey, F., Eichler, E. E., Gelb, B. D., Quertermous, T., Ashley, E. A., Portman, M. A. LIPPINCOTT WILLIAMS & WILKINS. 2013: E163
  • Genetic Variation Near HCRTR2 Associates With Dramatic Improvement of Heart Function in Patients With Heart Failure Perez, M. V., Pavlovic, A., Wheeler, M. T., Miller, C. L., Thanaporn, P., Dewey, F. E., Pan, S., Absher, D., Cretti, E., Southwick, A., Heidenreich, P., Sedehi, D., Brandimarto, J., Kao, D., Salisbury, H., Chan, K., Rosenthal, D., Bernstein, D., Fowler, M. B., Robbins, R. C., Meyers, R., Meyers, R., Quertermous, T., Cappola, T., Ashley, E. LIPPINCOTT WILLIAMS & WILKINS. 2013
  • Effects of respiratory exchange ratio on the prognostic value of peak oxygen consumption and ventilatory efficiency in patients with systolic heart failure. JACC. Heart failure Chase, P. J., Kenjale, A., Cahalin, L. P., Arena, R., Davis, P. G., Myers, J., Guazzi, M., Forman, D. E., Ashley, E., Peberdy, M. A., West, E., Kelly, C. T., Bensimhon, D. R. 2013; 1 (5): 427-432

    Abstract

    The purpose of this analysis was to evaluate the prognostic characteristics of peak oxygen consumption (Vo2) and the minute ventilation/carbon dioxide (VE/Vco2) slope of different peak respiratory exchange ratios (RERs) obtained from cardiopulmonary exercise testing in patients with heart failure (HF).For patients with HF, peak Vo2 and the VE/Vco2 slope are used for assessing prognosis. Peak Vo2 is assessed in association with peak RER ≥1.10, indicating maximal effort and prognostic sensitivity. Conversely, the VE/Vco2 slope provides effort-independent prognostic discrimination.Patients with HF scheduled to undergo cardiopulmonary exercise testing were enrolled. Patients were subclassified by peak RER (RER <1.00, RER 1.00 to 1.04, RER 1.05 to 1.09, RER ≥1.10) and followed for up to 3 years for major cardiac-related events (death, left ventricular assist device implantation, or cardiac transplantation).Included were 1,728 patients with HF (75% males; 40% ischemic etiology; age: 55 ± 14 years; left ventricular ejection fraction: 28 ± 10%). Two hundred seventy major events occurred, with no proportional differences across the RER subgroups. Multivariate Cox regression analysis indicated that the VE/Vco2 slope and peak Vo2 remained prognostic within each subgroup; the VE/Vco2 slope remained the strongest predictor. Receiver-operating characteristic analysis demonstrated equitable prognostic cutoffs for the VE/Vco2 slope (range: 34.9 to 35.7; area under the curve [AUC] range: 0.69 to 0.75) and peak Vo2 (range: 13.8 to 14.0 ml·kg(-1)·min(-1); AUC range: 0.68 to 0.75).Peak Vo2 provided a sensitive assessment of prognosis in patients with HF in all RER subgroups. The VE/Vco2 slope provided greater prognostic discrimination in all RER subgroups. Clinical consideration may be warranted for patients with low RER, low peak Vo2, and an elevated VE/Vco2 slope.

    View details for DOI 10.1016/j.jchf.2013.05.008

    View details for PubMedID 24621975

  • Effects of Respiratory Exchange Ratio on the Prognostic Value of Peak Oxygen Consumption and Ventilatory Efficiency in Patients With Systolic Heart Failure JACC-HEART FAILURE Chase, P. J., Kenjale, A., Cahalin, L. P., Arena, R., Davis, P. G., Myers, J., Guazzi, M., Forman, D. E., Ashley, E., Peberdy, M. A., West, E., Kelly, C. T., Bensimhon, D. R. 2013; 1 (5): 427-432

    Abstract

    The purpose of this analysis was to evaluate the prognostic characteristics of peak oxygen consumption (Vo2) and the minute ventilation/carbon dioxide (VE/Vco2) slope of different peak respiratory exchange ratios (RERs) obtained from cardiopulmonary exercise testing in patients with heart failure (HF).For patients with HF, peak Vo2 and the VE/Vco2 slope are used for assessing prognosis. Peak Vo2 is assessed in association with peak RER ≥1.10, indicating maximal effort and prognostic sensitivity. Conversely, the VE/Vco2 slope provides effort-independent prognostic discrimination.Patients with HF scheduled to undergo cardiopulmonary exercise testing were enrolled. Patients were subclassified by peak RER (RER <1.00, RER 1.00 to 1.04, RER 1.05 to 1.09, RER ≥1.10) and followed for up to 3 years for major cardiac-related events (death, left ventricular assist device implantation, or cardiac transplantation).Included were 1,728 patients with HF (75% males; 40% ischemic etiology; age: 55 ± 14 years; left ventricular ejection fraction: 28 ± 10%). Two hundred seventy major events occurred, with no proportional differences across the RER subgroups. Multivariate Cox regression analysis indicated that the VE/Vco2 slope and peak Vo2 remained prognostic within each subgroup; the VE/Vco2 slope remained the strongest predictor. Receiver-operating characteristic analysis demonstrated equitable prognostic cutoffs for the VE/Vco2 slope (range: 34.9 to 35.7; area under the curve [AUC] range: 0.69 to 0.75) and peak Vo2 (range: 13.8 to 14.0 ml·kg(-1)·min(-1); AUC range: 0.68 to 0.75).Peak Vo2 provided a sensitive assessment of prognosis in patients with HF in all RER subgroups. The VE/Vco2 slope provided greater prognostic discrimination in all RER subgroups. Clinical consideration may be warranted for patients with low RER, low peak Vo2, and an elevated VE/Vco2 slope.

    View details for DOI 10.1016/j.jchf.2013.05.008

    View details for Web of Science ID 000209535900009

  • The prognostic significance of heart rate recovery is not dependent upon maximal effort in patients with heart failure INTERNATIONAL JOURNAL OF CARDIOLOGY Cahalin, L. P., Forman, D. E., Chase, P., Guazzi, M., Myers, J., Bensimhon, D., Peberdy, M. A., Ashley, E., West, E., Arena, R. 2013; 168 (2): 1496-1501

    Abstract

    Heart rate recovery (HRR) has been observed to be a significant prognostic measure in patients with heart failure (HF). However, the prognostic value of HRR has not been examined in regard to the level of patient effort during exercise testing. Using the peak respiratory exchange ratio (RER) and a large multicenter HF database we examined the prognostic utility of HRR.Cardiopulmonary exercise testing (CPX) was performed in 806 HF patients who then underwent an active cool-down of at least 1 min. Peak oxygen consumption (VO2), ventilatory efficiency (VE/VCO2 slope), and peak RER were determined with subjects categorized into subgroups according to peak RER (<1.00, 1.00-1.09, ≥ 1.10). HRR was defined as the difference between heart rate at peak exercise and 1 min following test termination. Patients were followed for major cardiac events for up to four years post-CPX.There were 163 major cardiac events (115 deaths, 20 left ventricular assist device implantations, and 28 transplantations) during the four year tracking period. Univariate Cox regression analysis results identified HRR as a significant (p<0.05) univariate predictor of adverse events regardless of the RER achieved. Multivariate Cox regression analysis in the overall group revealed that the VE/VCO2 slope was the strongest predictor of adverse events (chi-square: 110.9, p<0.001) with both HRR (residual chi-square: 16.7, p<0.001) and peak VO2 (residual chi-square: 10.4, p<0.01) adding significant prognostic value.HRR after symptom-limited exercise testing performed at sub-maximal efforts using RER to categorize level of effort is as predictive as HRR after maximal effort in HF patients.

    View details for DOI 10.1016/j.ijcard.2012.12.102

    View details for Web of Science ID 000325412800152

    View details for PubMedID 23391698

  • Exercise capacity in patients with hypertrophic cardiomyopathy: non-invasive hemodynamic responses to exercise and association with clinical and imaging variables Finocchiaro, G., Haddad, F., Pavlovic, A., Sinagra, G., Wong, M., Knowles, J. K., Perez, M., Myers, J., Ashley, E. OXFORD UNIV PRESS. 2013: 532–33
  • Prognostic role of exercise echocardiography in patients with hypertrophic cardiomyopathy Finocchiaro, G., Haddad, F., Pavlovic, A., Sinagra, G., Magavern, E., Knowles, J. K., Ashley, E. OXFORD UNIV PRESS. 2013: 167
  • Race differences in ventricular remodeling and function among college football players. American journal of cardiology Haddad, F., Peter, S., Hulme, O., Liang, D., Schnittger, I., Puryear, J., Gomari, F. A., Finocchiaro, G., Myers, J., Froelicher, V., Garza, D., Ashley, E. A. 2013; 112 (1): 128-134

    Abstract

    Athletic training is associated with increases in ventricular mass and volume. Recent studies have shown that left ventricular mass increases proportionally in white athletes with a mass/volume ratio approaching unity. The objective of this study was to compare the proportionality in ventricular remodeling and ventricular function in black versus white National Collegiate Athletic Association Division I football players. From 2008 to 2011, football players at Stanford University underwent cardiovascular screening with a 12-point history and physical examination, electrocardiography, and focused echocardiography. Compared with white players, black players had on average higher left ventricular mass indexes (77 ± 11 vs 71 ± 11 g/m(2), p = 0.009), higher mass/volume ratios (1.18 ± 0.16 vs 1.06 ± 0.09 g/ml, p <0.001), and higher QRS vector magnitudes (3.2 ± 0.7 vs 2.7 ± 0.8, p = 0.002). Black race had an odds ratio of 14 (95% confidence interval 5 to 42, p <0.001) for a mass/volume ratio >1.2. Mass/volume ratio was inversely related to early diastolic tissue Doppler velocity e' (r = -0.50, p <0.001) but not to QRS vector magnitude (r = 0.065, p = 0.034). With regard to systolic indexes, there was no significant difference in the left ventricular ejection fraction, velocity of circumferential shortening, and isovolumic acceleration. In conclusion, black college football players exhibit more concentric ventricular remodeling, lower early diastolic annular velocities, and increased ventricular voltage compared with white players. Ventricular mass increases proportionally to volume in white players but not in black players.

    View details for DOI 10.1016/j.amjcard.2013.02.065

    View details for PubMedID 23602691

  • Taming Rare Variation With Known Biology in Long QT Syndrome. Circulation. Cardiovascular genetics Perez, M. V., Ashley, E. A. 2013; 6 (3): 227-229

    View details for DOI 10.1161/CIRCGENETICS.113.000199

    View details for PubMedID 23778589

  • Prevention of Sudden Cardiac Death With Implantable Cardioverter-Defibrillators in Children and Adolescents With Hypertrophic Cardiomyopathy JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY Maron, B. J., Spirito, P., Ackerman, M. J., Casey, S. A., Semsarian, C., Estes, N. A., Shannon, K. M., Ashley, E. A., Day, S. M., Pacileo, G., Formisano, F., Devoto, E., Anastasakis, A., Bos, J. M., Woo, A., Autore, C., Pass, R. H., Boriani, G., Garberich, R. F., Almquist, A. K., Russell, M. W., Boni, L., Berger, S., Maron, M. S., Link, M. S. 2013; 61 (14): 1527-1535

    Abstract

    The aim of this study was to determine the efficacy of implantable cardioverter-defibrillators (ICDs) in children and adolescents with hypertrophic cardiomyopathy (HCM).HCM is the most common cause of sudden death in the young. The availability of ICDs over the past decade for HCM has demonstrated the potential for sudden death prevention, predominantly in adult patients.A multicenter international registry of ICDs implanted (1987 to 2011) in 224 unrelated children and adolescents with HCM judged at high risk for sudden death was assembled. Patients received ICDs for primary (n = 188) or secondary (n = 36) prevention after undergoing evaluation at 22 referral and nonreferral institutions in the United States, Canada, Europe, and Australia.Defibrillators were activated appropriately to terminate ventricular tachycardia or ventricular fibrillation in 43 of 224 patients (19%) over a mean of 4.3 ± 3.3 years. ICD intervention rates were 4.5% per year overall, 14.0% per year for secondary prevention after cardiac arrest, and 3.1% per year for primary prevention on the basis of risk factors (5-year cumulative probability 17%). The mean time from implantation to first appropriate discharge was 2.9 ± 2.7 years (range to 8.6 years). The primary prevention discharge rate terminating ventricular tachycardia or ventricular fibrillation was the same in patients who underwent implantation for 1, 2, or ≥3 risk factors (12 of 88 [14%], 10 of 71 [14%], and 4 of 29 [14%], respectively, p = 1.00). Extreme left ventricular hypertrophy was the most common risk factor present (alone or in combination with other markers) in patients experiencing primary prevention interventions (17 of 26 [65%]). ICD-related complications, particularly inappropriate shocks and lead malfunction, occurred in 91 patients (41%) at 17 ± 5 years of age.In a high-risk pediatric HCM cohort, ICD interventions terminating life-threatening ventricular tachyarrhythmias were frequent. Extreme left ventricular hypertrophy was most frequently associated with appropriate interventions. The rate of device complications adds a measure of complexity to ICD decisions in this age group.

    View details for DOI 10.1016/j.jacc.2013.01.037

    View details for Web of Science ID 000317192300010

    View details for PubMedID 23500286

  • Physical Activity and Other Health Behaviors in Adults With Hypertrophic Cardiomyopathy AMERICAN JOURNAL OF CARDIOLOGY Reineck, E., Rolston, B., Bragg-Gresham, J. L., Salberg, L., Baty, L., Kumar, S., Wheeler, M. T., Ashley, E., Saberi, S., Day, S. M. 2013; 111 (7): 1034-1039

    Abstract

    The clinical expression of hypertrophic cardiomyopathy (HC) is undoubtedly influenced by modifying genetic and environmental factors. Lifestyle practices such as tobacco and alcohol use, poor nutritional intake, and physical inactivity are strongly associated with adverse cardiovascular outcomes and increased mortality in the general population. Before addressing the direct effect of such modifiable factors on the natural history of HC, it is critical to define their prevalence in this population. A voluntary survey, drawing questions in part from the 2007 to 2008 National Health and Nutrition Examination Survey (NHANES), was posted on the HC Association website and administered to patients with HC at the University of Michigan. Propensity score matching to NHANES participants was used. Dichotomous and continuous health behaviors were analyzed using logistic and linear regression, respectively, and adjusted for body mass index and propensity score quintile. Compared to the matched NHANES participants, the patients with HC reported significantly less alcohol and tobacco use but also less time engaged in physical activity at work and for leisure. Time spent participating in vigorous or moderate activity was a strong predictor of self-reported exercise capacity. The body mass index was greater in the HC cohort than in the NHANES cohort. Exercise restrictions negatively affected emotional well-being in most surveyed subjects. In conclusion, patients with HC are less active than the general United States population. The well-established relation of inactivity, obesity, and cardiovascular mortality might be exaggerated in patients with HC. More data are needed on exercise in those with HC to strike a balance between acute risks and the long-term health benefits of exercise.

    View details for DOI 10.1016/j.amjcard.2012.12.018

    View details for Web of Science ID 000316923700018

    View details for PubMedID 23340032

  • Prevalence and Clinical Correlates of Right Ventricular Dysfunction in Patients with Hypertrophic Cardiomyopathy Finocchiaro, G., Pavlovic, A., Sudini, N. L., Sinagra, G., Haddad, F., Ashley, E. ELSEVIER SCIENCE INC. 2013: S21–S22
  • WHAT IS THE PROGNOSTIC VALUE OF THE ST DEPRESSION CRITERIA FOR ISCHEMIA RECOMMENDED IN THE UNIVERSAL DEFINITION FOR MYOCARDIAL INFARCTION? 62nd Annual Scientific Session of the American-College-of-Cardiology Perino, A., Singh, N., Aggarwal, S., Perez, M., Ashley, E., Froelicher, V. ELSEVIER SCIENCE INC. 2013: E1166–E1166
  • PREVALENCE AND CLINICAL CORRELATES OF RIGHT VENTRICULAR DYSFUNCTION IN PATIENTS WITH HYPERTROPHIC CARDIOMYOPATHY Finocchiaro, G., Pavlovic, A., Shmargad, Y., Sinagra, G., Haddad, F., Ashley, E. ELSEVIER SCIENCE INC. 2013: E1273
  • A NEURAL NETWORK APPROACH TO PREDICTING OUTCOMES IN HEART FAILURE USING CARDIOPULMONARY EXERCISE TESTING Arena, R., Myers, J. N., de Souza, C., Silva, A., Guazzi, M., Chase, P., Bensimhon, D., Peberdy, M., Ashley, E., West, E., Cahalin, L., Forman, D. ELSEVIER SCIENCE INC. 2013: E1415
  • PAROXYSMAL ATRIAL FIBRILLATION IS ASSOCIATED WITH EXERCISE INTOLERANCE AMONG INDIVIDUALS WITH HYPERTROPHIC CARDIOMYOPATHY 62nd Annual Scientific Session of the American-College-of-Cardiology Azarbal, F., Singh, M., Finocchiaro, G., Le, V., Schnittger, I., Wang, P., Myers, J., Perez, M., Ashley, E. ELSEVIER SCIENCE INC. 2013: E1617–E1617
  • PATTERNS AND PROGNOSIS OF ALL COMPONENTS OF EARLY REPOLARIZATION IN ATHLETES AND AMBULATORY PATIENTS 62nd Annual Scientific Session of the American-College-of-Cardiology Muramoto, D., Singh, N., Aggarwal, S., Perez, M., Ashley, E., Hadley, D., Froelicher, V. ELSEVIER SCIENCE INC. 2013: E349–E349
  • Validation of a cardiopulmonary exercise test score in heart failure. Circulation. Heart failure Myers, J., Oliveira, R., Dewey, F., Arena, R., Guazzi, M., Chase, P., Bensimhon, D., Peberdy, M. A., Ashley, E., West, E., Cahalin, L. P., Forman, D. E. 2013; 6 (2): 211-218

    Abstract

    Cardiopulmonary exercise test (CPX) responses are strong predictors of outcomes in patients with heart failure. We recently developed a CPX score that integrated the additive prognostic information from CPX. The purpose of this study was to validate the score in a larger, independent sample of patients.A total of 2625 patients with heart failure underwent CPX and were followed for cardiovascular (CV) mortality and major CV events (death, transplantation, left ventricular assist device implantation). Net reclassification improvement (NRI) for the score and each of its components were determined at 3 years. The VE/VCO2 slope was the strongest predictor of risk and was attributed a relative weight of 7, with weighted scores for abnormal heart rate recovery, oxygen uptake efficiency slope, end-tidal CO2 pressure, and peak VO2 having scores of 5, 3, 3, and 2, respectively. A summed score of >15 was associated with an annual mortality rate of 12.2% and a relative risk >9 for total events, whereas a score of <5 was associated with an annual mortality rate of 1.2%. The composite score was the most accurate predictor of CV events among all CPX responses considered (C indexes, 0.70 for CV mortality and 0.72 for the composite outcome). Each component of the score provided significant NRI compared with peak VO2 (category-free NRI, 0.61-0.77), and the score provided significant NRI above clinical risk factors for both CV events and mortality (NRI, 0.63 and 0.65 for CPX score compared with clinical variables alone).These results validate the application of a simple, integrated multivariable score based on readily available CPX responses.

    View details for DOI 10.1161/CIRCHEARTFAILURE.112.000073

    View details for PubMedID 23392791

  • Impact of Cardiorespiratory Fitness on the Obesity Paradox in Patients With Heart Failure MAYO CLINIC PROCEEDINGS Lavie, C. J., Cahalin, L. P., Chase, P., Myers, J., Bensimhon, D., Peberdy, M. A., Ashley, E., West, E., Forman, D. E., Guazzi, M., Arena, R. 2013; 88 (3): 251-258

    Abstract

    To determine the impact of cardiorespiratory fitness (FIT) on survival in relation to the obesity paradox in patients with systolic heart failure (HF).We studied 2066 patients with systolic HF (body mass index [BMI] ≥18.5 kg/m(2)) between April 1, 1993 and May 11, 2011 (with 1784 [86%] tested after January 31, 2000) from a multicenter cardiopulmonary exercise testing database who were followed for up to 5 years (mean ± SD, 25.0±17.5 months) to determine the impact of FIT (peak oxygen consumption <14 vs ≥14 mL O2 ∙ kg(-1) ∙ min(-1)) on the obesity paradox.There were 212 deaths during follow-up (annual mortality, 4.5%). In patients with low FIT, annual mortality was 8.2% compared with 2.8% in those with high FIT (P<.001). After adjusting for age and sex, BMI was a significant predictor of survival in the low FIT subgroup when expressed as a continuous (P=.03) and dichotomous (<25.0 vs ≥25.0 kg/m(2)) (P=.01) variable. Continuous and dichotomous BMI expressions were not significant predictors of survival in the overall and high FIT groups after adjusting for age and sex. In patients with low FIT, progressively worse survival was noted with BMI of 30.0 or greater, 25.0 to 29.9, and 18.5 to 24.9 (log-rank, 11.7; P=.003), whereas there was no obesity paradox noted in those with high FIT (log-rank, 1.72; P=.42).These results indicate that FIT modifies the relationship between BMI and survival. Thus, assessing the obesity paradox in systolic HF may be misleading unless FIT is considered.

    View details for DOI 10.1016/j.mayocp.2012.11.020

    View details for Web of Science ID 000317331800009

    View details for PubMedID 23489451

  • Cardiopulmonary and Noninvasive Hemodynamic Responses to Exercise Predict Outcomes in Heart Failure JOURNAL OF CARDIAC FAILURE Myers, J., Wong, M., Adhikarla, C., Boga, M., Challa, S., Abella, J., Ashley, E. A. 2013; 19 (2): 101-107

    Abstract

    An impaired cardiac output response to exercise is a hallmark of chronic heart failure (HF). We determined the extent to which noninvasive estimates of cardiac hemodynamics during exercise in combination with cardiopulmonary exercise test (CPX) responses improved the estimation of risk for adverse events in patients with HF.CPX and impedance cardiography were performed in 639 consecutive patients (mean age 48 ± 14 years), evaluated for HF. Clinical, hemodynamic, and CPX variables were acquired at baseline and subjects were followed for a mean of 460 ± 332 days. Patients were followed for the composite outcome of cardiac-related death, hospitalization for worsening HF, cardiac transplantation, and left ventricular assist device implantation. Cox proportional hazards analyses including clinical, noninvasive hemodynamic, and CPX variables were performed to determine their association with the composite endpoint. There were 113 events. Among CPX variables, peak oxygen uptake (VO(2)) and the minute ventilation (VE)/carbon dioxide production (VCO(2)) slope were significant predictors of risk for adverse events (age-adjusted hazard ratio [HR] 1.08, 95% confidence interval [CI] 1.05-1.11 for both; P < .001). Among hemodynamic variables, peak cardiac index was the strongest predictor of risk (HR 1.08, 95% CI 1.0-1.16; P = .01). In a multivariate analysis including CPX and noninvasively determined hemodynamic variables, the most powerful predictive model included the combination of peak VO(2), peak cardiac index, and the VE/VCO(2) slope, with each contributing significantly and independently to predicting risk; an abnormal response for all 3 yielded an HR of 5.1 (P < .001).These findings suggest that noninvasive indices of cardiac hemodynamics complement established CPX measures in quantifying risk in patients with HF.

    View details for DOI 10.1016/j.cardfail.2012.11.010

    View details for Web of Science ID 000315017600006

    View details for PubMedID 23384635

  • Electrocardiographic interpretation in athletes: the 'Seattle Criteria' BRITISH JOURNAL OF SPORTS MEDICINE Drezner, J. A., Ackerman, M. J., Anderson, J., Ashley, E., Asplund, C. A., Baggish, A. L., Borjesson, M., Cannon, B. C., Corrado, D., Difiori, J. P., Fischbach, P., Froelicher, V., Harmon, K. G., Heidbuchel, H., Marek, J., Owens, D. S., Paul, S., Pelliccia, A., Prutkin, J. M., Salerno, J. C., Schmied, C. M., Sharma, S., Stein, R., Vetter, V. L., Wilson, M. G. 2013; 47 (3): 122-124

    Abstract

    Sudden cardiac death (SCD) is the leading cause of death in athletes during sport. Whether obtained for screening or diagnostic purposes, an ECG increases the ability to detect underlying cardiovascular conditions that may increase the risk for SCD. In most countries, there is a shortage of physician expertise in the interpretation of an athlete's ECG. A critical need exists for physician education in modern ECG interpretation that distinguishes normal physiological adaptations in athletes from abnormal findings suggestive of pathology. On 13-14 February 2012, an international group of experts in sports cardiology and sports medicine convened in Seattle, Washington, to define contemporary standards for ECG interpretation in athletes. The objective of the meeting was to develop a comprehensive training resource to help physicians distinguish normal ECG alterations in athletes from abnormal ECG findings that require additional evaluation for conditions associated with SCD.

    View details for DOI 10.1136/bjsports-2012-092067

    View details for Web of Science ID 000314349700002

    View details for PubMedID 23303758

  • Abnormal electrocardiographic findings in athletes: recognising changes suggestive of primary electrical disease BRITISH JOURNAL OF SPORTS MEDICINE Drezner, J. A., Ackerman, M. J., Cannon, B. C., Corrado, D., Heidbuchel, H., Prutkin, J. M., Salerno, J. C., Anderson, J., Ashley, E., Asplund, C. A., Baggish, A. L., Borjesson, M., Difiori, J. P., Fischbach, P., Froelicher, V., Harmon, K. G., Marek, J., Owens, D. S., Paul, S., Pelliccia, A., Schmied, C. M., Sharma, S., Stein, R., Vetter, V. L., Wilson, M. G. 2013; 47 (3): 153-?

    Abstract

    Cardiac channelopathies are potentially lethal inherited arrhythmia syndromes and an important cause of sudden cardiac death (SCD) in young athletes. Other cardiac rhythm and conduction disturbances also may indicate the presence of an underlying cardiac disorder. The 12-lead ECG is utilised as both a screening and a diagnostic tool for detecting conditions associated with SCD. Fundamental to the appropriate evaluation of athletes undergoing ECG is an understanding of the ECG findings that may indicate the presence of a pathological cardiac disease. This article describes ECG findings present in primary electrical diseases afflicting young athletes and outlines appropriate steps for further evaluation of these ECG abnormalities. The ECG findings defined as abnormal in athletes were established by an international consensus panel of experts in sports cardiology and sports medicine.

    View details for DOI 10.1136/bjsports-2012-092070

    View details for Web of Science ID 000314349700005

    View details for PubMedID 23303761

  • Abnormal electrocardiographic findings in athletes: recognising changes suggestive of cardiomyopathy BRITISH JOURNAL OF SPORTS MEDICINE Drezner, J. A., Ashley, E., Baggish, A. L., Borjesson, M., Corrado, D., Owens, D. S., Patel, A., Pelliccia, A., Vetter, V. L., Ackerman, M. J., Anderson, J., Asplund, C. A., Cannon, B. C., DiFiori, J., Fischbach, P., Froelicher, V., Harmon, K. G., Heidbuchel, H., Marek, J., Paul, S., Prutkin, J. M., Salerno, J. C., Schmied, C. M., Sharma, S., Stein, R., Wilson, M. 2013; 47 (3): 137-?

    Abstract

    Cardiomyopathies are a heterogeneous group of heart muscle diseases and collectively are the leading cause of sudden cardiac death (SCD) in young athletes. The 12-lead ECG is utilised as both a screening and diagnostic tool for detecting conditions associated with SCD. Fundamental to the appropriate evaluation of athletes undergoing ECG is an understanding of the ECG findings that may indicate the presence of an underlying pathological cardiac disorder. This article describes ECG findings present in cardiomyopathies afflicting young athletes and outlines appropriate steps for further evaluation of these ECG abnormalities. The ECG findings defined as abnormal in athletes were established by an international consensus panel of experts in sports cardiology and sports medicine.

    View details for DOI 10.1136/bjsports-2012-092069

    View details for Web of Science ID 000314349700004

    View details for PubMedID 23303760

  • Normal electrocardiographic findings: recognising physiological adaptations in athletes BRITISH JOURNAL OF SPORTS MEDICINE Drezner, J. A., Fischbach, P., Froelicher, V., Marek, J., Pelliccia, A., Prutkin, J. M., Schmied, C. M., Sharma, S., Wilson, M. G., Ackerman, M. J., Anderson, J., Ashley, E., Asplund, C. A., Baggish, A. L., Borjesson, M., Cannon, B. C., Corrado, D., Difiori, J. P., Harmon, K. G., Heidbuchel, H., Owens, D. S., Paul, S., Salerno, J. C., Stein, R., Vetter, V. L. 2013; 47 (3): 125-?

    Abstract

    Electrocardiographic changes in athletes are common and usually reflect benign structural and electrical remodelling of the heart as a physiological adaptation to regular and sustained physical training (athlete's heart). The ability to identify an abnormality on the 12-lead ECG, suggestive of underlying cardiac disease associated with sudden cardiac death (SCD), is based on a sound working knowledge of the normal ECG characteristics within the athletic population. This document will assist physicians in identifying normal ECG patterns commonly found in athletes. The ECG findings presented as normal in athletes were established by an international consensus panel of experts in sports cardiology and sports medicine.

    View details for DOI 10.1136/bjsports-2012-092068

    View details for Web of Science ID 000314349700003

    View details for PubMedID 23303759

  • A Clinical Approach to Inherited Hypertrophy The Use of Family History in Diagnosis, Risk Assessment, and Management CIRCULATION-CARDIOVASCULAR GENETICS Dunn, K. E., Caleshu, C., Cirino, A. L., Ho, C. Y., Ashley, E. A. 2013; 6 (1): 118-131
  • Abnormal Calcium Handling Properties Underlie Familial Hypertrophic Cardiomyopathy Pathology in Patient-Specific Induced Pluripotent Stem Cells CELL STEM CELL Lan, F., Lee, A. S., Liang, P., Sanchez-Freire, V., Nguyen, P. K., Wang, L., Han, L., Yen, M., Wang, Y., Sun, N., Abilez, O. J., Hu, S., Ebert, A. D., Navarrete, E. G., Simmons, C. S., Wheeler, M., Pruitt, B., Lewis, R., Yamaguchi, Y., Ashley, E. A., Bers, D. M., Robbins, R. C., Longaker, M. T., Wu, J. C. 2013; 12 (1): 101-113

    Abstract

    Familial hypertrophic cardiomyopathy (HCM) is a prevalent hereditary cardiac disorder linked to arrhythmia and sudden cardiac death. While the causes of HCM have been identified as genetic mutations in the cardiac sarcomere, the pathways by which sarcomeric mutations engender myocyte hypertrophy and electrophysiological abnormalities are not understood. To elucidate the mechanisms underlying HCM development, we generated patient-specific induced pluripotent stem cell cardiomyocytes (iPSC-CMs) from a ten-member family cohort carrying a hereditary HCM missense mutation (Arg663His) in the MYH7 gene. Diseased iPSC-CMs recapitulated numerous aspects of the HCM phenotype including cellular enlargement and contractile arrhythmia at the single-cell level. Calcium (Ca(2+)) imaging indicated dysregulation of Ca(2+) cycling and elevation in intracellular Ca(2+) ([Ca(2+)](i)) are central mechanisms for disease pathogenesis. Pharmacological restoration of Ca(2+) homeostasis prevented development of hypertrophy and electrophysiological irregularities. We anticipate that these findings will help elucidate the mechanisms underlying HCM development and identify novel therapies for the disease.

    View details for DOI 10.1016/j.stem.2012.10.010

    View details for Web of Science ID 000313839500014

    View details for PubMedID 23290139

    View details for PubMedCentralID PMC3638033

  • A meta-analysis of the prognostic significance of cardiopulmonary exercise testing in patients with heart failure HEART FAILURE REVIEWS Cahalin, L. P., Chase, P., Arena, R., Myers, J., Bensimhon, D., Peberdy, M. A., Ashley, E., West, E., Forman, D. E., Pinkstaff, S., Lavie, C. J., Guazzi, M. 2013; 18 (1): 79-94

    Abstract

    The objective of the study is to assess the role of cardiopulmonary exercise testing (CPX) variables, including peak oxygen consumption (VO(2)), which is the most recognized CPX variable, the minute ventilation/carbon dioxide production (VE/VCO(2)) slope, the oxygen uptake efficiency slope (OUES), and exercise oscillatory ventilation (EOV) in a current meta-analysis investigating the prognostic value of a broader list of CPX-derived variables for major adverse cardiovascular events in patients with HF. A search for relevant CPX articles was performed using standard meta-analysis methods. Of the initial 890 articles found, 30 met our inclusion criteria and were included in the final analysis. The total subject populations included were as follows: peak VO(2) (7,319), VE/VCO(2) slope (5,044), EOV (1,617), and OUES (584). Peak VO(2), the VE/VCO(2) slope and EOV were all highly significant prognostic markers (diagnostic odds ratios ≥ 4.10). The OUES also demonstrated promise as a prognostic marker (diagnostic odds ratio = 8.08) but only in a limited number of studies (n = 2). No other independent variables (including age, ejection fraction, and beta-blockade) had a significant effect on the meta-analysis results for peak VO(2) and the VE/VCO(2) slope. CPX is an important component in the prognostic assessment of patients with HF. The results of this meta-analysis strongly confirm this and support a multivariate approach to the application of CPX in this patient population.

    View details for DOI 10.1007/s10741-012-9332-0

    View details for Web of Science ID 000312882800007

    View details for PubMedID 22733204

  • Whole Exome Sequencing Identifies Novel Candidate Genes In A Cohort Of Patients With Idiopathic Pulmonary Arterial Hypertension Perez, V., Lyuksyutova, M., Dewey, F., Del Rosario, P., Ashley, E., Zamanian, R. T. AMER THORACIC SOC. 2013
  • Whole Exome Sequencing Identifies Carboxylesterase 1 As Aa Novel Candidate Gene In Patients With Methamphetamine Induced Pulmonary Hypertension Zamanian, R. T., Khurshudyan, A., Dewey, F., Orcholski, M., Ashley, E., Perez, V. AMER THORACIC SOC. 2013
  • ACTIVATION OF VEGFR-2 IN ADVENTITIAL STEM CELLS TRIGGERS VASCULAR REMODELLING Chang, C., Lin, C., Lin, C., Lehrer, J., Krampitz, G., Ikeno, F., Ali, Z., Wang, R., Ashley, E., Rabinovitch, M. KARGER. 2013: 15
  • Cardiac Structural and Sarcomere Genes Associated With Cardiomyopathy Exhibit Marked Intolerance of Genetic Variation CIRCULATION-CARDIOVASCULAR GENETICS Pan, S., Caleshu, C. A., Dunn, K. E., Foti, M. J., Moran, M. K., Soyinka, O., Ashley, E. A. 2012; 5 (6): 602-610

    Abstract

    The clinical significance of variants in genes associated with inherited cardiomyopathies can be difficult to determine because of uncertainty regarding population genetic variation and a surprising amount of tolerance of the genome even to loss-of-function variants. We hypothesized that genes associated with cardiomyopathy might be particularly resistant to the accumulation of genetic variation.We analyzed the rates of single nucleotide genetic variation in all known genes from the exomes of >5000 individuals from the National Heart, Lung, and Blood Institute's Exome Sequencing Project, as well as the rates of structural variation from the Database of Genomic Variants. Most variants were rare, with over half unique to 1 individual. Cardiomyopathy-associated genes exhibited a rate of nonsense variants, about 96.1% lower than other Mendelian disease genes. We tested the ability of in silico algorithms to distinguish between a set of variants in MYBPC3, MYH7, and TNNT2 with strong evidence for pathogenicity and variants from the Exome Sequencing Project data. Algorithms based on conservation at the nucleotide level (genomic evolutionary rate profiling, PhastCons) did not perform as well as amino acid-level prediction algorithms (Polyphen-2, SIFT). Variants with strong evidence for disease causality were found in the Exome Sequencing Project data at prevalence higher than expected.Genes associated with cardiomyopathy carry very low rates of population variation. The existence in population data of variants with strong evidence for pathogenicity suggests that even for Mendelian disease genetics, a probabilistic weighting of multiple variants may be preferred over the single gene causality model.

    View details for DOI 10.1161/CIRCGENETICS.112.963421

    View details for Web of Science ID 000312774800008

    View details for PubMedID 23074333

    View details for PubMedCentralID PMC3526690

  • Patients with Hypertrophic Cardiomyopathy are Less Physically Active than the General Population Rolston, B., Reineck, E., Bragg-Gresham, J., Salberg, L., Saberi, S., Baty, L., Wheeler, M., Ashley, E., Day, S. M. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • Race Differences in Ventricular Remodeling Among College Football Players: Implications for a Cardiovascular Screening Program Peter, S., Haddad, F., Hulme, O., Gomari, A., Myers, J., Froelicher, V., Ashley, E. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • Are T wave Inversions in the Anterior Precordial Leads Benign in African-Americans? Findley, C. M., Stein, R., Perez, M., Ashley, E., Froelicher, V. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • Impact of Cardiorespiratory Fitness on the Obesity Paradox in Patients with Heart Failure Lavie, C. J., Cahalin, L. P., Chase, P., Myers, J., Bensimhon, D., Peberdy, M., Ashley, E., West, E., Forman, D. E., Guazzil, M., Arena, R. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • Analysis of Cardiomyopathy Using Whole Genome Sequencing Golbus, J. R., Puckelwartz, M. J., Pesce, L. L., Wolfgeher, D., Dellefave-Castillo, L., Cappola, T. P., Ashley, E. A., Dorn, G. W., McNally, E. M. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • Prognostic value of capnography during rest and exercise in patients with heart failure. Congestive heart failure (Greenwich, Conn.) Arena, R., Guazzi, M., Myers, J., Chase, P., Bensimhon, D., Cahalin, L. P., Peberdy, M. A., Ashley, E., West, E., Forman, D. E. 2012; 18 (6): 302-307

    Abstract

    New variables obtained from cardiopulmonary exercise testing (CPX) have received attention in recent years, in particular the partial pressure of end-tidal carbon dioxide (P(ET) CO(2) ). The purpose of this study was to therefore comprehensively assess the ability of resting and exercise P(ET) CO(2) to predict major cardiac events in a heart failure (HF) cohort referred for CPX. A total of 963 patients with systolic HF undergoing symptom-limited CPX were included in the analysis. Resting and exercise P(ET) CO(2) along with other CPX variables were determined, and patients were followed for major adverse events. With regard to resting measures, multivariate analysis revealed that left ventricular ejection fraction was the most robust prognostic marker (P<.001) while resting P(ET) CO(2) added significant predictive value and was retained in the regression (P<.001). When exercise data were considered, the multivariate analysis revealed that the P(ET) CO(2) apex during exercise added predictive value and was retained (P<.05). In what is the largest evaluation of P(ET) CO(2) in the assessment of systolic HF patients to date, the authors substantiate prior (smaller) studies showing prognostic utility of P(ET) CO(2) , both as a resting measure (an important potential screening tool) and during exercise. These data add to the rationale to incorporate P(ET) CO(2) as a routine monitoring component in HF management.

    View details for DOI 10.1111/j.1751-7133.2012.00296.x

    View details for PubMedID 22537025

  • Ventilatory Power A Novel Index That Enhances Prognostic Assessment of Patients With Heart Failure CIRCULATION-HEART FAILURE Forman, D. E., Guazzi, M., Myers, J., Chase, P., Bensimhon, D., Cahalin, L. P., Peberdy, M. A., Ashley, E., West, E., Daniels, K. M., Arena, R. 2012; 5 (5): 621-626

    Abstract

    Minute ventilation/CO(2) production (VE/Vco(2)) slope is an index determined by cardiopulmonary exercise testing, which incorporates pertinent cardiac, pulmonary, and skeletal muscle physiology into a substantive composite assessment. The VE/Vco(2) slope has many applications, including utility as a well-validated prognostic gauge for patients with heart failure (HF). In this study, we combine VE/Vco(2) slope with systolic blood pressure, creating a novel index that we labeled ventilatory power. Ventilatory power links the combined physiology inherent in the VE/Vco(2) slope to peripheral pressure, adding an additional dimension pertinent to HF assessment. Whereas the related concept of circulatory power links peak oxygen consumption with peak systolic blood pressure as a prognostic index, we hypothesized that ventilatory power would provide greater prognostic discrimination than VE/Vco2 slope, peak oxygen consumption, and circulatory power for patients with systolic HF.Patients with systolic HF (left ventricular ejection fraction ≤35%) underwent symptom-limited cardiopulmonary exercise testing as part of routine management and were followed for up to 4 years for major cardiac events (mortality, left ventricular assist device implantation, and heart transplantation). Eight hundred seventy-five patients with HF (left ventricular ejection fraction, 26±9%; mean age, 55±14) were studied. Cardiopulmonary exercise testing indices peak oxygen consumption, VE/Vco(2) slope, circulatory power, and ventilatory power were all predictive of cardiac events (P<0.001). Multivariate analysis demonstrated that ventilatory power was the strongest indicator of prognosis.Although circulatory power and traditional cardiopulmonary exercise testing parameters can be used to predict prognosis among patients with HF, ventilatory power provides relatively greater prognostic discrimination and may constitute a relatively more useful composite tool.

    View details for DOI 10.1161/CIRCHEARTFAILURE.112.968529

    View details for Web of Science ID 000313579500014

    View details for PubMedID 22899767

  • Modeling Pathogenesis in Familial Hypertrophic Cardiomyopathy Using Patient-Specific Induced Pluripotent Stem Cells Basic Cardiovascular Sciences Scientific Session Lan, F., Lee, A., Liang, P., Navarrete, E., Wang, L., Leng, H., Sanchez, V., Yen, M., Wang, Y., Nguyen, P., Sun, N., Abilez, O., Lewis, R., Yamaguchi, Y., Ashley, E., Bers, D., Robbins, R., Longaker, M., Wu, J. LIPPINCOTT WILLIAMS & WILKINS. 2012
  • In Situ Optical Mapping of Voltage and Calcium in the Heart PLOS ONE Lee, P., Taghavi, F., Yan, P., Ewart, P., Ashley, E. A., Loew, L. M., Kohl, P., Bollensdorff, C., Woods, C. E. 2012; 7 (8)

    Abstract

    Electroanatomic mapping the interrelation of intracardiac electrical activation with anatomic locations has become an important tool for clinical assessment of complex arrhythmias. Optical mapping of cardiac electrophysiology combines high spatiotemporal resolution of anatomy and physiological function with fast and simultaneous data acquisition. If applied to the clinical setting, this could improve both diagnostic potential and therapeutic efficacy of clinical arrhythmia interventions. The aim of this study was to explore this utility in vivo using a rat model. To this aim, we present a single-camera imaging and multiple light-emitting-diode illumination system that reduces economic and technical implementation hurdles to cardiac optical mapping. Combined with a red-shifted calcium dye and a new near-infrared voltage-sensitive dye, both suitable for use in blood-perfused tissue, we demonstrate the feasibility of in vivo multi-parametric imaging of the mammalian heart. Our approach combines recording of electrophysiologically-relevant parameters with observation of structural substrates and is adaptable, in principle, to trans-catheter percutaneous approaches.

    View details for DOI 10.1371/journal.pone.0042562

    View details for Web of Science ID 000307184700055

    View details for PubMedID 22876327

    View details for PubMedCentralID PMC3411684

  • A public resource facilitating clinical use of genomes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ball, M. P., Thakuria, J. V., Zaranek, A. W., Clegg, T., Rosenbaum, A. M., Wu, X., Angrist, M., Bhak, J., Bobe, J., Callow, M. J., Cano, C., Chou, M. F., Chung, W. K., Douglas, S. M., Estep, P. W., Gore, A., Hulick, P., Labarga, A., Lee, J., Lunshof, J. E., Kim, B. C., Kim, J., Li, Z., Murray, M. F., Nilsen, G. B., Peters, B. A., Raman, A. M., Rienhoff, H. Y., Robasky, K., Wheeler, M. T., Vandewege, W., Vorhaus, D. B., Yang, J. L., Yang, L., Aach, J., Ashley, E. A., Drmanac, R., Kim, S., Li, J. B., Peshkin, L., Seidman, C. E., Seo, J., Zhang, K., Rehm, H. L., Church, G. M. 2012; 109 (30): 11920-11927

    Abstract

    Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain-we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.

    View details for DOI 10.1073/pnas.1201904109

    View details for Web of Science ID 000306992700018

    View details for PubMedID 22797899

    View details for PubMedCentralID PMC3409785

  • Personalized medicine: hope or hype? EUROPEAN HEART JOURNAL Salari, K., Watkins, H., Ashley, E. A. 2012; 33 (13): 1564-U29

    Abstract

    Medicine has always been personalized. For years, physicians have incorporated environmental, behavioural, and genetic factors that affect disease and drug response into patient management decisions. However, until recently, the 'genetic' data took the form of family history and self-reported race/ethnicity. As genome sequencing declines in cost, the availability of specific genomic information will no longer be limiting. Rather, our ability to parse these data and our decision whether to use it will become primary. As our understanding of genetic association with drug responses and diseases continues to improve, clinically useful genetic tests may emerge to improve upon our previous methods of assessing genetic risks. Indeed, genetic tests for monogenic disorders have already proven useful. Such changes may usher in a new era of personalized medicine. In this review, we will discuss the utility and limitations of personal genomic data in three domains: pharmacogenomics, assessment of genetic predispositions for common diseases, and identification of rare disease-causing genetic variants.

    View details for DOI 10.1093/eurheartj/ehs112

    View details for Web of Science ID 000306143000014

    View details for PubMedID 22659199

    View details for PubMedCentralID PMC3388016

  • The Prognostic Utility of Cardiopulmonary Exercise Testing Stands the Test of Time in Patients With Heart Failure JOURNAL OF CARDIOPULMONARY REHABILITATION AND PREVENTION Arena, R., Guazzi, M., Myers, J., Chase, P., Bensimhon, D., Cahalin, L. P., Peberdy, M. A., Ashley, E., West, E., Forman, D. E. 2012; 32 (4): 198-202

    Abstract

    While the medical management strategy for patients with heart failure (HF) has dramatically changed, cardiopulmonary exercise testing (CPX) procedures and the data obtained have remained relatively stable. We are unaware of any previous investigation that has assessed differences in the prognostic utility of CPX in HF according to time period, reflecting differences in the clinical management of systolic HF.Subjects (n = 381) underwent CPX between April 1, 1993, and December 31, 2005, and the remaining 511 were tested between January 1, 2006, and October 28, 2010. Peak oxygen uptake ((Equation is included in full-text article.)O2) and the minute ventilation/carbon dioxide production ((Equation is included in full-text article.)E/(Equation is included in full-text article.)CO2) slope were ascertained for all tests.Both the (Equation is included in full-text article.)E/(Equation is included in full-text article.)CO2 slope and peak (Equation is included in full-text article.)O2 were strong univariate predictors of adverse events in both subgroups. In the multivariate analysis, the (Equation is included in full-text article.)E/(Equation is included in full-text article.)CO2 slope was the strongest predictive marker while peak (Equation is included in full-text article.)O2 added predictive value and was retained in the regression for all scenarios. In subjects undergoing CPX before 2006, a (Equation is included in full-text article.)E/(Equation is included in full-text article.)CO2 slope 45 or greater and a peak (Equation is included in full-text article.)O2 of less than 10 mL · kg · min generated a hazard ratio of 4.2 (95% CI: 1.9-9.1, P < .001) when considering only mortality as an endpoint. In subjects undergoing CPX after 2006, a (Equation is included in full-text article.)E/(Equation is included in full-text article.)CO2 slope 45 or greater and a peak (Equation is included in full-text article.)O2 of less than 10 mL · kg · min generated a hazard ratio of 8.2 (95% CI: 4.7-14.3, P < .001) when considering only mortality as an endpoint.The results of this study indicate that CPX continues to be a valuable clinical assessment in the present-day HF management.

    View details for DOI 10.1097/HCR.0b013e318259f153

    View details for Web of Science ID 000306115400005

    View details for PubMedID 22760244

  • Prognostic Implications of Q Waves and T-Wave Inversion Associated With Early Repolarization MAYO CLINIC PROCEEDINGS Uberoi, A., Sallam, K., Perez, M., Jain, N. A., Ashley, E., Froelicher, V. 2012; 87 (7): 614-619

    Abstract

    To evaluate the prevalence of early polarization (ER) in a stable population and to evaluate the prognostic significance of the association or absence of Q waves or T-wave inversion (TWI).In this retrospective study performed at the university-affiliated Palo Alto Veterans Affairs Health Care Center from March 1, 1987, through December 31, 1999, we evaluated outpatient electrocardiograms. Vital status and cause of death were determined in all patients, with a mean ± SD follow-up of 7.6±3.8 years.Of the 29,281 patients, 87% were men and 13% were African American. Inferior or lateral ER was present in 664 patients (2.3%): in inferior leads in 185 (0.6%), in lateral leads in 479 (1.6%) , and in both inferior and lateral leads in 163 (0.6%). Only when Q waves or TWI accompanied ER was there an increased risk of cardiovascular death (Cox proportional hazards regression model, 5.0; 95% confidence interval, 3.4-7.2; P<.001).Common patterns of ER without concomitant Q waves or TWI are not associated with increased risk of cardiovascular death; however, when either occurs with ER, there is a hazard ratio of 5.0. These findings confirm that ER is a benign entity; however, the presence of Q waves or TWI with ER is predictive of increased cardiovascular death.

    View details for DOI 10.1016/j.mayocp.2012.04.009

    View details for PubMedID 22766081

  • Cell-Intrinsic Functional Effects of the alpha-Cardiac Myosin Arg-403-Gln Mutation in Familial Hypertrophic Cardiomyopathy BIOPHYSICAL JOURNAL Chuan, P., Sivaramakrishnan, S., Ashley, E. A., Spudich, J. A. 2012; 102 (12): 2782-2790

    Abstract

    Human familial hypertrophic cardiomyopathy is the most common Mendelian cardiovascular disease worldwide. Among the most severe presentations of the disease are those in families heterozygous for the mutation R403Q in β-cardiac myosin. Mice heterozygous for this mutation in the α-cardiac myosin isoform display typical familial hypertrophic cardiomyopathy pathology. Here, we study cardiomyocytes from heterozygous 403/+ mice. The effects of the R403Q mutation on force-generating capabilities and dynamics of cardiomyocytes were investigated using a dual carbon nanofiber technique to measure single-cell parameters. We demonstrate the Frank-Starling effect at the single cardiomyocyte level by showing that cell stretch causes an increase in amplitude of contraction. Mutant 403/+ cardiomyocytes exhibit higher end-diastolic and end-systolic stiffness than +/+ cardiomyocytes, whereas active force generation capabilities remain unchanged. Additionally, 403/+ cardiomyocytes show slowed relaxation dynamics. These phenotypes are consistent with increased end-diastolic and end-systolic chamber elastance, as well as diastolic dysfunction seen at the level of the whole heart. Our results show that these functional effects of the R403Q mutation are cell-intrinsic, a property that may be a general phenomenon in familial hypertrophic cardiomyopathy.

    View details for DOI 10.1016/j.bpj.2012.04.049

    View details for Web of Science ID 000305546500012

    View details for PubMedID 22735528

    View details for PubMedCentralID PMC3379014

  • Apelin Enhances Directed Cardiac Differentiation of Mouse and Human Embryonic Stem Cells PLOS ONE Wang, I. E., Wang, X., Ge, X., Anderson, J., Ho, M., Ashley, E., Liu, J., Butte, M. J., Yazawa, M., Dolmetsch, R. E., Quertermous, T., Yang, P. C. 2012; 7 (6)

    Abstract

    Apelin is a peptide ligand for an orphan G-protein coupled receptor (APJ receptor) and serves as a critical gradient for migration of mesodermal cells fated to contribute to the myocardial lineage. The present study was designed to establish a robust cardiac differentiation protocol, specifically, to evaluate the effect of apelin on directed differentiation of mouse and human embryonic stem cells (mESCs and hESCs) into cardiac lineage. Different concentrations of apelin (50, 100, 500 nM) were evaluated to determine its differentiation potential. The optimized dose of apelin was then combined with mesodermal differentiation factors, including BMP-4, activin-A, and bFGF, in a developmentally specific temporal sequence to examine the synergistic effects on cardiac differentiation. Cellular, molecular, and physiologic characteristics of the apelin-induced contractile embryoid bodies (EBs) were analyzed. It was found that 100 nM apelin resulted in highest percentage of contractile EB for mESCs while 500 nM had the highest effects on hESCs. Functionally, the contractile frequency of mESCs-derived EBs (mEBs) responded appropriately to increasing concentration of isoprenaline and diltiazem. Positive phenotype of cardiac specific markers was confirmed in the apelin-treated groups. The protocol, consisting of apelin and mesodermal differentiation factors, induced contractility in significantly higher percentage of hESC-derived EBs (hEBs), up-regulated cardiac-specific genes and cell surface markers, and increased the contractile force. In conclusion, we have demonstrated that the treatment of apelin enhanced cardiac differentiation of mouse and human ESCs and exhibited synergistic effects with mesodermal differentiation factors.

    View details for DOI 10.1371/journal.pone.0038328

    View details for PubMedID 22675543

  • Whole-Genome Sequencing in Personalized Therapeutics CLINICAL PHARMACOLOGY & THERAPEUTICS Cordero, P., Ashley, E. A. 2012; 91 (6): 1001-1009

    Abstract

    Eleven years since the initial drafts of the human genome were published, we have begun to see the first examples of the application of whole-genome sequencing to personalized diagnosis and therapeutics. The exponential decline in sequencing costs and the constant improvement in these technologies promise to further advance the use of a patient's full genetic profile in the clinic. However, realizing the potential benefit of such sequencing will require a concerted effort by science, medicine, law, and management. In this review, we discuss current approaches to decoding the 6 billion-letter genetic code of a whole genome in a clinical context, give current examples of translating this information into therapy-guiding knowledge, and list the challenges that will need to be surmounted before these powerful data can be fully exploited to forward the goals of personalized medicine.

    View details for DOI 10.1038/clpt.2012.51

    View details for Web of Science ID 000304245800018

    View details for PubMedID 22549284

  • Systems-Based Approaches to Cardiovascular Biomarker Discovery CIRCULATION-CARDIOVASCULAR GENETICS Azuaje, F. J., Dewey, F. E., Brutsaert, D. L., Devaux, Y., Ashley, E. A., Wagner, D. R. 2012; 5 (3): 360-367
  • Randomized Trial of Personal Genomics for Preventive Cardiology Design and Challenges CIRCULATION-CARDIOVASCULAR GENETICS Knowles, J. W., Assimes, T. L., Kiernan, M., Pavlovic, A., Goldstein, B. A., Yank, V., McConnell, M. V., Absher, D., Bustamante, C., Ashley, E. A., Ioannidis, J. P. 2012; 5 (3): 368-376

    View details for DOI 10.1161/CIRCGENETICS.112.962746

    View details for PubMedID 22715281

  • Clopidogrel: A Case for Indication-Specific Pharmacogenetics CLINICAL PHARMACOLOGY & THERAPEUTICS Johnson, J. A., Roden, D. M., Lesko, L. J., Ashley, E., Klein, T. E., Shuldiner, A. R. 2012; 91 (5): 774-776

    Abstract

    The CYP2C19*2 loss-of-function allele is associated with reduced generation of active metabolites of clopidogrel. However, meta-analyses have supported or discounted the impact of genotype on adverse cardiovascular outcomes during clopidogrel therapy, depending on studies included in the analysis. Here we review these data and conclude that evidence supports a differential effect of genotype on protection from major adverse cardiovascular outcomes following percutaneous coronary intervention (PCI), but not for other clopidogrel indications.

    View details for DOI 10.1038/clpt.2012.21

    View details for Web of Science ID 000303047400009

    View details for PubMedID 22513313

    View details for PubMedCentralID PMC3382015

  • Patient-Specific Induced Pluripotent Stem Cells as a Model for Familial Dilated Cardiomyopathy SCIENCE TRANSLATIONAL MEDICINE Sun, N., Yazawa, M., Liu, J., Han, L., Sanchez-Freire, V., Abilez, O. J., Navarrete, E. G., Hu, S., Wang, L., Lee, A., Pavlovic, A., Lin, S., Chen, R., Hajjar, R. J., Snyder, M. P., Dolmetsch, R. E., Butte, M. J., Ashley, E. A., Longaker, M. T., Robbins, R. C., Wu, J. C. 2012; 4 (130)

    Abstract

    Characterized by ventricular dilatation, systolic dysfunction, and progressive heart failure, dilated cardiomyopathy (DCM) is the most common form of cardiomyopathy in patients. DCM is the most common diagnosis leading to heart transplantation and places a significant burden on healthcare worldwide. The advent of induced pluripotent stem cells (iPSCs) offers an exceptional opportunity for creating disease-specific cellular models, investigating underlying mechanisms, and optimizing therapy. Here, we generated cardiomyocytes from iPSCs derived from patients in a DCM family carrying a point mutation (R173W) in the gene encoding sarcomeric protein cardiac troponin T. Compared to control healthy individuals in the same family cohort, cardiomyocytes derived from iPSCs from DCM patients exhibited altered regulation of calcium ion (Ca(2+)), decreased contractility, and abnormal distribution of sarcomeric α-actinin. When stimulated with a β-adrenergic agonist, DCM iPSC-derived cardiomyocytes showed characteristics of cellular stress such as reduced beating rates, compromised contraction, and a greater number of cells with abnormal sarcomeric α-actinin distribution. Treatment with β-adrenergic blockers or overexpression of sarcoplasmic reticulum Ca(2+) adenosine triphosphatase (Serca2a) improved the function of iPSC-derived cardiomyocytes from DCM patients. Thus, iPSC-derived cardiomyocytes from DCM patients recapitulate to some extent the morphological and functional phenotypes of DCM and may serve as a useful platform for exploring disease mechanisms and for drug screening.

    View details for DOI 10.1126/scitranslmed.3003552

    View details for Web of Science ID 000303045900004

    View details for PubMedID 22517884

    View details for PubMedCentralID PMC3657516

  • The prognostic value of early repolarization with ST-segment elevation in African Americans HEART RHYTHM Perez, M. V., Uberoi, A., Jain, N. A., Ashley, E., Turakhia, M. P., Froelicher, V. 2012; 9 (4): 558-565

    Abstract

    Increased prevalence of classic early repolarization, defined as ST-segment elevation (STE) in the absence of acute myocardial injury, in African Americans is well established. The prognostic value of this pattern in different ethnicities remains controversial.Measure association between early repolarization and cardiovascular mortality in African Americans.The resting electrocardiograms of 45,829 patients were evaluated at the Palo Alto Veterans Affairs Hospital. Subjects with inpatient status or electrocardiographic evidence of acute myocardial infarction were excluded, leaving 29,281 subjects. ST-segment elevation, defined as an elevation of >0.1 mV at the end of the QRS, was electronically flagged and visually adjudicated by 3 observers blinded to outcomes. An association between ethnicity and early repolarization was measured by using multivariate logistic regression. We analyzed associations between early repolarization and cardiovascular mortality by using the Cox proportional hazards regression analysis.Subjects were 13% women and 13.3% African Americans, with an average age of 55 years and followed for an average of 7.6 years, resulting in 1995 cardiovascular deaths. There were 479 subjects with lateral STE and 185 with inferior STE. After adjustment for age, sex, heart rate, and coronary artery disease, African American ethnicity was associated with lateral or inferior STE (odds ratio 3.1; P = .0001). While lateral or inferior STE in non-African Americans was independently associated with cardiovascular death (hazard ratio 1.6; P = .02), it was not associated with cardiovascular death in African Americans (hazard ratio 0.75; P = .50).Although early repolarization is more prevalent in African Americans, it is not predictive of cardiovascular death in this population and may represent a distinct electrophysiologic phenomenon.

    View details for DOI 10.1016/j.hrthm.2011.11.020

    View details for PubMedID 22094072

  • Independent Determinants of Septal Curvature in Patients with Pulmonary Arterial Hypertension Haddad, F., Denault, A. Y., Shkiri, M., Guihaire, J., Mercier, O., Gomari, F., Ashley, E., Fadel, E., Zamanian, R., Schnittger, I. ELSEVIER SCIENCE INC. 2012: S80
  • Activation of Aldehyde Dehydrogenase Type 2 (ALDH2) by Alda-1 Significantly Enhances the Function of the DCD Heart Taghavi, F. J., Thanaporn, P. K., Woods, C. E., Ali, A., Large, S. R., Chen, C., Mochly-Rosen, D., Ashley, E. ELSEVIER SCIENCE INC. 2012: S40
  • PROGNOSTIC IMPLICATIONS OF Q WAVES AND T WAVE INVERSION ASSOCIATED WITH EARLY REPOLARIZATION 61st Annual Scientific Session and Expo of the American-College-of-Cardiology (ACC)/Conference on ACC-i2 with TCT Uberoi, A. (., Sallam, K., Perez, M., Jain, N. A., Ashley, E., Froelicher, V. ELSEVIER SCIENCE INC. 2012: E567–E567
  • DNA Sequencing Clinical Applications of New DNA Sequencing Technologies CIRCULATION Dewey, F. E., Pan, S., Wheeler, M. T., Quake, S. R., Ashley, E. A. 2012; 125 (7): 931-944
  • The relationship between minute ventilation and oxygen consumption in heart failure: Comparing peak VE/VO2 and the oxygen uptake efficiency slope INTERNATIONAL JOURNAL OF CARDIOLOGY Arena, R., Guazzi, M., Myers, J., Chase, P., Bensimhon, D., Cahalin, L. P., Peberdy, M., Ashley, E., West, E., Forman, D. E. 2012; 154 (3): 384–85

    View details for DOI 10.1016/j.ijcard.2011.11.038

    View details for Web of Science ID 000299317900054

    View details for PubMedID 22188985

  • Image-Based Functional Assay to Screen Therapies for Inherited Heart Disease. Simmons, C., Zaleta-Rivera, K. L., Ribeiro, A., Ashley, E., Pruitt, B. L. AMER SOC CELL BIOLOGY. 2012
  • Exercise oscillatory ventilation reflects diminished quality of life and perceived functional capacity in patients with heart failure INTERNATIONAL JOURNAL OF CARDIOLOGY Arena, R., Guazzi, M., Myers, J., Chase, P., Bensimhon, D., Cahalin, L., Peberdy, M. A., Ashley, E., West, E., Forman, D. E. 2011; 153 (2): 213-214

    View details for DOI 10.1016/j.ijcard.2011.09.072

    View details for Web of Science ID 000297249400027

    View details for PubMedID 21993226

  • Personalized Medicine and Cardiovascular Disease: From Genome to Bedside CURRENT CARDIOVASCULAR RISK REPORTS Pan, S., Dewey, F. E., Perez, M. V., Knowles, J. W., Chen, R., Butte, A. J., Ashley, E. A. 2011; 5 (6): 542–51
  • Network Analysis Identifies the Orphan Receptor Tyrosine Kinase Ros1 as a Determinant of Glutathione Peroxidase-1 Mediated Vascular Remodeling Scientific Sessions of the American-Heart-Association/Resuscitation Science Symposium Ali, Z. A., Perez, V. D., Raiesdana, A., Leeper, N. J., Pan, S., Qu, X., Ali, A., Haghighat, R., Kato, K., Channon, K. M., Rabinovitch, M., Quertermous, T., Ashley, E. A. LIPPINCOTT WILLIAMS & WILKINS. 2011
  • Cardiovascular Magnetic Resonance Imaging Elucidates Genotype-Phenotype Relationships in Patients with Hypertrophic Cardiomyopathy Scientific Sessions of the American-Heart-Association/Resuscitation Science Symposium Heidary, S., Wheeler, M. T., Bennett, M. V., Chung, J., Pavlovic, A., Parent, M., Dash, R., McConnell, M. V., Ashley, E. A., Yang, P. C. LIPPINCOTT WILLIAMS & WILKINS. 2011
  • Patient-Specific Induced Pluripotent Stem Cell as a Model for Familial Dilated Cardiomyopathy Scientific Sessions of the American-Heart-Association/Resuscitation Science Symposium Sun, N., Yazawa, M., Liu, J., Han, L., Sanchez-Freire, V., Hu, S., Ricardo, D., Butte, M., Ashley, E., Longaker, M., Robbins, R., Wu, J. LIPPINCOTT WILLIAMS & WILKINS. 2011
  • Early Repolarization in an Ambulatory Clinical Population CIRCULATION Uberoi, A., Jain, N. A., Perez, M., Weinkopff, A., Ashley, E., Hadley, D., Turakhia, M. P., Froelicher, V. 2011; 124 (20): 2208-2214

    Abstract

    The significance of early repolarization, particularly regarding the morphology of the R-wave downslope, has come under question.We evaluated 29 281 resting ambulatory ECGs from the VA Palo Alto Health Care System. With PR interval as the isoelectric line and amplitude criteria ≥0.1 mV, ST-segment elevation is defined at the end of the QRS, J wave as an upward deflection, and slur as a conduction delay on the QRS downstroke. Associations of ST-segment elevation patterns, J waves, and slurs with cardiovascular mortality were analyzed with Cox analysis. With a median follow-up of 7.6 years, there were 1995 cardiac deaths. Of 29 281 subjects, 87% were male (55±14 years) and 13% were female (56±17 years); 13% were black, 6% were Hispanic, and 81% were white or other. Six hundred sixty-four (2.3%) had inferior or lateral ST-segment elevation: 185 (0.6%) in inferior leads and 479 (1.6%) in lateral leads, 163 (0.6%) in both, and 0.4% had global elevation. A total of 4041 ECGs were analyzed with enhanced display, and 583 (14%) had J waves or slurring, which were more prevalent in those with than in those without ST-segment elevation (61% versus 13%; P<0.001). ST-segment elevation occurred more in those with than in those without J waves or slurs (12% versus 1.3%; P<0.001). Except when involving only inferior leads, all components of early repolarization were more common in young individuals, male subjects, blacks, and those with bradycardia. All patterns and components of early repolarization were associated with decreased cardiovascular mortality, but this was not significant after adjustment for age.We found no significant association between any components of early repolarization and cardiac mortality.

    View details for DOI 10.1161/CIRCULATIONAHA.111.047191

    View details for PubMedID 21986288

  • Insights from Network Analysis: Deficiency of Glutathione Peroxidase-1 Increases In-stent Stenosis 23rd Annual Scientific Symposium of Transcatheter Cardiovascular Therapeutics (TCT) Ali, Z. A., Raiesdana, A., Qu, X., Patel, S., Keyghobadi, F., Saeed, A., Quertermous, T., Ashley, E. ELSEVIER SCIENCE INC. 2011: B122–B122
  • Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence PLOS GENETICS Dewey, F. E., Chen, R., Cordero, S. P., Ormond, K. E., Caleshu, C., Karczewski, K. J., Whirl-Carrillo, M., Wheeler, M. T., Dudley, J. T., Byrnes, J. K., Cornejo, O. E., Knowles, J. W., Woon, M., Sangkuhl, K., Gong, L., Thorn, C. F., Hebert, J. M., Capriotti, E., David, S. P., Pavlovic, A., West, A., Thakuria, J. V., Ball, M. P., Zaranek, A. W., Rehm, H. L., Church, G. M., West, J. S., Bustamante, C. D., Snyder, M., Altman, R. B., Klein, T. E., Butte, A. J., Ashley, E. A. 2011; 7 (9)

    Abstract

    Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs). We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

    View details for DOI 10.1371/journal.pgen.1002280

    View details for PubMedID 21935354

  • The Impact of ST Elevation on Athletic Screening CLINICAL JOURNAL OF SPORT MEDICINE Leo, T., Uberoi, A., Jain, N. A., Garza, D., Chowdhury, S., Freeman, J. V., Perez, M., Ashley, E., Froelicher, V. 2011; 21 (5): 433-440

    Abstract

    To demonstrate the prevalence and patterns of ST elevation (STE) in ambulatory individuals and athletes and compare the clinical outcomes.Retrospective cohort study. ST elevation was measured by computer algorithm and defined as ≥0.1 mV at the end of the QRS complex. Elevation was confirmed, and J waves and slurring were coded visually.Veterans Affairs Palo Alto Health Care System and Stanford University varsity athlete screening evaluation.Overall, 45 829 electrocardiograms (ECGs) were obtained from the clinical patient cohort and 658 ECGs from athletes. We excluded inpatients and those with ECG abnormalities, leaving 20 901 outpatients and 641 athletes.Electrocardiogram evaluation and follow-up for vital status.All-cause and cardiovascular mortality and cardiac events.ST elevation in the anterior and lateral leads was more prevalent in men and in African Americans and inversely related to age and resting heart rate. Athletes had a higher prevalence of early repolarization even when matched for age and gender with nonathletes. ST elevation greater than 0.2 mV (2 mm) was very unusual. ST elevation was not associated with cardiac death in the clinical population or with cardiac events or abnormal test results in the athletes.Early repolarization is not associated with cardiac death and has patterns that help distinguish it from STE associated with cardiac conditions, such as myocardial ischemia or injury, pericarditis, and the Brugada syndrome.

    View details for DOI 10.1097/JSM.0B013E31822CF105

    View details for PubMedID 21892017

  • Interpretation of the Electrocardiogram of Young Athletes CIRCULATION Uberoi, A., Stein, R., Perez, M. V., Freeman, J., Wheeler, M., Dewey, F., Peidro, R., Hadley, D., Drezner, J., Sharma, S., Pelliccia, A., Corrado, D., Niebauer, J., Estes, M., Ashley, E., Froelicher, V. 2011; 124 (6): 746-757

    View details for DOI 10.1161/CIRCULATIONAHA.110.013078

    View details for PubMedID 21824936

  • Hearts From DCD Donors Display Acceptable Biventricular Function After Heart Transplantation in Pigs AMERICAN JOURNAL OF TRANSPLANTATION Ali, A. A., White, P., Xiang, B., Lin, H., Tsui, S. S., Ashley, E., LEE, T. W., Klein, J. R., Kumar, K., Arora, R. C., Large, S. R., Tian, G., Freed, D. H. 2011; 11 (8): 1621-1632

    Abstract

    Cardiac transplantation is in decline, in contrast to other solid organs where the number of solid organ transplants from donors after circulatory death (DCD) is increasing. Hearts from DCD donors are not currently utilized due to concerns that they may suffer irreversible cardiac injury with resultant poor graft function. Using a large animal model, we tested the hypothesis that hearts from DCD donors would be suitable for transplantation. Donor pigs were subjected to hypoxic cardiac arrest (DCD) followed by 15 min of warm ischemia and resuscitation on cardiopulmonary bypass, or brainstem death (BSD) via intracerebral balloon inflation. Cardiac function was assessed through load-independent measures and magnetic resonance imaging and spectroscopy. After resuscitation, DCD hearts had near normal contractility, although stroke volume was reduced, comparable to BSD hearts. DCD hearts had a significant decline in phosphocreatine and increase in inorganic phosphate during the hypoxic period, with a return to baseline levels after reperfusion. After transplantation, cardiac function was comparable between BSD and DCD groups. Therefore, in a large animal model, the DCD heart maintains viability and recovers function similar to that of the BSD heart and may be suitable for clinical transplantation. Further study is warranted on optimal reperfusion strategies.

    View details for DOI 10.1111/j.1600-6143.2011.03622.x

    View details for Web of Science ID 000293340900015

    View details for PubMedID 21749639

  • Modulation of atrial electrophysiology and oxidative stress by the endogenous peptide hormone apelin: implications in human atrial fibrillation Kim, Y. M., Sachedina, A., Singh, M. H., Ray, S., Zhang, L., Ruiz-Lozano, P., Verma, S., Casadei, B., Ashley, E. A., Backx, P. H. OXFORD UNIV PRESS. 2011: 941–942
  • Systems biology of heart failure, challenges and hopes CURRENT OPINION IN CARDIOLOGY Dewey, F. E., Wheeler, M. T., Ashley, E. A. 2011; 26 (4): 314-321

    Abstract

    Heart failure remains a leading cause of morbidity and mortality in developed nations. Our current understanding of molecular pathways involved in heart failure reveals little of the multiscale biological systems at work. Here we consider recent advances in understanding the integrative multiscale biology, or systems biology, of heart failure and present a framework for future work in the area.Multiplexed assays of gene expression and the complex dynamics of protein-protein interactions in heart failure have illuminated key pathways important to myocardial adaptation. Modeling of complex systems has advanced to incorporate these dynamic data sources into networks that capture fundamental interactions on different biological scales. The complex syndrome of heart failure, like other complex disease syndromes, can be viewed as an emergent property of these multiscale systems.A comprehensive understanding of adaptive mechanisms in heart failure requires integration of multiple data sources on several biological scales. A combination of holistic systems biology approaches and traditional reductionist experimentation will be required for a nuanced understanding of this multifaceted disease process.

    View details for DOI 10.1097/HCO.0b013e328346597d

    View details for Web of Science ID 000291424400007

    View details for PubMedID 21478745

  • GENETIC DETERMINANTS OF DRAMATIC IMPROVEMENT IN LEFT VENTRICULAR FUNCTION IN PATIENTS WITH HEART FAILURE 60th Annual Scientific Session and Expo of the American-College-of-Cardiology (ACC) / I2 Summit / ACCF/Herman K. Gold Young Investigator's Award in Molecular and Cellular Cardiology Perez, M. V., Pavlovic, A., Wheeler, M. T., Dewey, F. E., Bernstein, D., Fowler, M. B., Robbins, R. C., Quertermous, T., Chan, K., Absher, D., Ho, M., Cretti, E., Southwick, A., Rosenthal, D., Myers, R. M., Heidenreich, P., Garrett, L., Sedehi, D., Kao, D., Salisbury, H., Ashley, E. A. ELSEVIER SCIENCE INC. 2011: E2041–E2041
  • PREVALENCE AND PATTERNS OF EARLY REPOLARIZATION 60th Annual Scientific Session and Expo of the American-College-of-Cardiology (ACC) / I2 Summit / ACCF/Herman K. Gold Young Investigator's Award in Molecular and Cellular Cardiology Leo, T., Uberoi, A., Chowdhury, S., Chan, K., Jain, N. A., Weinkopff, A., Freeman, J., Ashley, E., Froelicher, V. ELSEVIER SCIENCE INC. 2011: E124–E124
  • Hearts from DCD Donors Display Excellent Biventricular Function Following Transplantation 31st Annual Meeting and Scientific Sessions of the International-Society-for-Heart-and-Lung-Transplantation (ISHLT) Ali, A. A., White, P., Xiang, B., Arora, R., Lee, T., Ashley, E., Large, S. R., Tian, G., Freed, D. ELSEVIER SCIENCE INC. 2011: S120–S121
  • Intracellular Calcium Handling in the Donor Heart: Comparison between DCD and Brainstem Dead (BSD) Donor Hearts Taghavi, F. J., Ali, A. A., Woods, C., Large, S. R., Ashley, E. A. ELSEVIER SCIENCE INC. 2011: S199
  • Genetic Analysis in Cardiovascular Disease A Clinical Perspective 3rd International Conference on Women, Heart, Disease and Stroke Ho, E., Bhindi, R., Ashley, E. A., Figtree, G. A. LIPPINCOTT WILLIAMS & WILKINS. 2011: 81–89

    Abstract

    Many forms of cardiovascular disease (CVD) demonstrate heritability and thus a genetic contribution is likely. This is most evident when considering the "simple" Mendelian traits such as hypertrophic cardiomyopathy. However, family history also influences our asses