Chloe Reuter

All Publications

• Characterizing psychosocial assessments across genetic counseling sessions through qualitative content analysis. Journal of genetic counseling Ruiz, K., Narain, A., Nguyen, T. P., Pollard, E., Joseph, G., Moscarello, T., Campion, M., Reuter, C. 2026; 35 (1): e70161

  Abstract

  Although psychosocial support and assessment is a required competency of genetic counselors (GCs), how the psychosocial assessment is actualized in sessions is not well studied. We aimed to describe the landscape of psychosocial assessments in clinical genetic counseling sessions at a single institution through direct analysis of audio recordings. Clinical GCs at Stanford Medicine and their new English-speaking adult patients were eligible. After GCs and patients completed demographic surveys, we audio-recorded sessions for which the GCs and patients enrolled. Purposive sampling, prioritizing a breadth of GCs, specialties, indications, and patient demographics, was used to select audio recordings for transcription and analysis. We used a blended inductive and deductive approach to develop the codebook. Code frequency and memos were assessed for descriptive content analysis of psychosocial components of the sessions. We analyzed 23 audio recordings, representing nine GCs across cancer, cardiology, and prenatal. We identified three distinct psychosocial styles that GCs used: "Direct," "Informational," "Casual." While all styles incorporated emotion-focused conversation to some degree, only the "Direct Psychosocial Style" included an explicit psychosocial assessment of patients. Psychosocial assessments consisted of direct feelings questions, emotion-focused responses, and advanced empathy. The "Informational Psychosocial Style" was characterized by GC responses to patient feelings and sympathy statements, without consistent exploration of patient feelings throughout the session. The "Casual Psychosocial Style" was characterized by an observable rapport between the GC and patient that carried throughout the session, allowing for psychosocial issues to be explored organically. GCs varied in their use of each style across patients, specialty, and indication. In conclusion, we observed three distinct psychosocial styles, of which only the Direct Psychosocial Style had an overt psychosocial assessment. Further research is needed to examine patient outcomes within each style.

  View details for DOI 10.1002/jgc4.70161

  View details for PubMedID 41485198

• Assessing and attending to psychosocial concerns in genetic counseling: Proposing the BATHE method. Journal of genetic counseling Moscarello, T., Higgs, E., Pollard, E., Monroe, M., Nguyen, T. P., Campion, M., Reuter, C. M. 2024

  Abstract

  The process of identifying and responding to patients' social, emotional, and psychological concerns is a required skill for training and practicing genetic counselors. Patients' health outcomes are improved when genetic counselors attend to these "psychosocial" concerns. Still, the process of eliciting, assessing, and attending to patients' psychosocial concerns in the genetic counseling setting is not well defined in the literature nor is it performed consistently. Tools that do exist are often questionnaire-based, designed for research use, or occur outside of a genetic counseling appointment. Here we describe the complexities of defining "psychosocial assessment" in genetic counseling, its impact on patient outcomes, and summarize existing tools for psychosocial assessment. We identify a need for evidenced-based, verbally-administered psychosocial assessment tools in genetic counseling and explore the value of adapting an existing tool from primary care (the BATHE method) to genetic counseling. The BATHE method is a semi-structured psychosocial assessment tool that can be performed quickly within a patient appointment to gather context, emotional impact, the patient's primary concern, and coping strategies. Through our professional experiences we believe it is a beneficial psychosocial assessment tool as perceived by both patients and genetic counselors. Further work is needed to determine if the BATHE method could fill a gap in how genetic counselors conduct a psychosocial assessment.

  View details for DOI 10.1002/jgc4.1998

  View details for PubMedID 39535335

• Arrhythmogenic Cardiomyopathy: Mechanisms, Genetics, and Their Clinical Implications CURRENT CARDIOVASCULAR RISK REPORTS Reuter, C. M., Dries, A. M., Parikh, V. N. 2021; 15 (5)

  View details for DOI 10.1007/s12170-021-00669-5

  View details for Web of Science ID 000633384600001

• 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

• 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

• "It didn't feel like anything unusual because we had already been through so much": Disability-Related Research Experiences of Families with Children Enrolled in the Undiagnosed Diseases Network. Genetics in medicine : official journal of the American College of Medical Genetics Mintz, K. T., Altamirano, E. N., Halley, M. C., Barton, K. S., Cho, M. K., Bernstein, J. A., Carter, J. N., Undiagnosed Diseases Network, Tabor, H. K., Quinlan, A., Elkadri, A., Beggs, A. H., La Spada, A. R., Huang, A., Foksinska, A., Paul, A., Ward, A., Krokosky, A., Tran, A. A., Gropman, A., Vargas, A., Crouse, A. B., Stergachis, A., Hurst, A., Raper, A., Slavotinek, A., Nouraee, A., Tarakad, A., Andrews, A., McMinn, A., Iverson, A., Pusey Swerdzewski, B. N., Afzali, B., Solomon, B., Martin, B. A., Wilk, B. M., Mitchell, B., Lanpher, B. C., Lee, B. H., Fogel, B. L., Bordini, B., Graham, B. H., Gelb, B., Korf, B. R., Toro, C., Skraban, C., Bacino, C. A., Prada, C., Smith, C. A., Shyr, C., Esteves, C., Xiao, C., Cunningham-Rundles, C., Reuter, C. M., Eng, C. M., Mayhew, C., Chan, C., Wahl, C. E., Welt, C. K., Tifft, C. J., Ward, D. I., Kiley, D., Sayer, D., Rader, D. J., Wegner, D., Miller, D. E., Scott, D. A., Viskochil, D., Sweetser, D. A., Chiang, D., Adams, D. R., Barbouth, D., Rao, D. A., Oglesbee, D., Bonner, D., Basel, D., Novacic, D., Baldridge, D., Seto, E., Rosenthal, E., Worthey, E. A., Burke, E. A., Blue, E., Chao, E. C., Wohler, E., Macnamara, E. F., Balton, E., Glanton, E., Shelkowitz, E., Mendonca, E., Allenspach, E., Gamazon, E., Gayle, E., Klee, E., Vilain, E., Davis, E., Wishart, E. A., Conboy, E., Baldwin, E. E., Ashley, E. A., Cole, F. S., Pinto E Vairo, F., High, F., Vetrini, F., Bustos, F., Hisama, F. M., Marth, G., Jarvik, G. P., Mochida, G., Carvalho, G., Berry, G. T., Mirzaa, G., Sirugo, G., Kilich, G., Bademci, G., Mendez, H. R., Wood, H., Taylor, H., Tabor, H. K., Dai, H., Chao, H., Bellen, H. J., Glass, I., Lanza, I. R., Holm, I. A., Kohane, I. S., Chinn, I., Pallais, J. C., Sampson, J. B., Orengo, J. P., Verbsky, J., Sninsky, J., Hom, J., Schend, J., Kohler, J. N., Morgan, J., Schymick, J., Tousseau, J., Wambach, J., Fu, J., Rosenfeld, J. A., Shin, J., Jen, J., Gonzalez, J. M., Phillips, J. A., Carey, J., Gorzynski, J. E., Davis, J., Bernstein, J. A., Abdenur, J., Loscalzo, J., Cogan, J. D., Martinez-Agosto, J. A., Hoover-Fong, J., McCarrier, J., Darr, K., Lee Yap, K., Callaway, K., Leppig, K. A., Sisco, K. A., Page, K., Sullivan, K., Dipple, K., Treat, K. M., Regan-Fendt, K., Schoch, K., Smith, K. S., Liaqat, K., Worley, K., Ezell, K., LeBlanc, K., Latchman, K., Perera, L., Rodan, L. H., Keehan, L., Blieden, L., Briere, L. C., Jeffries, L., Wiel, L., Abi Farraj, L. F., Petcharet, L., Peart, L., Mantcheva, L., Solnica-Krezel, L., Burrage, L. C., Mulvihill, L., Bastarache, L., Schimmenti, L., Botto, L., Potocki, L., Bier, L., Rives, L., Wolfe, L. A., Barbosa, M., Steenari, M., Butte, M. J., Balwani, M., Delgado, M., Ortuno Romero, M. J., Silva, M. P., Acosta, M. T., Morimoto, M., Shadrina, M., Wener, M., Sabaii, M., Horike-Pyne, M., Martin, M. G., Rodriguez, M., Koziura, M., Velinder, M., Might, M., Robinson, M., Wheeler, M. T., Malicdan, M. C., Bell, M., Halley, M. C., Walker, M., Levanto, M., Bamshad, M., Wangler, M. F., Muriello, M., Zimmermann, M. T., Leitheiser, M., Mikati, M., Saifeddine, M., Hubshman, M. W., Lek, M., Westerfield, M., Tekin, M., Dorrani, N., Sobreira, N., Parker, N. H., Hanchard, N., Borja, N., Longo, N., Walley, N. M., Jean-Marie, O., Witmer, P. D., Goddard, P. C., Moretti, P., Dickson, P., McMullen, P., Auwaerter, P., Berger, P., Fisher, P. G., Liu, P., Byers, P., Bayrak-Toydemir, P., Lertwilaiwittaya, P., D'Souza, P., Tan, Q., Ungar, R. A., Evard, R., Li, R., Quarells, R. C., Rajagopalan, R., Alvarez, R. L., Blackburn, R., Spillmann, R. C., Ganetzky, R., Overbury, R., Barrick, R., Lewis, R. A., Chang, R., Hamid, R., Mao, R., Marom, R., Corona, R. I., Kumar, R., Butterfield, R., Attaripour, S., Nagamani, S., Shuman, S., Lalani, S. R., Perlman, S., Ketkar, S., Kobren, S. N., Yamamoto, S., Marwaha, S., Chanprasert, S., Nelson, S. F., Zuchner, S., Bivona, S., Ware, S. M., Montgomery, S. B., Pak, S. C., Boyden, S., Bachir, S., Shin, S., Mozaffar, T., Jensen, T. D., Beagle, T., Maurer, T., Washington, T., Serrano, T. J., Coakley, T. R., Cassini, T., Nicholas, T. J., Schedl, T., Truong, T., Vogel, T. P., Jobanputra, V., Maduro, V. V., Shashi, V., Sybert, V., Chung, W., Introne, W., Raskind, W., Thorson, W., Gahl, W. A., Byrd, W. E., Craigen, W. J., Timp, W., Huang, Y., Karasozen, Y., Chang, Y., Jiang, Y., Manabe, Y., Guo, Z. 2026: 102663

  Abstract

  PURPOSE: In recent years, researchers have brought attention to the underrepresentation of people with disabilities in biomedical research, including genomics research. However, little is known about how disability-related experiences influence participation in rare disease research. This omission is striking, because rare diseases are associated with disabling phenotypes that affect multiple body systems. As part of a study interrogating the relationship between rare disease status and disability identity, we conducted mixed-methods research to address this knowledge gap.METHODS: Parents of children enrolled in the UDN (n=25) completed semi-structured interviews to assess disability-related experiences in research participation. Directed content analysis was used to identify common themes.RESULTS: Participants' disability-related research experiences were characterized by: 1) disability-related facilitators to research participation, including benefits of research participation and disability-conscious approaches; 2) disability-related logistical barriers to research participation; and 3) research procedures, and the perception of research as minimally burdensome relative to clinical encounters.CONCLUSION: Parents of children in the UDN make considerable investments of time and resources to accommodate their children's disabilities to facilitate their participation. Future research should explore these issues in other genomic research studies and practical approaches to mitigating barriers and employing facilitators to disability-related research participation.

  View details for DOI 10.1016/j.gim.2026.102663

  View details for PubMedID 42439107

• Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing. Genome biology Ferrasse, A., Mendez, R., Gorzynski, J. E., Reuter, C., Carter, J. N., Blas, M., Bernstein, J. A., Wheeler, M. T., Banal, J. L., Ashley, E. A. 2026; 27 (1)

  Abstract

  Native long-read DNA sequencing simultaneously captures genetic variants and epigenetic modifications from single molecules, but preserving molecular length and base modifications currently depends on cold-chain infrastructure that limits access to well-resourced settings.We demonstrate that ensilication, the encapsulation of DNA within silica matrices, preserves DNA at ambient temperature for 30 days with sequencing performance equivalent to conventional - 80 °C freezing. Across three Genome-in-a-Bottle reference genomes, ensilicated and frozen samples show no significant differences in read length (N50 ~ 8,000-11,000 bp), variant-calling accuracy, or genome-wide CpG methylation. Single-read methylation calls benchmarked against an independent bisulfite-sequencing reference confirm that ensilication introduces no detectable bias, with per-read accuracy differing by less than 0.4% between preservation conditions. Ensilicated DNA tolerates repeated handling better than frozen samples and maintains fragment integrity under accelerated weathering. In two patients with rare genetic disorders, ambient-preserved DNA resolves a de novo variant in the segmentally duplicated GTF2I locus and detects methylation patterns consistent with KDM2A-related disorder.Ensilication enables diagnostic-quality native long-read sequencing without cold-chain infrastructure, supporting ambient storage and transport while preserving both sequence and methylation information.

  View details for DOI 10.1186/s13059-026-04137-4

  View details for PubMedID 42298673

  View details for PubMedCentralID 7006217

• Population-scale detection of methylation outliers from long-read genome sequencing. medRxiv : the preprint server for health sciences Jensen, T. D., Kaur, R., Bonner, D. E., Nguyen, J., Reuter, C. M., Ashley, E. A., Bernstein, J. A., Wheeler, M. T., Montgomery, S. B. 2026

  Abstract

  Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited.We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA.METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion.METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

  View details for DOI 10.64898/2026.06.09.26355279

  View details for PubMedID 42326780

  View details for PubMedCentralID PMC13278280

• Author Correction: Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes. Nature genetics Rius, R., Blakes, A. J., Chen, Y., De Jonghe, J., Lecoquierre, F., Dawes, R., Cogne, B., Kim, H. C., Alvi, J. R., Amblard, F., Ansari, M., Arlt, A., Austin-Tse, C., Baer, S., Balasubramanian, M., Balton, E. V., Barcia, G., Beleza-Meireles, A., Bernstein, J. A., Beygo, J., Blanc, P., Bramswig, N. C., Braun, F., Buchzik, D., Calame, D. G., Campbell, J., Coutton, C., Cunningham, C. A., Dargie, N., Depienne, C., Dipple, K. M., Dieux, A., Dixit, A., Dreyer, L., Du, H., El Chehadeh, S., Field, M., Ewans, L. J., Geiger, V., Gibbs, R. A., Glass, I., Grunewald, O., Gueguen, P., Haack, T. B., Hadj Abdallah, H., Harbuz, R., Helbig, I., Horvath, J., Hustinx, A., Isidor, B., Jacquemont, M. L., Jamie, F., Jeanne, M., Kessler, R., Klinkhammer, H., Korenke, G. C., Kotzaeridou, U., Krawitz, P., Laurie, S., Leventer, R. J., Levy, R. J., Lupski, J. R., Marijon, P., McGinnis, K. E., Mendez, R., Messaoud, O., Nava, C., Nizard, M., O'Donnell-Luria, A., O'Leary, M. C., Olivieri, S., Parida, A., Pehlivan, D., Prentice, A. J., Posey, J. E., Reuter, C. M., Satre, V., Schluth-Bolard, C., Smol, T., Sultan, T., Taylor, J., Thauvin-Robinet, C., Thevenon, J., Uebergang, E., Ueberberg, S., Vincent-Delorme, C., Wassmer, E., Westwood, E., Wheeler, M. T., Gulec, E. Y., Vanderver, A., Vossough, A., Sanders, S. J., Banka, S., Findlay, G. M., MacArthur, D. G., Simons, C., Whiffin, N. 2026

  View details for DOI 10.1038/s41588-026-02636-5

  View details for PubMedID 42151417

• Biallelic variants in the noncoding RNA gene RNU4-2 cause a recessive neurodevelopmental syndrome with distinct white matter changes. Nature genetics Rius, R., Blakes, A. J., Chen, Y., De Jonghe, J., Lecoquierre, F., Dawes, R., Cogne, B., Kim, H. C., Alvi, J. R., Amblard, F., Ansari, M., Arlt, A., Austin-Tse, C., Baer, S., Balasubramanian, M., Balton, E. V., Barcia, G., Beleza-Meireles, A., Bernstein, J. A., Beygo, J., Blanc, P., Bramswig, N. C., Braun, F., Buchzik, D., Calame, D. G., Campbell, J., Coutton, C., Cunningham, C. A., Dargie, N., Depienne, C., Dipple, K. M., Dieux, A., Dixit, A., Dreyer, L., Du, H., El Chehadeh, S., Field, M., Ewans, L. J., Geiger, V., Gibbs, R. A., Glass, I., Grunewald, O., Gueguen, P., Haack, T. B., Hadj Abdallah, H., Harbuz, R., Helbig, I., Horvath, J., Hustinx, A., Isidor, B., Jacquemont, M. L., Jamie, F., Jeanne, M., Kessler, R., Klinkhammer, H., Korenke, G. C., Kotzaeridou, U., Krawitz, P., Laurie, S., Leventer, R. J., Levy, R. J., Lupski, J. R., Marijon, P., McGinnis, K. E., Mendez, R., Messaoud, O., Nava, C., Nizard, M., O'Donnell-Luria, A., O'Leary, M. C., Olivieri, S., Parida, A., Pehlivan, D., Prentice, A. J., Posey, J. E., Reuter, C. M., Satre, V., Schluth-Bolard, C., Smol, T., Sultan, T., Taylor, J., Thauvin-Robinetvin, C., Thevenon, J., Uebergang, E., Ueberberg, S., Vincent-Delorme, C., Wassmer, E., Westwood, E., Wheeler, M. T., Gulec, E. Y., Vanderver, A., Vossough, A., Sanders, S. J., Banka, S., Findlay, G. M., MacArthur, D. G., Simons, C., Whiffin, N. 2026

  Abstract

  Genetic variants in RNU4-2, which is transcribed into the U4 small nuclear RNA component of the major spliceosome, were recently shown to cause ReNU syndrome, a prevalent dominant neurodevelopmental disorder (NDD). These variants almost exclusively arise de novo and cluster within 18 nucleotides of RNU4-2. Here we describe a new recessive NDD associated with homozygous and compound heterozygous variants in RNU4-2. We identify 38 individuals with biallelic variants outside the 18-nucleotide ReNU syndrome region that cluster within other functionally important elements of U4: Stem II, the k-turn and the Sm protein binding site. We characterize the clinical phenotype in 31 individuals, demonstrating that the recessive disorder is clinically distinct from ReNU syndrome and is associated with distinctive white matter abnormalities, including enlarged perivascular spaces. Finally, we find reduced RNU4-2 transcript levels in individuals with the recessive disorder, suggesting a loss-of-function disease mechanism that is distinct from the mechanism underlying ReNU syndrome. Together, these findings expand the genotypic and phenotypic spectrum of RNU4-2-associated NDDs.

  View details for DOI 10.1038/s41588-026-02554-6

  View details for PubMedID 41951959

  View details for PubMedCentralID 3119917

• A mixed methods approach to understanding patient outcomes in cardiovascular genetic counseling. Journal of genetic counseling Lewis, E., Naik, H., Cragun, D., Zierhut, H., Reuter, C., Ison, H. 2026; 35 (2): e70179

  Abstract

  Genetic counselors (GCs) utilize a variety of skills while counseling patients. However, it remains unclear whether the frequency or types of skills used impact patient outcomes. We explored the use of specific GC communication skills in cardiology and their impact on empowerment and therapeutic alliance. Adults attending an initial cardiovascular GC appointment completed pre-visit and post-visit surveys. Measures included the Genetic Counseling Outcomes Scale (GCOS) and the Working Alliance Inventory (WAI). GC appointments were audio-recorded, transcribed, and coded using the Genetic Counseling Skills Checklist (GCSC). WAI and change in GCOS scores following the GC visit were stratified into high- and low-scoring groups for comparative analyses. Descriptive analyses were used to identify GCSC code patterns across sessions with high and low WAI and GCOS scores. Seventeen participants (65% female, mean age: 61 years) completed the study. Cases from seven GCs were included across four indications: cardiomyopathy, arrhythmia, dyslipidemia, and aortopathy. There was an increase in empowerment after GC appointments (p = 0.0007), with nearly half (8/17) of participants exhibiting a clinically meaningful increase. Sessions showed a diverse set of skills used across eight domains on the GCSC. Skills around mutual agenda setting, focus on patients' emotions, and facilitating decision-making were used more frequently in higher WAI-scoring sessions. However, when comparing participants who exhibited clinically meaningful changes in empowerment to those who did not, there was little difference in the skills used in sessions, though some skills may have been used more frequently with patients who demonstrated smaller changes in empowerment (e.g., eliciting ways to overcome barriers to taking action). This is the first application of the GCSC in nonsimulated patient settings. We observed trends suggesting varying use of GC skills may contribute to differences in therapeutic alliance and that GCs alter the skills they use for different patients.

  View details for DOI 10.1002/jgc4.70179

  View details for PubMedID 41742399

• DNASE1L3 Deficiency With Novel Missense Variant: Enzymatic and Plasma Fragmentomic Evidence of Pathogenicity and Partial Response to JAK Blockade ACR OPEN RHEUMATOLOGY Tenorio, A., Sugio, T., Cheng, J., Bonner, D. E., Esfahani, M., Kasinathan, S., Hsu, J. J., Moyer, A., Vera, L., Carter, J., Reuter, C. M., Marwaha, S., Balboni, I., Wheeler, M. T., Bernstein, J. A., Alizadeh, A., Gomez-Ospina, N. 2026; 8 (2)

  View details for DOI 10.1002/acr2.70184

  View details for Web of Science ID 001697626100001

• DNASE1L3 Deficiency With Novel Missense Variant: Enzymatic and Plasma Fragmentomic Evidence of Pathogenicity and Partial Response to JAK Blockade. ACR open rheumatology Leon Tenorio, A. A., Sugio, T., Cheng, J., Bonner, D. E., Esfahani, M. S., Kasinathan, S., Hsu, J. J., Moyer, A., Pimentel Vera, L., Carter, J., Reuter, C. M., Marwaha, S., Balboni, I., Wheeler, M. T., Bernstein, J. A., Alizadeh, A., Gomez-Ospina, N. 2026; 8 (2): e70184

  Abstract

  Biallelic loss-of-function variants in DNASE1L3 cause inherited systemic lupus erythematosus and hypocomplementemic urticarial vasculitis. These disorders arise from defective clearance of extracellular chromatin, leading to autoantibody formation, immune complex deposition, and complement consumption. The full clinical and therapeutic spectrum of DNASE1L3 deficiency remains incompletely defined.We evaluated a 24-year-old woman with lifelong systemic inflammation characterized by polyarthritis, urticarial vasculitis, episcleritis, recurrent abdominal pain with intestinal angioedema, and persistent hypocomplementemia. Testing included autoantibody profiling, whole-exome sequencing, DNASE1L3 enzymatic assays in cell lysates and supernatants, and plasma analysis of cell-free DNA fragmentation.The patient lacked antinuclear, anti-double-stranded DNA, and anti-Smith antibodies, though antiphospholipid antibodies were intermittently positive. The disease was refractory to multiple immunosuppressive agents but showed partial improvement with JAK inhibition. Genetic analysis revealed compound heterozygous DNASE1L3 variants: a pathogenic frameshift (c.290_291delCA) and a novel missense change (c.179T>G, p.Ile60Ser). Functional testing showed markedly impaired DNA degradation for both variants, with residual activity in the missense mutant. Plasma DNA analysis demonstrated reduced mononucleosomal peaks, altered fragment length distribution, and loss of cytosine-cytosine-rich end motifs, confirming reduced nuclease activity in vivo.This case supports the pathogenicity of the DNASE1L3 p.Ile60Ser variant broadening the genetic spectrum. Plasma DNA fragment analysis provides a sensitive biomarker of impaired nuclease function, and JAK inhibition may offer partial therapeutic benefit in DNASE1L3-related systemic inflammation.

  View details for DOI 10.1002/acr2.70184

  View details for PubMedID 42396794

  View details for PubMedCentralID PMC12928082

• Stanford Center for Undiagnosed Diseases: a decade of advancing genetic diagnosis and discovery Bonner, D., Carter, J., Reuter, C., Marwaha, S., Kravets, E., Hom, J., Sampson, J., Fisher, P., Ashley, E., Tabor, H., Halley, M., Wheeler, M., Bernstein, J., The Undiagnosed Diseases Network SPRINGERNATURE. 2025: 877

  View details for Web of Science ID 001671157904285

• Clinical Validity of Autosomal Dominant ALPK3 Loss-of-Function Variants as a Cause of Hypertrophic Cardiomyopathy. Circulation. Genomic and precision medicine Hespe, S., Singer, E. S., Reuter, C., Murray, B., Jordan, E., Chowns, J., Peters, S., Mayers, M., Gray, B., Hershberger, R. E., Owens, A., Semsarian, C., Waddell, A., Asatryan, B., Owens, E., Thaxton, C., Adduru, M. L., Anderson, K., Brown, E. E., Hoffman-Andrews, L., Stafford, F., Bagnall, R. D., Bronicki, L., Callewaert, B., Chahal, C. A., James, C. A., Jarinova, O., Landstrom, A. P., McNally, E. M., Muiño-Mosquera, L., Parikh, V., Walsh, R., Wayburn, B., Ware, J. S., Parker, B. L., Porrello, E. R., Elliott, D. A., McNamara, J. W., Ingles, J. 2025: e004976

  View details for DOI 10.1161/CIRCGEN.124.004976

  View details for PubMedID 40255155

• Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. Genome research 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. 2025

  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 Technologies 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 2.4× 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 do not 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 toward improving the prioritization of functional SVs and TREs in rare disease patients.

  View details for DOI 10.1101/gr.279323.124

  View details for PubMedID 40113264

• Genes Associated With Hypertrophic Cardiomyopathy: A Reappraisal by the ClinGen Hereditary Cardiovascular Disease Gene Curation Expert Panel. Journal of the American College of Cardiology Hespe, S., Waddell, A., Asatryan, B., Owens, E., Thaxton, C., Adduru, M. L., Anderson, K., Brown, E. E., Hoffman-Andrews, L., Jordan, E., Josephs, K., Mayers, M., Peters, S., Stafford, F., Bagnall, R. D., Bronicki, L., Callewaert, B., Chahal, C. A., James, C. A., Jarinova, O., Landstrom, A. P., McNally, E. M., Murray, B., Muiño-Mosquera, L., Parikh, V., Reuter, C., Walsh, R., Wayburn, B., Ware, J. S., Ingles, J. 2025; 85 (7): 727-740

  Abstract

  Hypertrophic cardiomyopathy (HCM) is an inherited cardiac condition affecting ∼1 in 500 and exhibits marked genetic heterogeneity. Previously published in 2019, 57 HCM-associated genes were curated providing the first systematic evaluation of gene-disease validity.The authors report work by the Clinical Genome Resource Hereditary Cardiovascular Disease (HCVD) Gene Curation Expert Panel (GCEP) to reappraise the clinical validity of previously curated and new putative HCM genes.The Clinical Genome Resource systematic gene curation framework was used to reclassify the gene-disease relationships for HCM and related syndromic entities involving left ventricular hypertrophy. Genes previously curated were included if their classification was not definitive, and if the time since curation was >2 to 3 years. New genes with literature assertions for HCM were included for initial evaluation. Existing genes were curated for new inheritance patterns where evidence existed. Curations were presented on twice monthly calls, with the HCVD GCEP composed of 29 individuals from 21 institutions across 6 countries.Thirty-one genes were recurated and an additional 5 new potential HCM-associated genes were curated. Among the recurated genes, 17 (55%) genes changed classification: 1 limited and 4 disputed (from no known disease relationship), 9 disputed (from limited), and 3 definitive (from moderate). Among these, 3 (10%) genes had a clinically relevant upgrade, including TNNC1, a 9th sarcomere gene with definitive HCM association. With new evidence, 2 genes were curated for multiple inheritance patterns (TRIM63, disputed for autosomal dominant but moderate for autosomal recessive; ALPK3, strong for autosomal dominant and definitive for recessive). CSRP3 was curated for a semidominant mode of inheritance (definitive). Nine (29%) genes were downgraded to disputed, further discouraging clinical reporting of variants in these genes. Five genes recently reported to cause HCM were curated: RPS6KB1 and RBM20 (limited), KLHL24 and MT-TI (moderate), and FHOD3 (definitive).We report 29 genes with definitive, strong, or moderate evidence of causation for HCM or isolated left ventricular hypertrophy, including sarcomere, sarcomere-associated, and syndromic conditions.

  View details for DOI 10.1016/j.jacc.2024.12.010

  View details for PubMedID 39971408

• Arrhythmic Risk Stratification of Carriers of Filamin C Truncating Variants. JAMA cardiology Filamin C Registry Consortium, Gigli, M., Stolfo, D., Barbati, G., Graw, S., Chen, S. N., Merlo, M., Medo, K., Gregorio, C., Dal Ferro, M., Paldino, A., Perotto, M., Peter van Tintelen, J., Te Riele, A. S., Baas, A. F., Wilde, A. M., Amin, A. S., Houweling, A. C., Elliott, P., Cannie, D., Michels, M., Schoonvelde, S. A., Prasad, S., Tayal, P. U., Yazdani, M., Morris-Rosendahl, D., Garcia-Pavia, P., Cabrera-Romero, E., Bauce, B., Pilichou, K., Fatkin, D., Johnson, R., Judge, D. P., Foil, K. L., Heymans, S., Verdonschot, J. A., Stroeks, S. L., Lakdawala, N. K., Anisha, P., O'Neill, M., Shoemaker, M. B., Roden, D. M., Calkins, H., James, C. A., Murray, B., Parikh, V. N., Ashley, E. A., Reuter, C., Imazio, M., Canepa, M., Ameri, P., Song, J., Sinagra, G., Taylor, M. R., Mestroni, L. 2025

  Abstract

  Importance: Filamin C truncating variants (FLNCtv) are a rare cause of cardiomyopathy with heterogeneous phenotypic presentations. Despite a high incidence of life-threatening ventricular arrhythmias and sudden cardiac death (SCD), reliable risk predictors to stratify carriers of FLNCtv are lacking.Objective: To determine factors predictive of SCD/major ventricular arrhythmias (MVA) in carriers of FLNCtv.Design, Setting, and Participants: This was an international, multicenter, retrospective cohort study conducted from February 2023 to June 2024. The Filamin C Registry Consortium included 19 referral centers for genetic cardiomyopathies worldwide. Participants included carriers of pathogenic or likely pathogenic FLNCtv. Phenotype negative was defined as the absence of any pathological findings detected by 12-lead electrocardiogram (ECG), Holter ECG monitoring, echocardiography, or cardiac magnetic resonance.Exposures: Composite of SCD and MVA in carriers of FLNCtv.Main Outcomes and Measures: The primary outcome was a composite of SCD and MVA, the last including aborted SCD, sustained ventricular tachycardia, and appropriate implantable cardioverter-defibrillator (ICD) interventions.Results: Among 308 individuals (median [IQR] age, 45 [33-56] years; 160 male [52%]) with FLNCtv, 112 (36%) were probands, and 72 (23%) were phenotype negative. Median (IQR) left ventricular ejection fraction (LVEF) was 51% (38%-59%); 89 participants (34%) had LVEF less than 45%, and 50 (20%) had right ventricular dysfunction. During a median (IQR) follow-up of 34 (8-63) months, 57 individuals (19%) experienced SCD/MVA, with an annual incidence rate of 4 cases per 100 person-years (95% CI, 3-6). Incidence rates were higher in probands vs nonprobands and in phenotype-positive vs phenotype-negative individuals. A predictive model estimating SCD/MVA risk was derived from multivariable analysis, which included older age, male sex, previous syncope, nonsustained ventricular tachycardia, and LVEF with a time-dependent area under the curve (AUC) ranging between 0.76 (95% CI, 0.67-0.86) at 12 months and 0.78 (95% CI, 0.70-0.86) at 72 months. Notably, the association of LVEF with the SCD/MVA risk was not linear, showing significant lower risk for values of LVEF greater than 58%, and no increase for values less than 58%. Internal validation with bootstrapping confirmed good accuracy and calibration of the model. Results were consistent in subgroups analysis (ie, phenotype-positive carriers and phenotype-positive carriers without MVA at onset).Conclusions and Relevance: Results suggest that the risk of SCD/MVA in phenotype-positive carriers of FLNCtv was high. A 5-variable predictive model derived from this cohort allows risk estimation and could support clinicians in the shared decision for prophylactic ICD implantation. External cohort validation is warranted.

  View details for DOI 10.1001/jamacardio.2024.5543

  View details for PubMedID 39937464

• Researcher views on returning results from multi-omics data to research participants: insights from The Molecular Transducers of Physical Activity Consortium (MoTrPAC) Study. BMC medical ethics Ormond, K. E., Stanclift, C., Reuter, C. M., Carter, J. N., Murphy, K. E., Lindholm, M. E., Wheeler, M. T. 2025; 26 (1): 22

  Abstract

  There is growing consensus in favor of returning individual specific research results that are clinically actionable, valid, and reliable. However, deciding what and how research results should be returned remains a challenge. Researchers are key stakeholders in return of results decision-making and implementation. Multi-omics data contains medically relevant findings that could be considered for return. We sought to understand researchers' views regarding the potential for return of results for multi-omics data from a large, national consortium generating multi-omics data.Researchers from the Molecular Transducers of Physical Activity Consortium (MoTrPAC) were recruited for in-depth semi-structured interviews. To assess understanding of potential clinical utility for types of data collected and attitudes towards return of results in multi-omic clinical studies, we devised an interview guide focusing on types of results generated in the study for hypothetical return based on review of the literature and professional expertise of team members. The semi-structured interviews were recorded, transcribed verbatim and co-coded. Thematic trends were identified for reporting.We interviewed a total of 16 individuals representative of 11 sites and 6 research roles across MoTrPAC. Many respondents expressed positive attitudes regarding hypothetical multi-omics results return, citing participant rights to their data and perception of minimal harm. Ethical and logistical concerns around the return of multi-omics results were raised, and they often mirrored those in the published literature for genomic return of results including: uncertain clinical validity, a lack of expertise to communicate results, and an unclear obligation regarding whether to return multi-omics results. With the exception of privacy concerns, respondents were able to give examples within multi-omics of how each point was relevant. Further, researchers called for more guidance from funding agencies and increased researcher education regarding return of results.Overall, researchers expressed positive attitudes toward multi-omic return of results in principle, particularly if medically actionable. However, competing ethical considerations, logistical constraints, and need for more external guidance were raised as key implementation concerns. Future studies should consider views and experiences of other relevant stakeholders, specifically clinical genomics professionals and study participants, regarding the clinical utility of multi-omics information and multi-omics results return.

  View details for DOI 10.1186/s12910-025-01174-9

  View details for PubMedID 39920727

  View details for PubMedCentralID PMC11804059

• Detailed tandem repeat allele profiling in 1,027 long-read genomes reveals genome-wide patterns of pathogenicity. bioRxiv : the preprint server for biology Danzi, M. C., Xu, I. R., Fazal, S., Dolzhenko, E., Pellerin, D., Weisburd, B., Reuter, C., Sampson, J., Folland, C., Wheeler, M., O'Donnell-Luria, A., Wuchty, S., Ravenscroft, G., Eberle, M. A., Zuchner, S. 2025

  Abstract

  Tandem repeats are a highly polymorphic class of genomic variation that play causal roles in rare diseases but are notoriously difficult to sequence using short-read techniques1,2. Most previous studies profiling tandem repeats genome-wide have reduced the description of each locus to the singular value of the length of the entire repetitive locus3,4. Here we introduce a comprehensive database of 3.6 billion tandem repeat allele sequences from over one thousand individuals using HiFi long-read sequencing. We show that the previously identified pathogenic loci are among the most variable tandem repeat loci in the genome, when incorporating nucleotide resolution sequence content to measure the longest pure motif segment. More broadly, we introduce a novel measure, 'tandem repeat constraint', that assists in distinguishing potentially pathogenic from benign loci. Our approach of measuring variation as 'the length of the longest pure segment' successfully prioritizes pathogenic repeats within their previously published linkage regions. We also present evidence for two novel pathogenic repeat expansion candidates. In summary, this analysis significantly clarifies the potential for short tandem repeat pathogenicity at over 1.7 million tandem repeat loci and will aid the identification of disease-causing repeat expansions.

  View details for DOI 10.1101/2025.01.06.631535

  View details for PubMedID 39868092

  View details for PubMedCentralID PMC11760257

• Re-evaluating the clinical validity of hypertrophic cardiomyopathy genes Hespe, S., Waddell, A., Asatryan, B., Owens, E., Thaxton, C., Adduru, M., Anderson, K., Brown, E., Hoffman-Andrews, L., Jordan, E., Mayers, M., Peters, S., Stafford, F., Bagnall, R., Bronicki, L., Callewaert, B., Chahal, A., James, C., Jarinova, O., Landstrom, A., McNally, E., Murray, B., Mosquera, L., Parikh, V., Reuter, C., Walsh, R., Wayburn, B., Ware, J., Ingles, J. SPRINGERNATURE. 2024: 1393-1394

  View details for Web of Science ID 001407868902022

• Re-evaluating the clinical validity of hypertrophic cardiomyopathy genes Hespe, S., Waddell, A., Asatryan, B., Owens, E., Thaxton, C., Adduru, M., Anderson, K., Brown, E., Hoffman-Andrews, L., Jordan, E., Mayers, M., Peters, S., Stafford, F., Bagnall, R., Bronicki, L., Callewaert, B., Chahal, A., James, C., Jarinova, O., Landstrom, A., McNally, E., Murray, B., Mosquera, L., Parikh, V., Reuter, C., Walsh, R., Wayburn, B., Ware, J., Ingles, J. SPRINGERNATURE. 2024: 1393-1394

  View details for Web of Science ID 001421430502103

• The current landscape of clinical exome and genome reanalysis in the U.S. Journal of genetic counseling Frees, M., Carter, J. N., Wheeler, M. T., Reuter, C. 2024

  Abstract

  The majority of patients undergoing exome or genome sequencing receive a nondiagnostic result. Periodic reanalysis is known to increase diagnostic yield from exome sequencing, yet laboratory reanalysis practices are obscure. We sought to define the landscape of exome and genome reanalysis across clinical laboratories. Genetic testing registries were queried to identify eligible clinical genetic laboratories offering exome and/or genome sequencing in the United States. A survey administered to lab representatives investigated reanalysis offerings, policies, perceived uptake, bioinformatic steps, and billing options. The analysis consisted of descriptive statistics. Survey data were collected from 30 of 32 eligible laboratories (93%), comprising 28 exome products and 13 genome products. Reanalysis was widely available for both exomes (n = 27/28, 96%) and genomes (n = 12/13, 92%). Most participating laboratories required ordering providers to initiate reanalysis (n = 24/28, 86%). Most respondents estimated providers initiated reanalysis in less than 10% of all exomes (n = 12/22) or genomes (n = 6/9) sequenced. The approach to reanalysis varied greatly by laboratory. Laboratory approaches to exome and genome reanalysis are highly variable and typically require provider initiation. This could contribute to low reanalysis uptake and increased administrative burden on providers. Further work should emphasize development of clinical exome and genome reanalysis standards.

  View details for DOI 10.1002/jgc4.1968

  View details for PubMedID 39285507

• 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

• ClinGen Hereditary Cardiovascular Disease Gene Curation Expert Panel: Reappraisal of Genes associated with Hypertrophic Cardiomyopathy. medRxiv : the preprint server for health sciences Hespe, S., Waddell, A., Asatryan, B., Owens, E., Thaxton, C., Adduru, M. L., Anderson, K., Brown, E. E., Hoffman-Andrews, L., Jordan, E., Josephs, K., Mayers, M., Peters, S., Stafford, F., Bagnall, R. D., Bronicki, L., Callewaert, B., Chahal, C. A., James, C. A., Jarinova, O., Landstrom, A. P., McNally, E. M., Murray, B., Muiño-Mosquera, L., Parikh, V., Reuter, C., Walsh, R., Wayburn, B., Ware, J. S., Ingles, J. 2024

  Abstract

  Hypertrophic cardiomyopathy (HCM) is an inherited cardiac condition affecting ~1 in 500 and exhibits marked genetic heterogeneity. Previously published in 2019, 57 HCM-associated genes were curated providing the first systematic evaluation of gene-disease validity. Here we report work by the ClinGen Hereditary Cardiovascular Disorders Gene Curation Expert Panel (HCVD-GCEP) to reappraise the clinical validity of previously curated and new putative HCM genes.The ClinGen systematic gene curation framework was used to re-classify the gene-disease relationships for HCM and related syndromic entities involving left ventricular hypertrophy. Genes previously curated were included if their classification was not definitive, and if the time since curation was >2-3 years. New genes with literature assertions for HCM were included for initial evaluation. Existing genes were curated for new inheritance patterns where evidence existed. Curations were presented on twice monthly calls, with the HCVD-GCEP composed of 29 individuals from 21 institutions across 6 countries.Thirty-one genes were re-curated and an additional 5 new potential HCM-associated genes were curated. Among the re-curated genes, 17 (55%) genes changed classification: 1 limited and 4 disputed (from no known disease relationship), 9 disputed (from limited), and 3 definitive (from moderate). Among these, 3 (10%) genes had a clinically relevant upgrade, including TNNC1, a 9th sarcomere gene with definitive HCM association. With new evidence, two genes were curated for multiple inheritance patterns (TRIM63, disputed for autosomal dominant but moderate for autosomal recessive; ALPK3, strong for autosomal dominant and definitive for recessive). CSRP3 was curated for a semi-dominant mode of inheritance (definitive). Nine (29%) genes were downgraded to disputed, further discouraging clinical reporting of variants in these genes. Five genes recently reported to cause HCM were curated: RPS6KB1 and RBM20 (limited), KLHL24 and MT-TI (moderate), and FHOD3 (definitive).We report 29 genes with definitive, strong or moderate evidence of causation for HCM or isolated LVH, including sarcomere, sarcomere-associated and syndromic conditions.

  View details for DOI 10.1101/2024.07.29.24311195

  View details for PubMedID 39132495

  View details for PubMedCentralID PMC11312670

• De novo variants in the RNU4-2 snRNA cause a frequent neurodevelopmental syndrome. Nature Chen, Y., Dawes, R., Kim, H. C., Ljungdahl, A., Stenton, S. L., Walker, S., Lord, J., Lemire, G., Martin-Geary, A. C., Ganesh, V. S., Ma, J., Ellingford, J. M., Delage, E., D'Souza, E. N., Dong, S., Adams, D. R., Allan, K., Bakshi, M., Baldwin, E. E., Berger, S. I., Bernstein, J. A., Bhatnagar, I., Blair, E., Brown, N. J., Burrage, L. C., Chapman, K., Coman, D. J., Compton, A. G., Cunningham, C. A., D'Souza, P., Danecek, P., Délot, E. C., Dias, K. R., Elias, E. R., Elmslie, F., Evans, C. A., Ewans, L., Ezell, K., Fraser, J. L., Gallacher, L., Genetti, C. A., Goriely, A., Grant, C. L., Haack, T., Higgs, J. E., Hinch, A. G., Hurles, M. E., Kuechler, A., Lachlan, K. L., Lalani, S. R., Lecoquierre, F., Leitão, E., Fevre, A. L., Leventer, R. J., Liebelt, J. E., Lindsay, S., Lockhart, P. J., Ma, A. S., Macnamara, E. F., Mansour, S., Maurer, T. M., Mendez, H. R., Metcalfe, K., Montgomery, S. B., Moosajee, M., Nassogne, M. C., Neumann, S., O'Donoghue, M., O'Leary, M., Palmer, E. E., Pattani, N., Phillips, J., Pitsava, G., Pysar, R., Rehm, H. L., Reuter, C. M., Revencu, N., Riess, A., Rius, R., Rodan, L., Roscioli, T., Rosenfeld, J. A., Sachdev, R., Shaw-Smith, C. J., Simons, C., Sisodiya, S. M., Snell, P., St Clair, L., Stark, Z., Stewart, H. S., Tan, T. Y., Tan, N. B., Temple, S. E., Thorburn, D. R., Tifft, C. J., Uebergang, E., VanNoy, G. E., Vasudevan, P., Vilain, E., Viskochil, D. H., Wedd, L., Wheeler, M. T., White, S. M., Wojcik, M., Wolfe, L. A., Wolfenson, Z., Wright, C. F., Xiao, C., Zocche, D., Rubenstein, J. L., Markenscoff-Papadimitriou, E., Fica, S. M., Baralle, D., Depienne, C., MacArthur, D. G., Howson, J. M., Sanders, S. J., O'Donnell-Luria, A., Whiffin, N. 2024

  Abstract

  Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 115 individuals with NDD. Most individuals (77.4%) have the same highly recurrent single base insertion (n.64_65insT). In 54 individuals where it could be determined, the de novo variants were all on the maternal allele. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to RNU4-1 and other U4 homologs. Using RNA-sequencing, we show how 5' splice site usage is systematically disrupted in individuals with RNU4-2 variants, consistent with the known role of this region during spliceosome activation. Finally, we estimate that variants in this 18 bp region explain 0.4% of individuals with NDD. This work underscores the importance of non-coding genes in rare disorders and will provide a diagnosis to thousands of individuals with NDD worldwide.

  View details for DOI 10.1038/s41586-024-07773-7

  View details for PubMedID 38991538

• 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

• De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. medRxiv : the preprint server for health sciences Chen, Y., Dawes, R., Kim, H. C., Stenton, S. L., Walker, S., Ljungdahl, A., Lord, J., Ganesh, V. S., Ma, J., Martin-Geary, A. C., Lemire, G., D'Souza, E. N., Dong, S., Ellingford, J. M., Adams, D. R., Allan, K., Bakshi, M., Baldwin, E. E., Berger, S. I., Bernstein, J. A., Brown, N. J., Burrage, L. C., Chapman, K., Compton, A. G., Cunningham, C. A., D'Souza, P., Délot, E. C., Dias, K. R., Elias, E. R., Evans, C. A., Ewans, L., Ezell, K., Fraser, J. L., Gallacher, L., Genetti, C. A., Grant, C. L., Haack, T., Kuechler, A., Lalani, S. R., Leitão, E., Fevre, A. L., Leventer, R. J., Liebelt, J. E., Lockhart, P. J., Ma, A. S., Macnamara, E. F., Maurer, T. M., Mendez, H. R., Montgomery, S. B., Nassogne, M. C., Neumann, S., O'Leary, M., Palmer, E. E., Phillips, J., Pitsava, G., Pysar, R., Rehm, H. L., Reuter, C. M., Revencu, N., Riess, A., Rius, R., Rodan, L., Roscioli, T., Rosenfeld, J. A., Sachdev, R., Simons, C., Sisodiya, S. M., Snell, P., Clair, L., Stark, Z., Tan, T. Y., Tan, N. B., Temple, S. E., Thorburn, D. R., Tifft, C. J., Uebergang, E., VanNoy, G. E., Vilain, E., Viskochil, D. H., Wedd, L., Wheeler, M. T., White, S. M., Wojcik, M., Wolfe, L. A., Wolfenson, Z., Xiao, C., Zocche, D., Rubenstein, J. L., Markenscoff-Papadimitriou, E., Fica, S. M., Baralle, D., Depienne, C., MacArthur, D. G., Howson, J. M., Sanders, S. J., O'Donnell-Luria, A., Whiffin, N. 2024

  Abstract

  Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes1. Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome2. We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.

  View details for DOI 10.1101/2024.04.07.24305438

  View details for PubMedID 38645094

  View details for PubMedCentralID PMC11030480

• 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

• 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

• RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci. Genome biology Fazal, S., Danzi, M. C., Xu, I., Kobren, S. N., Sunyaev, S., Reuter, C., Marwaha, S., Wheeler, M., Dolzhenko, E., Lucas, F., Wuchty, S., Tekin, M., Züchner, S., Aguiar-Pulido, V. 2024; 25 (1): 39

  Abstract

  Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional pathogenic repeat expansions will narrow the diagnostic gap in many diseases. A growing number of TR expansions are being identified, and interpreting them is a challenge. We present RExPRT (Repeat EXpansion Pathogenicity pRediction Tool), a machine learning tool for distinguishing pathogenic from benign TR expansions. Our results demonstrate that an ensemble approach classifies TRs with an average precision of 93% and recall of 83%. RExPRT's high precision will be valuable in large-scale discovery studies, which require prioritization of candidate loci for follow-up studies.

  View details for DOI 10.1186/s13059-024-03171-4

  View details for PubMedID 38297326

  View details for PubMedCentralID 7425049

• Arrhythmias including Atrial Fibrillation and Congenital Heart Disease in Kleefstra Syndrome: a possible epigenetic link. 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 Vasireddi, S. K., Draksler, T. Z., Bouman, A., Kummeling, J., Wheeler, M., Reuter, C., Srivastava, S., Harris, J., Fisher, P. G., Narayan, S. M., Wang, P. J., Badhwar, N., Kleefstra, T., Perez, M. V. 2024

  Abstract

  BACKGROUND: Kleefstra syndrome (KS), often diagnosed in early childhood, is a rare genetic disorder due to haploinsufficiency of EHMT1 and is characterized by neuromuscular and intellectual developmental abnormalities. Although congenital heart disease (CHD) is common, the prevalence of arrhythmias and CHD subtypes in KS is unknown.METHODS: Inspired by a novel case series of KS patients with atrial tachyarrhythmias in the USA, we evaluate the two largest known KS registries for arrhythmias and CHD: Radboudumc (50 patients) based on health record review at Radboud University Medical Center in the Netherlands, and GenIDA (163 patients) based on world-wide surveys of patient families.RESULTS: Three KS patients (aged 17-25 years) presented with atrial tachyarrhythmias without manifest CHD. In the international KS registries, the median(IQR) age was considerably younger; GenIDA/Radboudumc at 10/13.5 (12/13) years respectively. Both registries had a 40% prevalence of cardiovascular abnormalities, the majority being CHD, including septal defects, vascular malformations, and valvular disease. Interestingly, 4 (8%) patients in the Radboudumc registry reported arrhythmias without CHD, including one AF, two with supraventricular tachycardias (SVTs), and one with non-sustained ventricular tachycardia. The GenIDA registry reported one patient with AF and another with chronic ectopic atrial tachycardia. In total, atrial tachyarrhythmias were noted in six young KS patients (6/213 or 3%) with at least four (3 AF and 1 AT) without structural heart disease.CONCLUSION: In addition to a high prevalence of CHD, evolving data reveals early-onset atrial tachyarrhythmias in young KS patients, including AF, even in the absence of structural heart disease.

  View details for DOI 10.1093/europace/euae003

  View details for PubMedID 38195854

• 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

• Beyond the exome: What's next in diagnostic testing for Mendelian conditions. American journal of human genetics Wojcik, M. H., Reuter, C. M., Marwaha, S., Mahmoud, M., Duyzend, M. H., Barseghyan, H., Yuan, B., Boone, P. M., Groopman, E. E., Délot, E. C., Jain, D., Sanchis-Juan, A., Starita, L. M., Talkowski, M., Montgomery, S. B., Bamshad, M. J., Chong, J. X., Wheeler, M. T., Berger, S. I., O'Donnell-Luria, A., Sedlazeck, F. J., Miller, D. E. 2023; 110 (8): 1229-1248

  Abstract

  Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.

  View details for DOI 10.1016/j.ajhg.2023.06.009

  View details for PubMedID 37541186

• 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

• 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

• A concurrent dual analysis of genomic data augments diagnoses: experiences of two clinical sites in the Undiagnosed Diseases Network. Genetics in medicine : official journal of the American College of Medical Genetics Spillmann, R. C., Tan, Q. K., Reuter, C., Schoch, K., Kohler, J., Bonner, D., Zastrow, D., Alkelai, A., Baugh, E., Cope, H., Marwaha, S., Wheeler, M. T., Bernstein, J. A., Shashi, V. 2022

  Abstract

  Next generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultra-rare conditions. However, diagnosis rates differ between analytical pipelines. In the NIH-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice.A retrospective review was performed at two UDN clinical sites, to compare variants, and diagnoses/candidate genes identified with the dual analyses of the NGS data.Ninety-five individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, while the clinical sites prioritized more research variants/candidate genes (p <0.001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the two pipelines were more often due to variant prioritization disparities, than variant detection.The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provides a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.

  View details for DOI 10.1016/j.gim.2022.12.001

  View details for PubMedID 36481303

• Patient experiences with clinical confirmatory genetic testing after using direct-to-consumer raw DNA and third-party genetic interpretation services. Translational behavioral medicine Nguyen Dolphyn, T. T., Ormond, K. E., Weissman, S. M., Kim, H. J., Reuter, C. M. 2022

  Abstract

  The availability of raw DNA and genetic interpretation tools allow individuals to access genetic health risk information, where analytical false-positives exist. Little is known about the experience of individuals who receive pathogenic or likely pathogenic variant(s) through raw DNA interpretation and follow-up with clinical confirmatory genetic testing. This qualitative study set out to describe the experiences of individuals who pursued clinical confirmatory genetic testing, including their perception of the process. Participants were recruited from social media and eligible if they discovered a potential pathogenic or likely pathogenic variant in a raw DNA interpretation report, completed clinical confirmatory genetic testing in the U.S., and provided documentation of those results. Individuals participated in semi-structured interviews, which were transcribed and inductively coded to identify themes. Of the 12 participants, 3 received clinical genetic testing results that confirmed pathogenic or likely pathogenic variants noted in raw DNA interpretation reports (confirmation positive), and 9 were not confirmed. Nearly all (n = 11) participants described emotional distress and information-seeking behavior as a coping mechanism after discovering a pathogenic or likely pathogenic variant in raw DNA interpretation. When pursuing confirmatory genetic testing, many (n = 9) faced challenges with finding knowledgeable healthcare providers and obtaining insurance coverage. Despite reporting concerns over raw DNA interpretation and a desire for more safeguards, almost all (n = 10) participants stated interest in using the service again. Overall, participants' experiences reveal they find personal utility in raw DNA interpretation results and provide insight into opportunities for patient and provider education.

  View details for DOI 10.1093/tbm/ibac083

  View details for PubMedID 36327324

• 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

• 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

• Correction to: The genetic architecture of Plakophilin 2 cardiomyopathy. Genetics in medicine : official journal of the American College of Medical Genetics Dries, A. M., Kirillova, A., Reuter, C. M., Garcia, J., Zouk, H., Hawley, M., Murray, B., Tichnell, C., Pilichou, K., Protonotarios, A., Medeiros-Domingo, A., Kelly, M. A., Baras, A., Ingles, J., Semsarian, C., Bauce, B., Celeghin, R., Basso, C., Jongbloed, J. D., Nussbaum, R. L., Funke, B., Cerrone, M., Mestroni, L., Taylor, M. R., Sinagra, G., Merlo, M., Saguner, A. M., Elliott, P. M., Syrris, P., van Tintelen, J. P., Regeneron Genetics Center, James, C. A., Haggerty, C. M., Parikh, V. N. 2021

  View details for DOI 10.1038/s41436-021-01298-4

  View details for PubMedID 34408292

• 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

• The genetic architecture of Plakophilin 2 cardiomyopathy. Genetics in medicine : official journal of the American College of Medical Genetics Dries, A. M., Kirillova, A., Reuter, C. M., Garcia, J., Zouk, H., Hawley, M., Murray, B., Tichnell, C., Pilichou, K., Protonotarios, A., Medeiros-Domingo, A., Kelly, M. A., Baras, A., Ingles, J., Semsarian, C., Bauce, B., Celeghin, R., Basso, C., Jongbloed, J. D., Nussbaum, R. L., Funke, B., Cerrone, M., Mestroni, L., Taylor, M. R., Sinagra, G., Merlo, M., Saguner, A. M., Elliott, P. M., Syrris, P., van Tintelen, J. P., Regeneron Genetics Center, James, C. A., Haggerty, C. M., Parikh, V. N. 2021

  Abstract

  PURPOSE: The genetic architecture of Plakophilin 2 (PKP2) cardiomyopathy can inform our understanding of its variant pathogenicity and protein function.METHODS: We assess the gene-wide and regional association of truncating and missense variants in PKP2 with arrhythmogenic cardiomyopathy (ACM), and arrhythmogenic right ventricular cardiomyopathy (ARVC) specifically. A discovery data set compares genetic testing requisitions to gnomAD. Validation is performed in a rigorously phenotyped definite ARVC cohort and non-ACM individuals in the Geisinger MyCode cohort.RESULTS: The etiologic fraction (EF) of ACM-related diagnoses from truncating variants in PKP2 is significant (0.85 [0.80,0.88], p<2*10-16), increases for ARVC specifically (EF=0.96 [0.94,0.97], p<2*10-16), and is highest in definite ARVC versus non-ACM individuals (EF=1.00 [1.00,1.00], p<2*10-16). Regions of missense variation enriched for ACM probands include known functional domains and the C-terminus, which was not previously known to contain a functional domain. No regional enrichment was identified for truncating variants.CONCLUSION: This multicohort evaluation of the genetic architecture of PKP2 demonstrates the specificity of PKP2 truncating variants for ARVC within the ACM disease spectrum. We identify the PKP2 C-terminus as a potential functional domain and find that truncating variants likely cause disease irrespective of transcript position.

  View details for DOI 10.1038/s41436-021-01233-7

  View details for PubMedID 34120153

• "Doctors can read about it, they can know about it, but they've never lived with it": How parents use social media throughout the diagnostic odyssey. Journal of genetic counseling Deuitch, N. T., Beckman, E., Halley, M. C., Young, J. L., Reuter, C. M., Kohler, J., Bernstein, J. A., Wheeler, M. T., Undiagnosed Diseases Network, Ormond, K. E., Tabor, H. K. 2021

  Abstract

  Parents of children with undiagnosed conditions struggle to obtain information about how to treat and support their children. It can be particularly challenging to find communities and other parents who share their experiences and can provide emotional and informational support. This study sought to characterize how parents use social media, both throughout the diagnostic odyssey and post-diagnosis, to meet their informational, social, and emotional support needs. We conducted qualitative semi-structured interviews with 14 parents from the Stanford site of the Undiagnosed Diseases Network (UDN), including five whose children had received a diagnosis through study participation. Interview recordings were analyzed using inductive, team-based coding and thematic analysis based in grounded theory using Dedoose qualitative analysis software. Through this process, we identified four key themes related to social media use. First, parents struggled to find the "right" community, often seeking out groups of similar patients based on symptoms or similar conditions. Second, though they found much valuable information through social media about caring for their child, they also struggled to interpret the relevance of the information to their own child's condition. Third, the social support and access to other patients' and families' lived experiences were described as both highly valued and emotionally challenging, particularly in the case of poor outcomes for similar families. Finally, parents expressed the need to balance concerns about their child's privacy with the value of transparency and data sharing for diagnosis. Our results suggest that the needs and experiences of undiagnosed patients and families differ from those with diagnosed diseases and highlight the need for support in best utilizing social media resources at different stages of the diagnostic odyssey.

  View details for DOI 10.1002/jgc4.1438

  View details for PubMedID 34096130

• 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. D. 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. G. 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. G. 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. L. 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

• 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

• 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

• 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

• 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

• Understanding variants of uncertain significance in the era of multigene panels: Through the eyes of the patient JOURNAL OF GENETIC COUNSELING Reuter, C., Chun, N., Pariani, M., Hanson-Kahn, A. 2019; 28 (4): 878–86

  View details for DOI 10.1002/jgc4.1130

  View details for Web of Science ID 000482136400016

• 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. 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. G. S., Papp, J. C., Parker, N. H., Pena, L. D. 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

  View details for DOI 10.1002/ajmg.a.61134

  View details for Web of Science ID 000468322800015

• 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. G. 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

• 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

• 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

• Direct-to-consumer raw genetic data and third-party interpretation services: more burden than bargain? GENETICS IN MEDICINE Moscarello, T., Murray, B., Reuter, C. M., Demo, E. 2019; 21 (3): 539-541

  View details for DOI 10.1038/s41436-018-0097-2

  View details for Web of Science ID 000460274400007

  View details for PubMedID 29997392

  View details for PubMedCentralID PMC6752274

• 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. G., Mestroni, L., Merlo, M., Sinagra, G., Semsarian, C., Meder, B., Judge, D. P., Ashley, E. 2019; 12 (3)

  View details for DOI 10.1161/CIRCHEARTFAILURE.118.005371

  View details for Web of Science ID 000469339500003

• 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

• 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

• 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

• Understanding variants of uncertain significance in the era of multigene panels: Through the eyes of the patient. Journal of genetic counseling Reuter, C. n., Chun, N. n., Pariani, M. n., Hanson-Kahn, A. n. 2019

  Abstract

  Variants of uncertain significance (VUSs) are often disclosed to patients despite ambiguous association with disease risk and lack of clinical actionability. It is important to understand how patients understand a VUS result, but few studies have assessed this. Our qualitative study explored patient recall, reaction to, and interpretation of a VUS in the context of multigene panels. We conducted 11 semi-structured phone interviews with adults who had a VUS identified on multigene panel testing in a hereditary oncology clinic, with questions focusing on the VUS result, personal and family history, and motivations for and expectations of genetic testing. Transcripts were coded iteratively, using both deductive and inductive codes. Overall, participants usually recalled that they had a VUS, despite variation in the vocabulary used. Participants responded both emotionally and intellectually to receiving information about having a VUS, which was often a result of their expectations and motivations prior to testing. Overall, participants understood the lack of clinical significance of a VUS, yet often interpreted the etiologic significance of a VUS within the context of the personal and family history. Our study provides insight into a process by which patients translate uncertain genetic testing results into a construct that fits within their current belief framework and which may be facilitated by a genetic counselor.

  View details for PubMedID 31050105

• 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

• 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

  View details for DOI 10.1056/NEJMoa1714458

  View details for Web of Science ID 000451402500008

• 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

  View details for Web of Science ID 000528619405020

• Clinical Cardiovascular Genetic Counselors Take a Leading Role in Team-based Variant Classification JOURNAL OF GENETIC COUNSELING Reuter, C., Grove, M. E., Orland, K., Spoonamore, K., Caleshu, C. 2018; 27 (4): 751–60

  Abstract

  We sought to delineate the genetic test review and interpretation practices of clinical cardiovascular genetic counselors. A one-time anonymous online survey was taken by 46 clinical cardiovascular genetic counselors recruited through the National Society of Genetic Counselors Cardiovascular Special Interest Group. Nearly all (95.7%) gather additional information on variants reported on clinical genetic test reports and most (81.4%) assess the classification of such variants. Clinical cardiovascular genetic counselors typically (81.0%) classify variants in collaboration with cardiologist and/or geneticist colleagues, with the genetic counselor as the team member who is primarily responsible. Variant classification is a relatively recent (mean 3.2 years) addition to practice. Most genetic counselors learned classification skills on the job from clinical and laboratory colleagues. Recent graduates were more likely to have learned this in graduate school (p < 0.001). Genetic counselors are motivated to take responsibility for the classification of variants because of prior experiences with variant reclassification, inconsistencies between laboratories, and incomplete laboratory reports. They are also driven by a sense of professional duty and their proximity to the clinical context. This practice represents a broadening of the skill set of clinical cardiovascular genetic counselors and a unique expertise that they contribute to the interdisciplinary teams in which they work.

  View details for PubMedID 29234989

• 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

  View details for DOI 10.1016/j.jacc.2018.05.029

  View details for Web of Science ID 000438942300010

• 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. L. 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

• 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

• Clinical Characteristics of the GLA N215S Variant and Implications for the Diagnosis and Management of Nonclassic Fabry Disease CIRCULATION-CARDIOVASCULAR GENETICS Reuter, C., Platt, J. 2017; 10 (5)

  View details for DOI 10.1161/CIRCGENETICS.117.001918

  View details for Web of Science ID 000424292400024

  View details for PubMedID 29018007