Swaroop Aradhya

All Publications

• Clinical utility of comprehensive gene panel testing for common and rare causes of skeletal dysplasia and other skeletal disorders: Results from the largest cohort to date. American journal of medical genetics. Part A MacCarrick, G., Aradhya, S., Bailey, M., Chu, D., Hunt, A., Izzo, E., Krakow, D., Mackenzie, W., Poll, S., Raggio, C., Shediac, R., White, K. K., McLaughlin, H. M., Seratti, G. 2024: e63646

  Abstract

  Molecular genetics enables more precise diagnoses of skeletal dysplasia and other skeletal disorders (SDs). We investigated the clinical utility of multigene panel testing for 5011 unrelated individuals with SD in the United States (December 2019-April 2022). Median (range) age was 8 (0-90) years, 70.5% had short stature and/or disproportionate growth, 27.4% had a positive molecular diagnosis (MDx), and 30 individuals received two MDx. Genes most commonly contributing to MDx were FGFR3 (16.9%), ALPL (13.0%), and COL1A1 (10.3%). Most of the 112 genes associated with ≥1 MDx were primarily involved in signal transduction (n = 35), metabolism (n = 23), or extracellular matrix organization (n = 17). There were implications associated with specific care/treatment options for 84.4% (1158/1372) of MDx-positive individuals; >50% were linked to conditions with targeted therapy approved or in clinical development, including osteogenesis imperfecta, achondroplasia, hypophosphatasia, and mucopolysaccharidosis. Forty individuals with initially inconclusive results became MDx-positive following family testing. Follow-up mucopolysaccharidosis enzyme activity testing was positive in 14 individuals (10 of these were not MDx-positive). Our findings showed that inclusion of metabolic genes associated with SD increased the clinical utility of a gene panel and confirmed that integrated use of comprehensive gene panel testing with orthogonal testing reduced the burden of inconclusive results.

  View details for DOI 10.1002/ajmg.a.63646

  View details for PubMedID 38702915

• Early genetic testing in pediatric epilepsy: Diagnostic and cost implications. Epilepsia open Swartwood, S. M., Morales, A., Hatchell, K. E., Moretz, C., McKnight, D., Demmer, L., Chagnon, S., Aradhya, S., Esplin, E. D., Bonkowsky, J. L. 2024; 9 (1): 439-444

  Abstract

  The identification of numerous genetically based epilepsies has resulted in the widespread use of genetic testing to inform epilepsy etiology. Our study aims to investigate whether a difference exists in the diagnostic evaluation and healthcare-related cost expenditures of pediatric patients with epilepsy of unknown etiology who receive a genetic diagnosis through multigene epilepsy panel (MEP) testing and comparing those who underwent early (EGT) versus late genetic testing (LGT). Testing was defined as early (less than 1 year), or late (more than 1 year), following clinical epilepsy diagnosis. A retrospective chart review of pediatric individuals (1-17 years) with epilepsy of unknown etiology who underwent multigene epilepsy panel (MEP) testing identified 28 of 226 (12%) individuals with a pathogenic epilepsy variant [EGT n = 8 (29%); LGT n = 20 (71%)]. The average time from clinical epilepsy diagnosis to genetic diagnosis was 0.25 years (EGT), compared with 7.1 years (LGT). The EGT cohort underwent fewer metabolic tests [EGT n = 0 (0%); LGT n = 16 (80%) (P < 0.01)] and invasive procedures [EGT n = 0 (0%); LGT n = 5 (25%) (P = 0.06)]. Clinical management changes implemented due to genetic diagnosis occurred in 10 (36%) patients [EGT n = 2 (25%); LGT n = 8 (40%) (P = 0.76)]. Early genetic testing with a MEP in pediatric patients with epilepsy of unknown etiology who receive a genetic diagnosis is associated with fewer non-diagnostic tests and invasive procedures and reduced estimated overall healthcare-related costs. PLAIN LANGUAGE SUMMARY: This study aims to investigate whether a difference exists in the diagnostic evaluation and cost expenditures of pediatric patients (1-17 years) with epilepsy of unknown cause who are ultimately diagnosed with a genetic cause of epilepsy through multigene epilepsy panel testing and comparing those who underwent early testing (less than 1 year) versus late testing (more than 1 year) after clinical epilepsy diagnosis. Of the 28 of 226 individuals with a confirmed genetic cause of epilepsy on multigene epilepsy panel testing, performing early testing was associated with fewer non-diagnostic tests, fewer invasive procedures and reduced estimated overall healthcare-related costs.

  View details for DOI 10.1002/epi4.12878

  View details for PubMedID 38071479

  View details for PubMedCentralID PMC10839360

• The myth of the "Genetic Wallflower": in reproductive carrier screening, for every Papageno there is always a Papagena Burnett, L., Gruzin, M., Lee, E., Hobbs, M., Poll, S., Faulkner, N., Aradhya, S. SPRINGERNATURE. 2024: 758

  View details for Web of Science ID 001147414903509

• Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA network open Chen, E., Facio, F. M., Aradhya, K. W., Rojahn, S., Hatchell, K. E., Aguilar, S., Ouyang, K., Saitta, S., Hanson-Kwan, A. K., Capurro, N. N., Takamine, E., Jamuar, S. S., McKnight, D., Johnson, B., Aradhya, S. 2023; 6 (10): e2339571

  Abstract

  Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty.To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them.This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023.The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs.The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification.This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.

  View details for DOI 10.1001/jamanetworkopen.2023.39571

  View details for PubMedID 37878314

• THE AMERICAN COLLEGE OF MEDICAL GENETICS AND GENOMICS (ACMG) TIERED APPROACH TO CARRIER SCREENING: EXPERIENCE WITHIN A DIVERSE PATIENT POPULATION Neitzel, D., Poll, S., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2023: E279

  View details for Web of Science ID 001084670200660

• High-Throughput Splicing Assays Identify Known and Novel WT1 Exon 9 Variants in Nephrotic Syndrome. Kidney international reports Smith, C., Burugula, B. B., Dunn, I., Aradhya, S., Kitzman, J. O., Yee, J. L. 2023; 8 (10): 2117-2125

  Abstract

  Frasier syndrome (FS) is a rare Mendelian form of nephrotic syndrome (NS) caused by variants which disrupt the proper splicing of WT1. This key transcription factor gene is alternatively spliced at exon 9 to produce 2 isoforms ("KTS+" and "KTS-"), which are normally expressed in the kidney at a ∼2:1 (KTS+:KTS-) ratio. FS results from variants that reduce this ratio by disrupting the splice donor of the KTS+ isoform. FS is extremely rare, and it is unclear whether any variants beyond the 8 already known could cause FS.To prospectively identify other splicing-disruptive variants, we leveraged a massively parallel splicing assay. We tested every possible single nucleotide variant (n = 519) in and around WT1 exon 9 for effects upon exon inclusion and KTS+/- ratio.Splice disruptive variants (SDVs) made up 11% of the tested point variants overall and were tightly concentrated near the canonical acceptor and the KTS+/- alternate donors. Our map successfully identified all 8 known FS or focal segmental glomerulosclerosis (FSGS) variants and 16 additional novel variants which were comparably disruptive to these known pathogenic variants. We also identified 19 variants that, conversely, increased the KTS+/KTS- ratio, of which 2 are observed in unrelated individuals with 46,XX ovotesticular disorder of sex development (46,XX OTDSD).This splicing effect map can serve as functional evidence to guide the clinical interpretation of newly observed variants in and around WT1 exon 9.

  View details for DOI 10.1016/j.ekir.2023.07.033

  View details for PubMedID 37850022

  View details for PubMedCentralID PMC10577367

• 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

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

  Abstract

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

  View details for DOI 10.1016/j.gim.2023.100947

  View details for PubMedID 37534744

• Applications of artificial intelligence in clinical laboratory genomics. American journal of medical genetics. Part C, Seminars in medical genetics Aradhya, S., Facio, F. M., Metz, H., Manders, T., Colavin, A., Kobayashi, Y., Nykamp, K., Johnson, B., Nussbaum, R. L. 2023

  Abstract

  The transition from analog to digital technologies in clinical laboratory genomics is ushering in an era of "big data" in ways that will exceed human capacity to rapidly and reproducibly analyze those data using conventional approaches. Accurately evaluating complex molecular data to facilitate timely diagnosis and management of genomic disorders will require supportive artificial intelligence methods. These are already being introduced into clinical laboratory genomics to identify variants in DNA sequencing data, predict the effects of DNA variants on protein structure and function to inform clinical interpretation of pathogenicity, link phenotype ontologies to genetic variants identified through exome or genome sequencing to help clinicians reach diagnostic answers faster, correlate genomic data with tumor staging and treatment approaches, utilize natural language processing to identify critical published medical literature during analysis of genomic data, and use interactive chatbots to identify individuals who qualify for genetic testing or to provide pre-test and post-test education. With careful and ethical development and validation of artificial intelligence for clinical laboratory genomics, these advances are expected to significantly enhance the abilities of geneticists to translate complex data into clearly synthesized information for clinicians to use in managing the care of their patients at scale.

  View details for DOI 10.1002/ajmg.c.32057

  View details for PubMedID 37507620

• Response to Spurdle et al. Genetics in medicine : official journal of the American College of Medical Genetics Riggs, E. R., Andersen, E. F., Kantarci, S., Kearney, H., Patel, A., Raca, G., Ritter, D. I., South, S. T., Thorland, E. C., Pineda-Alvarez, D., Aradhya, S., Martin, C. L. 2023: 100869

  View details for DOI 10.1016/j.gim.2023.100869

  View details for PubMedID 37261438

• The impact of machine learning models in reducing variants of uncertain significance for individuals from underrepresented populations who are undergoing testing for inborn errors of immunity Johnson, B., Morales, A., Facio, F., Fresard, L., McKnight, D., Kobayashi, Y., Reuter, J., Aradhya, S., Nykamp, K., Colavin, A. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2023: 66-67

  View details for DOI 10.1016/j.clim.2023.109469

  View details for Web of Science ID 001038057600123

• Genetic testing outcomes in a cohort of 21,159 children with heart disease Nussbaum, R., Facio, F., Morales, A., Mitchell, A., Garcia, J., McKnight, D., Callis, T., Moretz, C., Vatta, M., Aradhya, S. SPRINGERNATURE. 2023: 410-411

  View details for Web of Science ID 001050507001348

• Healthcare Utilization In Cardiomyopathy Patients Who Had Genetic Testing Before Or After Diagnosis Moretz, C., Smith, E. M., Aradhya, S., Callis, T., Esplin, E., Hatchell, K., Hall, T., Nussbaum, R., Morales, A., Regalado, E., Ren, S., Rojahn, S., Vatta, M., Murillo, J. CHURCHILL LIVINGSTONE INC MEDICAL PUBLISHERS. 2023: 571

  View details for Web of Science ID 001009258900064

• Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. American journal of human genetics Truty, R., Rojahn, S., Ouyang, K., Kautzer, C., Kennemer, M., Pineda-Alvarez, D., Johnson, B., Stafford, A., Basel-Salmon, L., Saitta, S., Slavotinek, A., Chandrasekharappa, S. C., Suarez, C. J., Burnett, L., Nussbaum, R. L., Aradhya, S. 2023

  Abstract

  DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred to for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.

  View details for DOI 10.1016/j.ajhg.2023.02.013

  View details for PubMedID 36933558

• THE IMPACT OF MACHINE LEARNING MODELS IN REDUCING VARIANTS OF UNCERTAIN SIGNIFICANCE (VUS) FOR INDIVIDUALS FROM UNDERREPRESENTED POPULATIONS WHO ARE UNDERGOING TESTING FOR INHERITED METABOLIC DISORDERS Johnson, B., Facio, F., Morales, A., Fresard, L., McKnight, D., Kobayashi, Y., Reuter, J., Aradhya, S., Nykamp, K., Colavin, A. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2023: 59

  View details for DOI 10.1016/j.ymgme.2023.107433

  View details for Web of Science ID 001175367500060

• Scalable detection of technically challenging variants through modified next-generation sequencing. Molecular genetics & genomic medicine Rojahn, S., Hambuch, T., Adrian, J., Gafni, E., Gileta, A., Hatchell, H., Johnson, B., Kallman, B., Karfilis, K., Kautzer, C., Kennemer, M., Kirk, L., Kvitek, D., Lettes, J., Macrae, F., Mendez, F., Paul, J., Pellegrino, M., Preciado, R., Risinger, J., Schultz, M., Spurka, L., Swamy, S., Truty, R., Usem, N., Velenich, A., Aradhya, S. 2022; 10 (12): e2072

  Abstract

  Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions).We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes.Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats.NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.

  View details for DOI 10.1002/mgg3.2072

  View details for PubMedID 36251442

  View details for PubMedCentralID PMC9747563

• Genetic Testing to Inform Epilepsy Treatment Management From an International Study of Clinical Practice. JAMA neurology McKnight, D., Morales, A., Hatchell, K. E., Bristow, S. L., Bonkowsky, J. L., Perry, M. S., Berg, A. T., Borlot, F., Esplin, E. D., Moretz, C., Angione, K., Rios-Pohl, L., Nussbaum, R. L., Aradhya, S., ELEVIATE Consortium, Haldeman-Englert, C. R., Levy, R. J., Parachuri, V. G., Lay-Son, G., de Montellano, D. J., Ramirez-Garcia, M. A., Benitez Alonso, E. O., Ziobro, J., Chirita-Emandi, A., Felix, T. M., Kulasa-Luke, D., Megarbane, A., Karkare, S., Chagnon, S. L., Humberson, J. B., Assaf, M. J., Silva, S., Zarroli, K., Boyarchuk, O., Nelson, G. R., Palmquist, R., Hammond, K. C., Hwang, S. T., Boutlier, S. B., Nolan, M., Batley, K. Y., Chavda, D., Reyes-Silva, C. A., Miroshnikov, O., Zuccarelli, B., Amlie-Wolf, L., Wheless, J. W., Seinfeld, S., Kanhangad, M., Freeman, J. L., Monroy-Santoyo, S., Rodriguez-Vazquez, N., Ryan, M. M., Machie, M., Guerra, P., Hassan, M. J., Candee, M. S., Bupp, C. P., Park, K. L., Muller, E. 2., Lupo, P., Pedersen, R. C., Arain, A. M., Murphy, A., Schatz, K., Mu, W., Kalika, P. M., Plaza, L., Kellogg, M. A., Lora, E. G., Carson, R. P., Svystilnyk, V., Venegas, V., Luke, R. R., Jiang, H., Stetsenko, T., Duenas-Roque, M. M., Trasmonte, J., Burke, R. J., Hurst, A. C., Smith, D. M., Massingham, L. J., Pisani, L., Costin, C. E., Ostrander, B., Filloux, F. M., Ananth, A. L., Mohamed, I. S., Nechai, A., Dao, J. M., Fahey, M. C., Aliu, E., Falchek, S., Press, C. A., Treat, L., Eschbach, K., Starks, A., Kammeyer, R., Bear, J. J., Jacobson, M., Chernuha, V., Meibos, B., Wong, K., Sweney, M. T., Espinoza, A. C., Van Orman, C. B., Weinstock, A., Kumar, A., Soler-Alfonso, C., Nolan, D. A., Raza, M., Rojas Carrion, M. D., Chari, G., Marsh, E. D., Shiloh-Malawsky, Y., Parikh, S., Gonzalez-Giraldo, E., Fulton, S., Sogawa, Y., Burns, K., Malets, M., Montiel Blanco, J. D., Habela, C. W., Wilson, C. A., Guzman, G. G., Pavliuk, M. 2022

  Abstract

  Importance: It is currently unknown how often and in which ways a genetic diagnosis given to a patient with epilepsy is associated with clinical management and outcomes.Objective: To evaluate how genetic diagnoses in patients with epilepsy are associated with clinical management and outcomes.Design, Setting, and Participants: This was a retrospective cross-sectional study of patients referred for multigene panel testing between March 18, 2016, and August 3, 2020, with outcomes reported between May and November 2020. The study setting included a commercial genetic testing laboratory and multicenter clinical practices. Patients with epilepsy, regardless of sociodemographic features, who received a pathogenic/likely pathogenic (P/LP) variant were included in the study. Case report forms were completed by all health care professionals.Exposures: Genetic test results.Main Outcomes and Measures: Clinical management changes after a genetic diagnosis (ie, 1 P/LP variant in autosomal dominant and X-linked diseases; 2 P/LP variants in autosomal recessive diseases) and subsequent patient outcomes as reported by health care professionals on case report forms.Results: Among 418 patients, median (IQR) age at the time of testing was 4 (1-10) years, with an age range of 0 to 52 years, and 53.8% (n = 225) were female individuals. The mean (SD) time from a genetic test order to case report form completion was 595(368) days (range, 27-1673 days). A genetic diagnosis was associated with changes in clinical management for 208 patients (49.8%) and usually (81.7% of the time) within 3 months of receiving the result. The most common clinical management changes were the addition of a new medication (78 [21.7%]), the initiation of medication (51 [14.2%]), the referral of a patient to a specialist (48 [13.4%]), vigilance for subclinical or extraneurological disease features (46 [12.8%]), and the cessation of a medication (42 [11.7%]). Among 167 patients with follow-up clinical information available (mean [SD] time, 584[365] days), 125 (74.9%) reported positive outcomes, 108 (64.7%) reported reduction or elimination of seizures, 37 (22.2%) had decreases in the severity of other clinical signs, and 11 (6.6%) had reduced medication adverse effects. A few patients reported worsening of outcomes, including a decline in their condition (20 [12.0%]), increased seizure frequency (6 [3.6%]), and adverse medication effects (3 [1.8%]). No clinical management changes were reported for 178 patients (42.6%).Conclusions and Relevance: Results of this cross-sectional study suggest that genetic testing of individuals with epilepsy may be materially associated with clinical decision-making and improved patient outcomes.

  View details for DOI 10.1001/jamaneurol.2022.3651

  View details for PubMedID 36315135

• PGT-SR OBSERVED SEGREGATION PATTERNS ALOWS FOR TAILORED RISK ASSESSMENT Walters-Sen, L., Neitzel, D., Wilkinson, J., Poll, S., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2022: E19

  View details for Web of Science ID 000891804600047

• Systematic use of phenotype evidence in clinical genetic testing reduces the frequency of variants of uncertain significance. American journal of medical genetics. Part A Johnson, B., Ouyang, K., Frank, L., Truty, R., Rojahn, S., Morales, A., Aradhya, S., Nykamp, K. 2022; 188 (9): 2642-2651

  Abstract

  Guidelines for variant interpretation include criteria for incorporating phenotype evidence, but this evidence is inconsistently applied. Systematic approaches to using phenotype evidence are needed. We developed a method for curating disease phenotypes as highly or moderately predictive of variant pathogenicity based on the frequency of their association with disease-causing variants. To evaluate this method's accuracy, we retrospectively reviewed variants with clinical classifications that had evolved from uncertain to definitive in genes associated with curated predictive phenotypes. To demonstrate the clinical validity and utility of this approach, we compared variant classifications determined with and without predictive phenotype evidence. The curation method was accurate for 93%-98% of eligible variants. Among variants interpreted using highly predictive phenotype evidence, the percentage classified as pathogenic or likely pathogenic was 80%, compared with 46%-54% had the evidence not been used. Positive results among individuals harboring variants with highly predictive phenotype-guided interpretations would have been missed in 25%-37% of diagnostic tests and 39%-50% of carrier screens had other approaches to phenotype evidence been used. In summary, predictive phenotype evidence associated with specific curated genes can be systematically incorporated into variant interpretation to reduce uncertainty and increase the clinical utility of genetic testing.

  View details for DOI 10.1002/ajmg.a.62779

  View details for PubMedID 35570716

  View details for PubMedCentralID PMC9544038

• A cross-disorder dosage sensitivity map of the human genome. Cell Collins, R. L., Glessner, J. T., Porcu, E., Lepamets, M., Brandon, R., Lauricella, C., Han, L., Morley, T., Niestroj, L. M., Ulirsch, J., Everett, S., Howrigan, D. P., Boone, P. M., Fu, J., Karczewski, K. J., Kellaris, G., Lowther, C., Lucente, D., Mohajeri, K., Nõukas, M., Nuttle, X., Samocha, K. E., Trinh, M., Ullah, F., Võsa, U., Hurles, M. E., Aradhya, S., Davis, E. E., Finucane, H., Gusella, J. F., Janze, A., Katsanis, N., Matyakhina, L., Neale, B. M., Sanders, D., Warren, S., Hodge, J. C., Lal, D., Ruderfer, D. M., Meck, J., Mägi, R., Esko, T., Reymond, A., Kutalik, Z., Hakonarson, H., Sunyaev, S., Brand, H., Talkowski, M. E. 2022; 185 (16): 3041-3055.e25

  Abstract

  Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. In this study, we aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome. We harmonized and meta-analyzed rCNVs from nearly one million individuals to construct a genome-wide catalog of dosage sensitivity across 54 disorders, which defined 163 dosage sensitive segments associated with at least one disorder. These segments were typically gene dense and often harbored dominant dosage sensitive driver genes, which we were able to prioritize using statistical fine-mapping. Finally, we designed an ensemble machine-learning model to predict probabilities of dosage sensitivity (pHaplo & pTriplo) for all autosomal genes, which identified 2,987 haploinsufficient and 1,559 triplosensitive genes, including 648 that were uniquely triplosensitive. This dosage sensitivity resource will provide broad utility for human disease research and clinical genetics.

  View details for DOI 10.1016/j.cell.2022.06.036

  View details for PubMedID 35917817

  View details for PubMedCentralID PMC9742861

• The genomic basis of sporadic and recurrent pregnancy loss: a comprehensive in-depth analysis of 24,900 miscarriages. Reproductive biomedicine online Finley, J., Hay, S., Oldzej, J., Meredith, M. M., Dzidic, N., Slim, R., Aradhya, S., Hovanes, K., Sahoo, T. 2022; 45 (1): 125-134

  Abstract

  What is the genetic cause of sporadic and recurrent pregnancy loss and does the frequency and nature of chromosomal abnormalities play a role? Types and frequency of all identifiable chromosomal abnormalities were determined to inform our understanding, medical management and recurrence risk for patients experiencing pregnancy loss.Genome-wide single-nucleotide polymorphism-based chromosomal microarray (SNP-CMA) were used to evaluate 24,900 products of conception samples from various forms of pregnancy losses.Sporadic miscarriage (64.7%) or recurrent pregnancy loss (RPL) (22%) were the most common referrals. Clinically significant abnormalities were observed in 55.8% (13,910) of samples, variants of uncertain significance in 1.8%, and normal results in 42.4%. In addition to autosomal trisomies (in 36% of samples), polyploidy and large segmental imbalances were identified in 7.8% and 2.8% of samples, respectively. Analysis of sequential samples from 1103 patients who had experienced RPL provided important insight into possible predispositions to RPL.This expansive chromosomal microarray analyses of pregnancy loss samples illuminates our understanding of the full spectrum, relative frequencies and the role of genomic abnormalities in pregnancy loss. The empiric observations described here provide useful insight for clinicians and highlight the importance of high-resolution genomic testing for comprehensive evaluation and risk assessment of individuals experiencing pregnancy loss.

  View details for DOI 10.1016/j.rbmo.2022.03.014

  View details for PubMedID 35523710

• Value of genetic testing for pediatric epilepsy: Driving earlier diagnosis of ceroid lipofuscinosis type 2 Batten disease. Epilepsia Leal-Pardinas, F., Truty, R., McKnight, D. A., Johnson, B., Morales, A., Bristow, S. L., Yar Pang, T., Cohen-Pfeffer, J., Izzo, E., Sankar, R., Koh, S., Wirrell, E. C., Millichap, J. J., Aradhya, S. 2022; 63 (7): e68-e73

  Abstract

  This study assessed the effectiveness of genetic testing in shortening the time to diagnosis of late infantile neuronal ceroid lipofuscinosis type 2 (CLN2) disease. Individuals who received epilepsy gene panel testing through Behind the Seizure® , a sponsored genetic testing program (Cohort A), were compared to children outside of the sponsored testing program during the same period (Cohort B). Two cohorts were analyzed: children aged ≥24 to ≤60 months with unprovoked seizure onset at ≥24 months between December 2016 and January 2020 (Cohort 1) and children aged 0 to ≤60 months at time of testing with unprovoked seizure onset at any age between February 2019 and January 2020 (Cohort 2). The diagnostic yield in Cohort 1A (n = 1814) was 8.4% (n = 153). The TPP1 diagnostic yield within Cohort 1A was 2.9-fold higher compared to Cohort 1B (1.0%, n = 18/1814 vs. .35%, n = 8/2303; p = .0157). The average time from first symptom to CLN2 disease diagnosis was significantly shorter than previously reported (9.8 vs. 22.7 months, p < .001). These findings indicate that facilitated access to early epilepsy gene panel testing helps to increase diagnostic yield for CLN2 disease and shortens the time to diagnosis, enabling earlier intervention.

  View details for DOI 10.1111/epi.17269

  View details for PubMedID 35474188

  View details for PubMedCentralID PMC9545603

• Global Expansion of Jeffrey's Insights: Jeffrey Modell Foundation's Genetic Sequencing Program for Primary Immunodeficiency. Frontiers in immunology Quinn, J., Modell, V., Johnson, B., Poll, S., Aradhya, S., Orange, J. S., Modell, F. 2022; 13: 906540

  Abstract

  Genetic disorders that impair the immune system, known as Primary Immunodeficiencies (PI), include over 450 single-gene inborn errors of immunity. Timely and appropriate diagnosis and treatment is vital to quality of life (QOL) and sometimes survival, as patients are susceptible to frequent, persistent, severe, and sometimes life-threatening infections or autoimmunity. Suspected PI patients that do not have a genetic diagnosis often endure a prolonged, onerous, inefficient, and expensive experience, known as a diagnostic odyssey. The resulting diagnostic delay prohibits proper disease management and treatment, causing unnecessary distress and diminished QOL. Next-generation sequencing (NGS) offers relief from the distress of the diagnostic odyssey, but because of cost and barriers to access, it is regularly unobtainable. The Jeffrey Modell Foundation (JMF) introduced "Jeffrey's Insights", a no-charge genetic sequencing pilot program, in January 2019 for patients within the Jeffrey Modell Centers Network (JMCN) with an underlying PI, but no genetic diagnosis. Building on the success of the pilot program, JMF expanded it globally to more than 400 Centers in the JMCN in early 2020. The most current version of Invitae's PI Panel available was used for this program. All participating clinicians were invited to complete a brief questionnaire assessing prior impediments to access and post-sequencing alterations in disease management and treatment. A total of 1,398 patients were tested, with 20.3% receiving a molecular diagnosis and many more receiving helpful diagnostic leads. Results obtained from genetic sequencing led to an alteration of clinical diagnosis, disease management, treatment, and genetic counseling in 39%, 38%, 35%, and 53% of patients, respectively. The global expansion of this program further underscores the crucial need for NGS for PI, along with its efficiency and potential cost savings. The results of this program to date further define rationale for the availability of comprehensive diagnostic NGS for patients with PI when requisitioned by an expert immunologist.

  View details for DOI 10.3389/fimmu.2022.906540

  View details for PubMedID 35757720

  View details for PubMedCentralID PMC9226364

• The KIDNEYCODE Program: Diagnostic Yield and Clinical Features of Individuals with CKD. Kidney360 Lieberman, K. V., Chang, A. R., Block, G. A., Robinson, K., Bristow, S. L., Morales, A., Mitchell, A., McCalley, S., McKay, J., Pollak, M. R., Aradhya, S., Warady, B. A. 2022; 3 (5): 900-909

  Abstract

  Despite increasing recognition that CKD may have underlyi ng genetic causes, genetic testing remains limited. This study evaluated the diagnostic yield and phenotypic spectrum of CKD in individuals tested through the KIDNEYCODE sponsored genetic testing program.Unrelated individuals who received panel testing (17 genes) through the KIDNEYCODE sponsored genetic testing program were included. Individuals had to meet at least one of the following eligibility criteria: eGFR ≤90 ml/min per 1.73m2 and hematuria or a family history of kidney disease; or suspected/biopsy-confirmed Alport syndrome or FSGS in tested individuals or relatives.Among 859 individuals, 234 (27%) had molecular diagnoses in genes associated with Alport syndrome (n=209), FSGS (n=12), polycystic kidney disease (n=6), and other disorders (n=8). Among those with positive findings in a COL4A gene, the majority were in COL4A5 (n=157, 72 hemizygous male and 85 heterozygous female individuals). A positive family history of CKD, regardless of whether clinical features were reported, was more predictive of a positive finding than was the presence of clinical features alone. For the 248 individuals who had kidney biopsies, a molecular diagnosis was returned for 49 individuals (20%). Most (n=41) individuals had a molecular diagnosis in a COL4A gene, 25 of whom had a previous Alport syndrome clinical diagnosis, and the remaining 16 had previous clinical diagnoses including FSGS (n=2), thin basement membrane disease (n=9), and hematuria (n=1). In total, 491 individuals had a previous clinical diagnosis, 148 (30%) of whom received a molecular diagnosis, the majority (89%, n=131) of which were concordant.Although skewed to identify individuals with Alport syndrome, these findings support the need to improve access to genetic testing for patients with CKD-particularly in the context of family history of kidney disease, hematuria, and hearing loss.

  View details for DOI 10.34067/KID.0004162021

  View details for PubMedID 36128480

  View details for PubMedCentralID PMC9438426

• Topological mapping of variant-intolerant domains in SCN1A using a novel functional modeling platform Vatta, M., McKnight, D., Ouyang, K., Morales, A., Aradhya, S. SPRINGERNATURE. 2022: 277

  View details for Web of Science ID 000779367701190

• Carrier screening in the Mexican Jewish community using a pan-ethnic expanded carrier screening NGS panel. Genetics in medicine : official journal of the American College of Medical Genetics Morgenstern-Kaplan, D., Raijman-Policar, J., Majzner-Aronovich, S., Aradhya, S., Pineda-Alvarez, D. E., Aguinaga, M., García-Vences, E. E. 2022; 24 (4): 821-830

  Abstract

  The Mexican Jewish community (MJC) is a previously uncharacterized, genetically isolated group composed of Ashkenazi and Sephardi-Mizrahi Jews who migrated in the early 1900s. We aimed to determine the heterozygote frequency of disease-causing variants in 302 genes in this population.We conducted a cross-sectional study of the MJC involving individuals representing Ashkenazi Jews, Sephardi-Mizrahi Jews, or mixed-ancestry Jews. We offered saliva-based preconception pan-ethnic expanded carrier screening, which examined 302 genes. We analyzed heterozygote frequencies of pathogenic/likely pathogenic variants and compared them with those in the Genome Aggregation Database (gnomAD).We recruited 208 participants. The carrier screening results showed that 72.1% were heterozygous for at least 1 severe disease-causing variant in 1 of the genes analyzed. The most common genes with severe disease-causing variants were CFTR (16.8% of participants), MEFV (11.5%), WNT10A (6.7%), and GBA (6.7%). The allele frequencies were compared with those in the gnomAD; 85% of variant frequencies were statistically different from those found in gnomAD (P <.05). Finally, 6% of couples were at risk of having a child with a severe disorder.The heterozygote frequency of at least 1 severe disease-causing variant in the MJC was 72.1%. The use of carrier screening in the MJC and other understudied populations could help parents make more informed decisions.

  View details for DOI 10.1016/j.gim.2021.11.019

  View details for PubMedID 34961661

• Clinical utility of a sponsored, no-cost skeletal dysplasia gene panel testing program: Results from 850 tests Seratti, G., Pansare, V., Pang, T., Izzo, E., Mackenzie, W., Raggio, C., White, K., Truty, R., Johnson, B., Aradhya, S. SPRINGERNATURE. 2022: 170

  View details for Web of Science ID 000779367700449

• A cross-disorder dosage sensitivity map of the human genome Collins, R., Glessner, J. T., Porcu, E., Niestroj, L., Ulirsch, J., Kellaris, G., Howrigan, D. P., Everett, S., Mohajeri, K., Nuttle, X., Lowther, C., Fu, J., Boone, P. M., Ullah, F., Samocha, K. E., Karczewski, K., Lucente, D., Gusella, J. F., Finucane, H., Matyakhina, L., Aradhya, S., Meck, J., Lal, D., Neale, B. M., Hodge, J. C., Reymond, A., Kutalik, Z., Katsanis, N., Davis, E. E., Hakonarson, H., Sunyaev, S., Brand, H., Talkowski, M. E., Epi25 Consortium SPRINGERNATURE. 2022: 4

  View details for Web of Science ID 000779367700005

• Clinical utility of a sponsored gene panel testing program for pediatric epilepsy and CLN2 disease diagnosis: Results from 10,853 tests Pang, T., Truty, R., McKnight, D. A., Johnson, B., Morales, A., Bristow, S. L., Izzo, E., Seratti, G., Koh, S., Wirrell, E. C., Millichap, J. J., Aradhya, S. SPRINGERNATURE. 2022: 216

  View details for Web of Science ID 000779367701037

• Deriving risk estimates for balanced rearrangement carriers utilizing PGT-SR data Walters-Sen, L., Neitzel, D., Wilkinson, J., Poll, S., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2022: S299-S300

  View details for DOI 10.1016/j.gim.2022.01.505

  View details for Web of Science ID 000796586200244

• The landscape of peripheral neuropathy genetics: When common causes are not actually the cause Roggenbuck, J., Mitchel, A., Morales, A., Stetler, M., Tan, C., Aradhya, S., McKnight, D. A., Winder, T., Esplin, E. ELSEVIER SCIENCE INC. 2022: S74-S75

  View details for DOI 10.1016/j.gim.2022.01.155

  View details for Web of Science ID 000788465500110

• Genetics professionals ' perspectives on the reporting of Variants of Uncertain Significance (VUS): Should they always be reported? Esplin, E., Fox, M., Saitta, S., Santani, A., Aradhya, S., Bernstein, J., Nussbaum, R. ELSEVIER SCIENCE INC. 2022: S269

  View details for DOI 10.1016/j.gim.2022.01.464

  View details for Web of Science ID 000796586200203

• Experience analysing over 190,000 embryo trophectoderm biopsies using a novel FAST-SeqS preimplantation genetic testing assay. Reproductive biomedicine online Walters-Sen, L., Neitzel, D., Bristow, S. L., Mitchell, A., Alouf, C. A., Aradhya, S., Faulkner, N. 2022; 44 (2): 228-238

  Abstract

  Is FAST-SeqS an accurate methodology for preimplantation genetic testing for whole-chromosome aneuploidy (PGT-A)? What additional types of chromosomal abnormalities can be assessed? What are the observed aneuploidy rates in a large clinical cohort?FAST-SeqS, a next-generation sequencing (NGS)-based assay amplifying genome-wide LINE1 repetitive sequences, was validated using reference samples. Sensitivity and specificity were calculated. Clinically derived trophectoderm biopsies submitted for PGT-A were assessed, and aneuploidy and mosaicism rates among biopsies were determined. Clinician-provided outcome rates were calculated.Sensitivity and specificity were over 95% for all aneuploidy types tested in the validation. Comparison of FAST-SeqS with VeriSeq showed high concordance (98.5%). Among embryos with actionable results (n = 182,827), 46.2% were aneuploid. Whole-chromosome aneuploidies were most observed (72.9% without or 8.7% with a segmental aneuploidy), with rates increasing with egg age; segmental aneuploidy rates did not. Segmental aneuploidy (n = 20,557) was observed on all chromosomes (most commonly deletions), with frequencies associated with chromosome length. Mosaic-only abnormalities constituted 10.1% (n = 3862/38145) of samples. Abnormal ploidy constituted 1.8% (n = 2370/128,991) of samples, triploidy being the most common (73.6%). Across 3297 frozen embryo transfers, the mean clinical pregnancy rate was 62% (range 38-80%); the mean combined ongoing pregnancy and live birth rate was 57% (range 38-72%).FAST-SeqS is a clinically reliable and scalable method for PGT-A, is comparable to whole-genome amplification-based platforms, and detects additional information related to ploidy using SNP analysis. Results suggest ongoing benefit of PGT-A using FAST-SeqS, consistent with other platforms.

  View details for DOI 10.1016/j.rbmo.2021.06.022

  View details for PubMedID 35039224

• Molecular Diagnoses of X-Linked and Other Genetic Hypophosphatemias: Results From a Sponsored Genetic Testing Program. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Rush, E. T., Johnson, B., Aradhya, S., Beltran, D., Bristow, S. L., Eisenbeis, S., Guerra, N. E., Krolczyk, S., Miller, N., Morales, A., Ramesan, P., Sarafrazi, S., Truty, R., Dahir, K. 2022; 37 (2): 202-214

  Abstract

  X-linked hypophosphatemia (XLH), a dominant disorder caused by pathogenic variants in the PHEX gene, affects both sexes of all ages and results in elevated serum fibroblast growth factor 23 (FGF23) and below-normal serum phosphate. In XLH, rickets, osteomalacia, short stature, and lower limb deformity may be present with muscle pain and/or weakness/fatigue, bone pain, joint pain/stiffness, hearing difficulty, enthesopathy, osteoarthritis, and dental abscesses. Invitae and Ultragenyx collaborated to provide a no-charge sponsored testing program using a 13-gene next-generation sequencing panel to confirm clinical XLH or aid diagnosis of suspected XLH/other genetic hypophosphatemia. Individuals aged ≥6 months with clinical XLH or suspected genetic hypophosphatemia were eligible. Of 831 unrelated individuals tested between February 2019 and June 2020 in this cross-sectional study, 519 (62.5%) individuals had a pathogenic or likely pathogenic variant in PHEX (PHEX-positive). Among the 312 PHEX-negative individuals, 38 received molecular diagnoses in other genes, including ALPL, CYP27B1, ENPP1, and FGF23; the remaining 274 did not have a molecular diagnosis. Among 319 patients with a provider-reported clinical diagnosis of XLH, 88.7% (n = 283) had a reportable PHEX variant; 81.5% (n = 260) were PHEX-positive. The most common variant among PHEX-positive individuals was an allele with both the gain of exons 13-15 and c.*231A>G (3'UTR variant) (n = 66/519). Importantly, over 80% of copy number variants would have been missed by traditional microarray analysis. A positive molecular diagnosis in 41 probands (4.9%; 29 PHEX positive, 12 non-PHEX positive) resulted in at least one family member receiving family testing. Additional clinical or family member information resulted in variant(s) of uncertain significance (VUS) reclassification to pathogenic/likely pathogenic (P/LP) in 48 individuals, highlighting the importance of segregation and clinical data. In one of the largest XLH genetic studies to date, 65 novel PHEX variants were identified and a high XLH diagnostic yield demonstrated broad insight into the genetic basis of XLH. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

  View details for DOI 10.1002/jbmr.4454

  View details for PubMedID 34633109

  View details for PubMedCentralID PMC9298723

• Multigene Panel Testing in a Large Cohort of Adults With Epilepsy: Diagnostic Yield and Clinically Actionable Genetic Findings. Neurology. Genetics McKnight, D., Bristow, S. L., Truty, R. M., Morales, A., Stetler, M., Westbrook, M. J., Robinson, K., Riethmaier, D., Borlot, F., Kellogg, M., Hwang, S. T., Berg, A., Aradhya, S. 2022; 8 (1): e650

  Abstract

  Although genetic testing among children with epilepsy has demonstrated clinical utility and become a part of routine testing, studies in adults are limited. This study reports the diagnostic yield of genetic testing in adults with epilepsy.Unrelated individuals aged 18 years and older who underwent diagnostic genetic testing for epilepsy using a comprehensive, next-generation sequencing-based, targeted gene panel (range 89-189 genes) were included in this cross-sectional study. Clinical information, provided at the discretion of the ordering clinician, was reviewed and analyzed. Diagnostic yield was calculated for all individuals including by age at seizure onset and comorbidities based on clinician-reported information. The proportion of individuals with clinically actionable genetic findings, including instances when a specific treatment would be indicated or contraindicated due to a diagnostic finding, was calculated.Among 2,008 individuals, a diagnostic finding was returned for 218 adults (10.9%), with clinically actionable findings in 55.5% of diagnoses. The highest diagnostic yield was in adults with seizure onset during infancy (29.6%, 0-1 year), followed by in early childhood (13.6%, 2-4 years), late childhood (7.0%, 5-10 years), adolescence (2.4%, 11-17 years), and adulthood (3.7%, ≥18 years). Comorbid intellectual disability (ID) or developmental delay resulted in a high diagnostic yield (16.0%), most notably for females (19.6% in females vs 12.3% in males). Among individuals with pharmacoresistant epilepsy, 13.5% had a diagnostic finding, and of these, 57.4% were clinically actionable genetic findings.These data reinforce the utility of genetic testing for adults with epilepsy, particularly for those with childhood-onset seizures, ID, and pharmacoresistance. This is an important consideration due to longer survival and the complexity of the transition from pediatric to adult care. In addition, more than half of diagnostic findings in this study were considered clinically actionable, suggesting that genetic testing could have a direct impact on clinical management and outcomes.

  View details for DOI 10.1212/NXG.0000000000000650

  View details for PubMedID 34926809

  View details for PubMedCentralID PMC8678910

• Correction to: Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC medicine Haverfield, E. V., Esplin, E. D., Aguilar, S. J., Hatchell, K. E., Ormond, K. E., Hanson-Kahn, A., Atwal, P. S., Macklin-Mantia, S., Hines, S., Sak, C. W., Tucker, S., Bleyl, S. B., Hulick, P. J., Gordon, O. K., Velsher, L., Gu, J. Y., Weissman, S. M., Kruisselbrink, T., Abel, C., Kettles, M., Slavotinek, A., Mendelsohn, B. A., Green, R. C., Aradhya, S., Nussbaum, R. L. 2021; 19 (1): 288

  View details for DOI 10.1186/s12916-021-02141-y

  View details for PubMedID 34732190

• Clinical utility of a sponsored gene panel testing program for pediatric epilepsy and CLN2 disease diagnosis: Results from 10,853 tests Pang, T., Poll, S., McKnight, D. A., Johnson, B., Morales, A., Bristow, S. L., Izzo, E., Seratti, G., Koh, S., Wirrell, E., Millichap, J. J., Aradhya, S. WILEY. 2021: 287-288

  View details for Web of Science ID 000714115400543

• Genetic testing for adults with epilepsy reveals a significant diagnostic yield and precision medicine implications for many individuals with a molecular diagnosis Narravula, A., Mcknight, D., Bristow, S., Truty, R., Morales, A., Westbrook, J., Robinson, K., Riethmaier, D., Borlot, F., Kellogg, M., Hwang, S., Berg, A., Aradhya, S. ELSEVIER. 2021

  View details for DOI 10.1016/j.jns.2021.117707

  View details for Web of Science ID 000713637300074

• Genetic testing guides clinical management of epilepsy and improves patient outcomes Narravula, A., Mcknight, D., Morales, A., Hatchell, K., Bristow, S., Esplin, E., Moretz, C., Aradhya, S. ELSEVIER. 2021

  View details for DOI 10.1016/j.jns.2021.117711

  View details for Web of Science ID 000713637300078

• CLINICAL UTILITY OF HUMAN REVIEW: EXPERIENCE WITH PREVIOUSLY UNKNOWN REARRANGEMENT CARRIERS USING FAST-SEQS, A NEXT-GENERATION SEQUENCING PGT ASSAY. Walters-Sen, L., Neitzel, D., Wilkinson, J., Poll, S., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2021: E398

  View details for Web of Science ID 000699951501477

• Elucidating clinical phenotypic variability associated with the polyT tract and TG repeats in CFTR. Human mutation Nykamp, K., Truty, R., Riethmaier, D., Wilkinson, J., Bristow, S. L., Aguilar, S., Neitzel, D., Faulkner, N., Aradhya, S. 2021; 42 (9): 1165-1172

  Abstract

  Biallelic pathogenic variants in CFTR manifest as cystic fibrosis (CF) or other CFTR-related disorders (CFTR-RDs). The 5T allele, causing alternative splicing and reduced protein activity, is modulated by the adjacent TG repeat element, though previous data have been limited to small, selective cohorts. Here, the risk and spectrum of phenotypes associated with the CFTR TG-T5 haplotype variants (TG11T5, TG12T5, and TG13T5) in the absence of the p.Arg117His variant are evaluated. Individuals who received physician-ordered next-generation sequencing of CFTR were included. TG[11-13]T5 variant frequencies (biallelic or with another CF-causing variant [CFvar]) were calculated. Clinical information reported by the ordering provider or the individual was examined. Among 548,300 individuals, the T5 minor allele frequency (MAF) was 4.2% (TG repeat distribution: TG11 = 68.1%, TG12 = 29.5%, TG13 = 2.4%). When present with a CFvar, each TG[11-13]T5 variant was significantly enriched in individuals with a high suspicion of CF or CFTR-RD (personal/family history of CF/CFTR-RD) compared to those with a low suspicion for CF or CFTR-RD (hereditary cancer screening, CFTR not requisitioned). Compared to CFvar/CFvar individuals, those with TG[11-13]T5/CFvar generally had single-organ involvement, milder symptoms, variable expressivity, and reduced penetrance. These data improve our understanding of disease risks associated with TG[11-13]T5 variants and have important implications for reproductive genetic counseling.

  View details for DOI 10.1002/humu.24250

  View details for PubMedID 34196078

  View details for PubMedCentralID PMC9292755

• Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC medicine Haverfield, E. V., Esplin, E. D., Aguilar, S. J., Hatchell, K. E., Ormond, K. E., Hanson-Kahn, A., Atwal, P. S., Macklin-Mantia, S., Hines, S., Sak, C. W., Tucker, S., Bleyl, S. B., Hulick, P. J., Gordon, O. K., Velsher, L., Gu, J. Y., Weissman, S. M., Kruisselbrink, T., Abel, C., Kettles, M., Slavotinek, A., Mendelsohn, B. A., Green, R. C., Aradhya, S., Nussbaum, R. L. 2021; 19 (1): 199

  Abstract

  BACKGROUND: The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings.METHODS: Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates' correction.RESULTS: Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility.CONCLUSIONS: This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.

  View details for DOI 10.1186/s12916-021-01999-2

  View details for PubMedID 34404389

• One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation. Genetics in medicine : official journal of the American College of Medical Genetics Lincoln, S. E., Hambuch, T., Zook, J. M., Bristow, S. L., Hatchell, K., Truty, R., Kennemer, M., Shirts, B. H., Fellowes, A., Chowdhury, S., Klee, E. W., Mahamdallie, S., Cleveland, M. H., Vallone, P. M., Ding, Y., Seal, S., DeSilva, W., Tomson, F. L., Huang, C., Garlick, R. K., Rahman, N., Salit, M., Kingsmore, S. F., Ferber, M. J., Aradhya, S., Nussbaum, R. L. 2021

  Abstract

  PURPOSE: To evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small copy-number variants (CNVs), complex alterations, and variants in low-complexity or segmentally duplicated regions.METHODS: An interlaboratory pilot study used synthetic specimens to assess detection of challenging variant types by various next-generation sequencing (NGS)-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients.RESULTS: In the interlaboratory study, only 2 of 13 challenging variants were detected by all 10 workflows, and just 3 workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests.CONCLUSION: The analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.

  View details for DOI 10.1038/s41436-021-01187-w

  View details for PubMedID 34007000

• SMA Identified: Clinical and Molecular Findings From a Sponsored Testing Program for Spinal Muscular Atrophy in More Than 2,000 Individuals. Frontiers in neurology Bowen, B. M., Truty, R., Aradhya, S., Bristow, S. L., Johnson, B. A., Morales, A., Tan, C. A., Westbrook, M. J., Winder, T. L., Chavez, J. C. 2021; 12: 663911

  Abstract

  Background: Spinal muscular atrophy (SMA) linked to chromosome 5q is an inherited progressive neuromuscular disorder with a narrow therapeutic window for optimal treatment. Although genetic testing provides a definitive molecular diagnosis that can facilitate access to effective treatments, limited awareness and other barriers may prohibit widespread testing. In this study, the clinical and molecular findings of SMA Identified-a no-charge sponsored next-generation sequencing (NGS)-based genetic testing program for SMA diagnosis-are reported. Methods: Between March 2018 and March 2020, unrelated individuals who had a confirmed or suspected SMA diagnosis or had a family history of SMA were eligible. All individuals underwent diagnostic genetic testing for SMA at clinician discretion. In total, 2,459 individuals were tested and included in this analysis. An NGS-based approach interrogated sequence and copy number of SMN1 and SMN2. Variants were confirmed by multiplex ligation-dependent probe amplification sequencing. Individuals were categorized according to genetic test results: diagnostic (two pathogenic SMN1 variants), nearly diagnostic (SMN1 exon-7 deletion with a variant of uncertain significance [VUS] in SMN1 or SMN2), indeterminate VUS (one VUS in SMN1 or SMN2), carrier (heterozygous SMN1 deletion only), or negative (no pathogenic variants or VUS in SMN1 or SMN2). Diagnostic yield was calculated. Genetic test results were analyzed based on clinician-reported clinical features and genetic modifiers (SMN2 copy number and SMN2 c.859G>C). Results: In total, 2,459 unrelated individuals (mean age 24.3 ± 23.0 years) underwent diagnostic testing. The diagnostic yield for diagnostic plus nearly diagnostic results was 31.3% (n = 771/2,459). Age of onset and clinical presentation varied considerably for individuals and was dependent on SMN2 copy number. Homozygous deletions represented the most common genetic etiology (96.2%), with sequence variants also observed in probands with clinical diagnoses of SMA. Conclusions: Using a high-yield panel test in a no-charge sponsored program early in the diagnostic odyssey may open the door for medical interventions in a substantial number of individuals with SMA. These findings have potential implications for clinical management of probands and their families.

  View details for DOI 10.3389/fneur.2021.663911

  View details for PubMedID 34025568

  View details for PubMedCentralID PMC8134668

• A web-based educational program to support the updated ACMG/ClinGen technical standards for constitutional copy number variant classification Riggs, E., Good, M., Andersen, E., Kantarci, S., Kearney, H., Patel, A., Raca, G., Ritter, D., Thorland, E., Pineda-Alvarez, D., Aradhya, S., Martin, C. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2021: S235

  View details for Web of Science ID 000639219800359

• Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. American journal of human genetics Truty, R., Ouyang, K., Rojahn, S., Garcia, S., Colavin, A., Hamlington, B., Freivogel, M., Nussbaum, R. L., Nykamp, K., Aradhya, S. 2021; 108 (4): 696-708

  Abstract

  The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.

  View details for DOI 10.1016/j.ajhg.2021.03.006

  View details for PubMedID 33743207

  View details for PubMedCentralID PMC8059334

• PATH4WARD: A Genetic Testing Program for Primary Immunodeficiencies With Neutropenia Including WHIM Syndrome Johnson, B., Connelly, J., Cohen, S., Dillinger, L., Badarau, A., Aradhya, S., Morales, A., Newburger, P. SPRINGER/PLENUM PUBLISHERS. 2021: S70

  View details for Web of Science ID 000639851600116

• Clinical utility of a sponsored, no-cost skeletal dysplasia gene panel testing program: results from 850 tests Seratti, G., Pang, T., Pansare, V., Izzo, E., Mackenzie, W., Raggio, C., White, K., Truty, R., Johnson, B., Aradhya, S. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2021: S201

  View details for Web of Science ID 000639219800310

• Clinical utility of a sponsored gene panel testing program for pediatric epilepsy and CLN2 disease diagnosis: results from 10,853 tests Pang, T., Truty, R., McKnight, D. A., Johnson, B., Morales, A., Bristow, S. L., Izzo, E., Seratti, G., Koh, S., Wirrell, E. C., Millichap, J. J., Aradhya, S. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2021: S204

  View details for Web of Science ID 000639219800313

• Correction: Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genetics in medicine : official journal of the American College of Medical Genetics Riggs, E. R., Andersen, E. F., Cherry, A. M., Kantarci, S., Kearney, H., Patel, A., Raca, G., Ritter, D. I., South, S. T., Thorland, E. C., Pineda-Alvarez, D., Aradhya, S., Martin, C. L. 2021

  View details for DOI 10.1038/s41436-021-01150-9

  View details for PubMedID 33731880

• Democratizing genomics: Leveraging software to make genetics an integral part of routine care. American journal of medical genetics. Part C, Seminars in medical genetics Snir, M., Nazareth, S., Simmons, E., Hayward, L., Ashcraft, K., Bristow, S. L., Esplin, E. D., Aradhya, S. 2021; 187 (1): 14-27

  Abstract

  Genetic testing can provide definitive molecular diagnoses and guide clinical management decisions from preconception through adulthood. Innovative solutions for scaling clinical genomics services are necessary if they are to transition from a niche specialty to a routine part of patient care. The expertise of specialists, like genetic counselors and medical geneticists, has traditionally been relied upon to facilitate testing and follow-up, and while ideal, this approach is limited in its ability to integrate genetics into primary care. As individuals, payors, and providers increasingly realize the value of genetics in mainstream medicine, several implementation challenges need to be overcome. These include electronic health record integration, patient and provider education, tools to stay abreast of guidelines, and simplification of the test ordering process. Currently, no single platform offers a holistic view of genetic testing that streamlines the entire process across specialties that begins with identifying at-risk patients in mainstream care settings, providing pretest education, facilitating consent and test ordering, and following up as a "genetic companion" for ongoing management. We describe our vision for using software that includes clinical-grade chatbots and decision support tools, with direct access to genetic counselors and pharmacists within a modular, integrated, end-to-end testing journey.

  View details for DOI 10.1002/ajmg.c.31866

  View details for PubMedID 33296144

• Clinical utility of a sponsored, no-cost skeletal dysplasia gene panel testing program: Results from 850 tests Seratti, G., Pansare, V., Pang, T., Izzo, E., Mackenzie, W., Raggio, C., White, K., Truty, R., Johnson, B., Aradhya, S. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2021: S98

  View details for DOI 10.1016/j.ymgme.2020.12.238

  View details for Web of Science ID 000614651500234

• Common Variants in KCNE1, KCNH2, and SCN5A May Impact Cardiac Arrhythmia Risk. Circulation. Genomic and precision medicine Vatta, M., Truty, R., Garcia, J., Callis, T. E., Hatchell, K., Rojahn, S., Morales, A., Aradhya, S., Nussbaum, R. 2021; 14 (1): e003206

  View details for DOI 10.1161/CIRCGEN.120.003206

  View details for PubMedID 33517668

• Clinical utility of a sponsored gene panel testing program for pediatric epilepsy and CLN2 disease diagnosis: Results from 4246 tests Pang, T., Leal-Pardinas, F., Truty, R., McKnight, D. A., Johnson, B., Morales, A., Bristow, S. L., Izzo, E., Cohen-Pfeffer, J., Sankar, R., Koh, S., Wirrell, E. C., Millichap, J. J., Aradhya, S. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2021: S82

  View details for DOI 10.1016/j.ymgme.2020.12.194

  View details for Web of Science ID 000614651500190

• Utility of RNA Sequencing Analysis in the Context of Genetic Testing CURRENT GENETIC MEDICINE REPORTS Tahiliani, J., Leisk, J., Aradhya, K., Ouyang, K., Aradhya, S., Nykamp, K. 2020; 8 (4): 140-146

  View details for DOI 10.1007/s40142-020-00195-7

  View details for Web of Science ID 000592282700001

• Correspondence on "Is there a duty to reinterpret genetic data? The ethical dimensions" by Appelbaum et al. GENETICS IN MEDICINE Faulkner, N., Aradhya, S., Aradhya, K. W., Nussbaum, R. L. 2021; 23 (1): 232-233

  View details for DOI 10.1038/s41436-020-00954-5

  View details for Web of Science ID 000565179300002

  View details for PubMedID 32873930

• GENETIC SCREENING IN REPRODUCTIVE AGE WOMEN IDENTIFIES A HIGH POSITIVE RATE OF ACTIONABLE RESULTS. Aguilar, S., Haverfield, E., Esplin, E., Nussbaum, R. L., Aradhya, S. ELSEVIER SCIENCE INC. 2020: E19

  View details for Web of Science ID 000579355300047

• EXPERIENCE WITH CARRIER SCREENING FOR X-LINKED CONDITIONS. Neitzel, D., Leahey, J., Aguilar, S., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2020: E18

  View details for Web of Science ID 000579355300044

• SEGMENTAL ANEUPLOIDY RATES OBSERVED IN ∼192,000 BLASTOCYSTS BY FAST-SEQS SUPPORT INCLUSION IN PGT-A ASSAYS. Walters-Sen, L., Neitzel, D., Bristow, S. L., Mitchell, A. D., Faulkner, N., Aradhya, S. ELSEVIER SCIENCE INC. 2020: E32-E33

  View details for Web of Science ID 000579355300079

• IDENTITY MARKER ANALYSIS DEMONSTRATES THAT MOST INITIAL AND RE-BIOPSY PAIRS ARE CONCORDANT. Walters-Sen, L., Neitzel, D., Bristow, S. L., Mitchell, A. D., Alouf, C. A., Aradhya, S. ELSEVIER SCIENCE INC. 2020: E30-E31

  View details for Web of Science ID 000579355300075

• Severe SOPH syndrome due to a novel NBAS mutation in a 27-year-old woman-Review of this pleiotropic, autosomal recessive disorder: Mystery solved after two decades. American journal of medical genetics. Part A Lacassie, Y., Johnson, B., Lay-Son, G., Quintana, R., King, A., Cortes, F., Alvarez, C., Gomez, R., Vargas, A., Chalew, S., King, A., Guardia, S., Sorensen, R. U., Aradhya, S. 2020; 182 (7): 1767-1775

  Abstract

  Autosomal recessive SOPH syndrome was first described in the Yakuts population of Asia by Maksimova et al. in 2010. It arises from biallelic pathogenic variants in the NBAS gene and is characterized by severe postnatal growth retardation, senile facial appearance, small hands and feet, optic atrophy with loss of visual acuity and color vision, and normal intelligence (OMIM #614800). The presence of Pelger-Hüet anomaly in this disorder led to its name as an acronym for Short stature, Optic nerve atrophy, and Pelger-Hüet anomaly. Recent publications have further contributed to the characterization of this syndrome through additional phenotype-genotype correlations. We review the clinical features described in these publications and report on a 27-year-old woman with dwarfism with osteolysis and multiple skeletal problems, minor anomalies, immunodeficiency, diabetes mellitus, and multiple secondary medical problems. Her condition was considered an unknown autosomal recessive disorder for many years until exome sequencing provided the diagnosis by revealing a founder disease-causing variant that was compound heterozygous with a novel pathogenic variant in NBAS. Based on the major clinical features of this individual and others reported earlier, a revision of the acronym is warranted to facilitate clinical recognition.

  View details for DOI 10.1002/ajmg.a.61597

  View details for PubMedID 32297715

• Jeffrey's insights: Jeffrey Modell Foundation's global genetic sequencing pilot program to identify specific primary immunodeficiency defects to optimize disease management and treatment. Immunologic research Quinn, J., Modell, V., Holle, J., Truty, R., Aradhya, S., Johnson, B., Orange, J., Modell, F. 2020; 68 (3): 126-134

  Abstract

  Primary immunodeficiencies (PI) are genetic defects of the immune system that result in chronic and often life-threatening infections and/or life-threatening autoimmunity if not diagnosed and treated. Patients with a suspected PI, but without a genetic diagnosis, commonly undergo a diagnostic odyssey that is costly, time-consuming, and arduous. This delay in diagnosis prevents appropriate disease management and treatment, contributing to prolonged suffering and decreased quality of life. Although next generation sequencing (NGS) can provide these patients with relief from such a diagnostic odyssey, it is often unavailable, mainly due to cost and inaccessibility. In January 2019, the Jeffrey Modell Foundation (JMF) launched a free genetic sequencing pilot program for Jeffrey Modell Centers Network (JMCN) patients clinically diagnosed with an underlying PI. A total of 21 sites within the JMCN were invited to participate. JMF collaborated with Invitae, and testing was comprised of Invitae's Primary Immunodeficiency Panel, which currently includes 207 genes. A questionnaire was disseminated to each participating physician to evaluate barriers to access to genetic sequencing and changes in disease management and treatment after testing. One hundred fifty-eight patients and 29 family members were tested in this pilot study. Twenty-one percent of patients with a suspected monogenic disorder received a molecular diagnosis, and others received potentially useful diagnostic leads. Based on the results of genetic sequencing, clinical diagnosis was altered in 45% of patients, disease management was altered in 40%, treatment was altered in 36%, and genetic counseling was altered in 62%. The results of this pilot program demonstrate the utility, cost-efficiency, and critical importance of NGS for PI and make the case for broad scale sequence-based diagnostics for PI patients when requested by expert immunologists.

  View details for DOI 10.1007/s12026-020-09131-x

  View details for PubMedID 32462469

  View details for PubMedCentralID PMC7335369

• Clinical utility of multigene analysis in over 25,000 patients with neuromuscular disorders. Neurology. Genetics Winder, T. L., Tan, C. A., Klemm, S., White, H., Westbrook, J. M., Wang, J. Z., Entezam, A., Truty, R., Nussbaum, R. L., McNally, E. M., Aradhya, S. 2020; 6 (2): e412

  Abstract

  Molecular genetic testing for hereditary neuromuscular disorders is increasingly used to identify disease subtypes, determine prevalence, and inform management and prognosis, and although many small disease-specific studies have demonstrated the utility of genetic testing, comprehensive data sets are better positioned to assess the complexity of genetic analysis.Using high depth-of-coverage next-generation sequencing (NGS) with simultaneous detection of sequence variants and copy number variants (CNVs), we tested 25,356 unrelated individuals for subsets of 266 genes.A definitive molecular diagnosis was obtained in 20% of this cohort, with yields ranging from 4% among individuals with congenital myasthenic syndrome to 33% among those with a muscular dystrophy. CNVs accounted for as much as 39% of all clinically significant variants, with 10% of them occurring as rare, private pathogenic variants. Multigene testing successfully addressed differential diagnoses in at least 6% of individuals with positive results. Even for classic disorders like Duchenne muscular dystrophy, at least 49% of clinically significant results were identified through gene panels intended for differential diagnoses rather than through single-gene analysis. Variants of uncertain significance (VUS) were observed in 53% of individuals. Only 0.7% of these variants were later reclassified as clinically significant, most commonly in RYR1, GDAP1, SPAST, and MFN2, providing insight into the types of evidence that support VUS resolution and informing expectations of reclassification rates.These data provide guidance for clinicians using genetic testing to diagnose neuromuscular disorders and represent one of the largest studies demonstrating the utility of NGS-based testing for these disorders.

  View details for DOI 10.1212/NXG.0000000000000412

  View details for PubMedID 32337338

  View details for PubMedCentralID PMC7164976

• Update on a no-cost epilepsy gene panel for seizure onset between 2 and 4 years of age: Results from 682 tests Pang, T. Y., Leal-Pardinas, F., Bailey, M., Koh, S., Millichap, J. J., Truty, R., Wirrell, E. C., Aradhya, S. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2020: S126

  View details for DOI 10.1016/j.ymgme.2019.11.330

  View details for Web of Science ID 000510805200340

• Shortening the time between symptom onset and diagnosis for CLN2 disease: Results from Behind the Seizure™, a no-cost epilepsy gene panel testing program Volz, A., Chu, D., Gurnon, S., Johnson, T., Ly, C., Truty, R., Aradhya, S., Leal-Pardinas, F. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2020: S157

  View details for DOI 10.1016/j.ymgme.2019.11.417

  View details for Web of Science ID 000510805200427

• Molecular diagnostic findings of lysosomal diseases as a result of "Detect Lysosomal Storage Diseases", a no-charge sponsored testing program Hubert, L., Truty, R., Beltran, D., Gillon, J., Mehta, G., Rangel-Miller, V., Silveira, N., Pivirotto, D., Anderson, D., Aradhya, S., Johnson, B. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2020: S76

  View details for DOI 10.1016/j.ymgme.2019.11.184

  View details for Web of Science ID 000510805200194

• Response to Maya et al. Genetics in medicine : official journal of the American College of Medical Genetics Riggs, E. R., Andersen, E. F., Kantarci, S. n., Kearney, H. n., Patel, A. n., Raca, G. n., Ritter, D. I., South, S. T., Thorland, E. C., Pineda-Alvarez, D. n., Aradhya, S. n., Martin, C. L. 2020

  View details for DOI 10.1038/s41436-020-0796-3

  View details for PubMedID 32341575

• Clinical true negative and true positive results of non-invasive prenatal screening Strecker, M., Guiltinan, J., Sahoo, T., Hay, S., Travis, M., Oldzej, J., Proffitt, J., O'Toole, E., Dzidic, N., Aradhya, S., Hovanes, K. MOSBY-ELSEVIER. 2020: S230-S231

  View details for DOI 10.1016/j.ajog.2019.11.359

  View details for Web of Science ID 000504997300342

• Cytogenomic analysis of molar pregnancies as a frequent cause of sporadic and recurrent pregnancy loss Sahoo, T., Dzidic, N., Guiltinan, J., Oldzej, J., Slim, R., Aradhya, S., Hovanes, K. MOSBY-ELSEVIER. 2020: S737

  View details for DOI 10.1016/j.ajog.2019.11.1210

  View details for Web of Science ID 000504997301516

• Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria (vol 74, pg 258, 2019) GENETICS IN MEDICINE Nykamp, K., Anderson, M., Powers, M., Garcia, J., Herrera, B., Ho, Y., Kobayashi, Y., Patil, N., Thusberg, J., Westbrook, M., Topper, S., Aguilar, S., Aradhya, S., Beltran, D., Bunker, B., Daly, A., Deucher, A., Ekstein, T., Entezam, A., Erhard, K., Esplin, E., Fulbright, J., Fuller, A., Gibson, K., Hambuch, T., Harte, R., Hartshorne, C., Haverfield, E., Heidari, N., Hogue, M., Iacoboni, D., Johnson, B., Kang, H., Lewis, R., Martin, S., McCalmon, S., Michalski, S., Morgan, C., Murillo, L., Nicolosi, P., Ouyang, K., Pardo, C., Quintana, R., Rabideau, M., Riethmaier, D., Stafford, A., Tahiliani, J., Tan, C., Taylor, S., Wang, S., White, H., Wilson, I., Winder, T., Zeman, M. K., Invitae Clinical Genomics Grp 2020; 22 (1): 240

  Abstract

  An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  View details for DOI 10.1038/s41436-019-0624-9

  View details for Web of Science ID 000510943400031

  View details for PubMedID 31346256

  View details for PubMedCentralID PMC6944637

• Response to "The use of ACMG secondary findings recommendations for general population screening: a policy statement of the American College of Medical Genetics and Genomics (ACMG)" GENETICS IN MEDICINE Nussbaum, R. L., Haverfield, E., Esplin, E. D., Aradhya, S. 2019; 21 (12): 2836-2837

  View details for DOI 10.1038/s41436-019-0572-4

  View details for Web of Science ID 000500923300024

  View details for PubMedID 31239557

• Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genetics in medicine : official journal of the American College of Medical Genetics Riggs, E. R., Andersen, E. F., Cherry, A. M., Kantarci, S., Kearney, H., Patel, A., Raca, G., Ritter, D. I., South, S. T., Thorland, E. C., Pineda-Alvarez, D., Aradhya, S., Martin, C. L. 2019

  Abstract

  PURPOSE: Copy-number analysis to detect disease-causing losses and gains across the genome is recommended for the evaluation of individuals with neurodevelopmental disorders and/or multiple congenital anomalies, as well as for fetuses with ultrasound abnormalities. In the decade that this analysis has been in widespread clinical use, tremendous strides have been made in understanding the effects of copy-number variants (CNVs) in both affected individuals and the general population. However, continued broad implementation of array and next-generation sequencing-based technologies will expand the types of CNVs encountered in the clinical setting, as well as our understanding of their impact on human health.METHODS: To assist clinical laboratories in the classification and reporting of CNVs, irrespective of the technology used to identify them, the American College of Medical Genetics and Genomics has developed the following professional standards in collaboration with the National Institutes of Health (NIH)-funded Clinical Genome Resource (ClinGen) project.RESULTS: This update introduces a quantitative, evidence-based scoring framework; encourages the implementation of the five-tier classification system widely used in sequence variant classification; and recommends "uncoupling" the evidence-based classification of a variant from its potential implications for a particular individual.CONCLUSION: These professional standards will guide the evaluation of constitutional CNVs and encourage consistency and transparency across clinical laboratories.

  View details for DOI 10.1038/s41436-019-0686-8

  View details for PubMedID 31690835

• Possible precision medicine implications from genetic testing using combined detection of sequence and intragenic copy number variants in a large cohort with childhood epilepsy. Epilepsia open Truty, R., Patil, N., Sankar, R., Sullivan, J., Millichap, J., Carvill, G., Entezam, A., Esplin, E. D., Fuller, A., Hogue, M., Johnson, B., Khouzam, A., Kobayashi, Y., Lewis, R., Nykamp, K., Riethmaier, D., Westbrook, J., Zeman, M., Nussbaum, R. L., Aradhya, S. 2019; 4 (3): 397-408

  Abstract

  Molecular genetic etiologies in epilepsy have become better understood in recent years, creating important opportunities for precision medicine. Building on these advances, detailed studies of the complexities and outcomes of genetic testing for epilepsy can provide useful insights that inform and refine diagnostic approaches and illuminate the potential for precision medicine in epilepsy.We used a multi-gene next-generation sequencing (NGS) panel with simultaneous sequence and exonic copy number variant detection to investigate up to 183 epilepsy-related genes in 9769 individuals. Clinical variant interpretation was performed using a semi-quantitative scoring system based on existing professional practice guidelines.Molecular genetic testing provided a diagnosis in 14.9%-24.4% of individuals with epilepsy, depending on the NGS panel used. More than half of these diagnoses were in children younger than 5 years. Notably, the testing had possible precision medicine implications in 33% of individuals who received definitive diagnostic results. Only 30 genes provided 80% of molecular diagnoses. While most clinically significant findings were single-nucleotide variants, ~15% were other types that are often challenging to detect with traditional methods. In addition to clinically significant variants, there were many others that initially had uncertain significance; reclassification of 1612 such variants with parental testing or other evidence contributed to 18.5% of diagnostic results overall and 6.1% of results with precision medicine implications.Using an NGS gene panel with key high-yield genes and robust analytic sensitivity as a first-tier test early in the diagnostic process, especially for children younger than 5 years, can possibly enable precision medicine approaches in a significant number of individuals with epilepsy.

  View details for DOI 10.1002/epi4.12348

  View details for PubMedID 31440721

  View details for PubMedCentralID PMC6698688

• Novel heterozygous mutation in the PTEN gene associated with ovarian germ cell tumor complicated by growing teratoma syndrome and overgrowth in a two-year-old female. Pediatric blood & cancer Tullius, B. P., Shankar, S. P., Cole, S., Triano, V., Aradhya, S., Huang, E. C., Sanchez, T., Pawar, A. 2019; 66 (8): e27788

  Abstract

  Growing teratoma syndrome (GTS) is a condition in which mature teratoma with negative tumor markers arises at the site of a treated malignant germ cell tumor. Pathogenic variants in PTEN have been reported to cause autosomal dominant cancer predisposition syndromes and are associated with germ cell tumors. We report the association of a novel heterozygous pathogenic variant in PTEN and very early onset ovarian germ cell tumor complicated by GTS as well as overgrowth syndrome. This marks the youngest reported patient to have developed GTS following treatment of her primary malignant ovarian germ cell tumor.

  View details for DOI 10.1002/pbc.27788

  View details for PubMedID 31038288

• Secondary findings on virtual panels: opportunities, challenges, and potential for preventive medicine GENETICS IN MEDICINE Esplin, E. D., Haverfield, E., Yang, S., Aradhya, S., Nussbaum, R. L. 2019; 21 (5): 1250-1251

  View details for DOI 10.1038/s41436-018-0302-3

  View details for Web of Science ID 000466707400028

  View details for PubMedID 30245515

• Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genetics in medicine : official journal of the American College of Medical Genetics Truty, R., Paul, J., Kennemer, M., Lincoln, S. E., Olivares, E., Nussbaum, R. L., Aradhya, S. 2019; 21 (1): 114-123

  Abstract

  We investigated the frequencies and characteristics of intragenic copy-number variants (CNVs) in a deep sampling of disease genes associated with monogenic disorders.Subsets of 1507 genes were tested using next-generation sequencing to simultaneously detect sequence variants and CNVs in >143,000 individuals referred for genetic testing. We analyzed CNVs in gene panels for hereditary cancer syndromes and cardiovascular, neurological, or pediatric disorders.Our analysis identified 2844 intragenic CNVs in 384 clinically tested genes. CNVs were observed in 1.9% of the entire cohort but in a disproportionately high fraction (9.8%) of individuals with a clinically significant result. CNVs accounted for 4.7-35% of pathogenic variants, depending on clinical specialty. Distinct patterns existed among CNVs in terms of copy number, location, exons affected, clinical classification, and genes affected. Separately, analysis of de-identified data for 599 genes unrelated to the clinical phenotype yielded 4054 CNVs. Most of these CNVs were novel rare events, present as duplications, and enriched in genes associated with recessive disorders or lacking loss-of-function mutational mechanisms.Universal intragenic CNV analysis adds substantial clinical sensitivity to genetic testing. Clinically relevant CNVs have distinct properties that distinguish them from CNVs contributing to normal variation in human disease genes.

  View details for DOI 10.1038/s41436-018-0033-5

  View details for PubMedID 29895855

  View details for PubMedCentralID PMC6752305

• Genetics in mainstream medicine: Finally within grasp to influence healthcare globally MOLECULAR GENETICS & GENOMIC MEDICINE Aradhya, S., Nussbaum, R. L. 2018; 6 (4): 473–80

  Abstract

  A modern genomics ecosystem has emerged. This commentary describes recent trends in clinical genomics that enable its successful integration in mainstream medicine. The rapid expansion of clinical genomics will have a positive impact on the healthcare of individuals worldwide.

  View details for PubMedID 29807392

• An interlaboratory study of complex mutation detection in genes associated with hereditary breast and ovarian cancer highlights both successes and current challenges Lincoln, S., Zook, J., Truty, R., Chowdhury, S., Fellowes, A., Mahamdallie, S., Ferber, M., Cleveland, M., Huang, C., Tomson, F., Klee, E., DeSilva, W., Seal, S., Aradhya, S., Nussbaum, R., Garlick, R., Kingsmore, S., Rahman, N., Salit, M., Shirts, B. AMER ASSOC CANCER RESEARCH. 2018

  View details for Web of Science ID 000425489401192

• Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria GENETICS IN MEDICINE Nykamp, K., Anderson, M., Powers, M., Garcia, J., Herrera, B., Ho, Y., Kobayashi, Y., Patil, N., Thusberg, J., Westbrook, M., Topper, S., Invitae Clinical Genomics Grp 2017; 19 (10): 1105–17

  Abstract

  PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification.MethodsWe undertook an iterative process of refining the ACMG-AMP guidelines. We used the guidelines to classify more than 40,000 clinically observed variants, assessed the outcome, and refined the classification criteria to capture exceptions and edge cases. During this process, the criteria evolved through eight major and minor revisions.ResultsOur implementation: (i) separated ambiguous ACMG-AMP criteria into a set of discrete but related rules with refined weights; (ii) grouped certain criteria to protect against the overcounting of conceptually related evidence; and (iii) replaced the "clinical criteria" style of the guidelines with additive, semiquantitative criteria.ConclusionSherloc builds on the strong framework of 33 rules established by the ACMG-AMP guidelines and introduces 108 detailed refinements, which support a more consistent and transparent approach to variant classification.

  View details for DOI 10.1038/gim.2017.37

  View details for Web of Science ID 000412303300005

  View details for PubMedID 28492532

  View details for PubMedCentralID PMC5632818

• Noninvasive prenatal screening for aneuploidy: positive predictive values based on cytogenetic findings AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY Meck, J. M., Dugan, E. K., Matyakhina, L., Aviram, A., Trunca, C., Pineda-Alvarez, D., Aradhya, S., Klein, R. T., Cherry, A. M. 2015; 213 (2)

  Abstract

  We sought to determine the positive predictive value (PPV) of noninvasive prenatal screening (NIPS) for various aneuploidies based on cases referred for follow-up cytogenetic testing. Secondarily, we wanted to determine the false-negative (FN) rate for those cases with a negative NIPS result.We compared the cytogenetic findings (primarily from chromosome analysis) from 216 cases referred to our laboratories with either a positive or negative NIPS result, and classified NIPS results as true positive, false positive, true negative, or FN. Diagnostic cytogenetic testing was performed on the following tissue types: amniotic fluid (n = 137), chorionic villi (n = 69), neonatal blood (n = 6), and products of conception (n = 4).The PPV for NIPS were as follows: 93% for trisomy (T)21 (n = 99; 95% confidence interval [CI], 86-97.1%), 58% for T18 (n = 24; 95% CI, 36.6-77.9%), 45% for T13 (n = 11; 95% CI, 16.7-76.6%), 23% for monosomy X (n = 26; 95% CI, 9-43.6%), and 67% for XXY (n = 6; 95% CI, 22.3-95.7%). Of the 26 cases referred for follow-up cytogenetics after a negative NIPS result, 1 (4%) was FN (T13). Two cases of triploidy, a very serious condition but one not claimed to be detectable by the test providers, were among those classified as true negatives.T21, which has the highest prevalence of all aneuploidies, demonstrated a high true-positive rate, resulting in a high PPV. However, the other aneuploidies, with their lower prevalence, displayed relatively high false-positive rates and, therefore, lower PPV. Patients and physicians must fully understand the limitations of this screening test and the need in many cases to follow up with appropriate diagnostic testing to obtain an accurate diagnosis.

  View details for DOI 10.1016/j.ajog.2015.04.001

  View details for Web of Science ID 000358550900024

• Assessing copy number from exome sequencing and exome array CGH based on CNV spectrum in a large clinical cohort. Genetics in medicine : official journal of the American College of Medical Genetics Retterer, K., Scuffins, J., Schmidt, D., Lewis, R., Pineda-Alvarez, D., Stafford, A., Schmidt, L., Warren, S., Gibellini, F., Kondakova, A., Blair, A., Bale, S., Matyakhina, L., Meck, J., Aradhya, S., Haverfield, E. 2015; 17 (8): 623-9

  Abstract

  Detection of copy-number variation (CNV) is important for investigating many genetic disorders. Testing a large clinical cohort by array comparative genomic hybridization provides a deep perspective on the spectrum of pathogenic CNV. In this context, we describe a bioinformatics approach to extract CNV information from whole-exome sequencing and demonstrate its utility in clinical testing.Exon-focused arrays and whole-genome chromosomal microarray analysis were used to test 14,228 and 14,000 individuals, respectively. Based on these results, we developed an algorithm to detect deletions/duplications in whole-exome sequencing data and a novel whole-exome array.In the exon array cohort, we observed a positive detection rate of 2.4% (25 duplications, 318 deletions), of which 39% involved one or two exons. Chromosomal microarray analysis identified 3,345 CNVs affecting single genes (18%). We demonstrate that our whole-exome sequencing algorithm resolves CNVs of three or more exons.These results demonstrate the clinical utility of single-exon resolution in CNV assays. Our whole-exome sequencing algorithm approaches this resolution but is complemented by a whole-exome array to unambiguously identify intragenic CNVs and single-exon changes. These data illustrate the next advancements in CNV analysis through whole-exome sequencing and whole-exome array.Genet Med 17 8, 623-629.

  View details for DOI 10.1038/gim.2014.160

  View details for PubMedID 25356966

• Noninvasive prenatal screening for aneuploidy: positive predictive values based on cytogenetic findings. American journal of obstetrics and gynecology Meck, J. M., Kramer Dugan, E., Matyakhina, L., Aviram, A., Trunca, C., Pineda-Alvarez, D., Aradhya, S., Klein, R. T., Cherry, A. M. 2015; 213 (2): 214 e1-5

  Abstract

  We sought to determine the positive predictive value (PPV) of noninvasive prenatal screening (NIPS) for various aneuploidies based on cases referred for follow-up cytogenetic testing. Secondarily, we wanted to determine the false-negative (FN) rate for those cases with a negative NIPS result.We compared the cytogenetic findings (primarily from chromosome analysis) from 216 cases referred to our laboratories with either a positive or negative NIPS result, and classified NIPS results as true positive, false positive, true negative, or FN. Diagnostic cytogenetic testing was performed on the following tissue types: amniotic fluid (n = 137), chorionic villi (n = 69), neonatal blood (n = 6), and products of conception (n = 4).The PPV for NIPS were as follows: 93% for trisomy (T)21 (n = 99; 95% confidence interval [CI], 86-97.1%), 58% for T18 (n = 24; 95% CI, 36.6-77.9%), 45% for T13 (n = 11; 95% CI, 16.7-76.6%), 23% for monosomy X (n = 26; 95% CI, 9-43.6%), and 67% for XXY (n = 6; 95% CI, 22.3-95.7%). Of the 26 cases referred for follow-up cytogenetics after a negative NIPS result, 1 (4%) was FN (T13). Two cases of triploidy, a very serious condition but one not claimed to be detectable by the test providers, were among those classified as true negatives.T21, which has the highest prevalence of all aneuploidies, demonstrated a high true-positive rate, resulting in a high PPV. However, the other aneuploidies, with their lower prevalence, displayed relatively high false-positive rates and, therefore, lower PPV. Patients and physicians must fully understand the limitations of this screening test and the need in many cases to follow up with appropriate diagnostic testing to obtain an accurate diagnosis.

  View details for DOI 10.1016/j.ajog.2015.04.001

  View details for PubMedID 25843063

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

  View details for DOI 10.1056/NEJMsr1406261

  View details for PubMedID 26014595

• A novel variant in GABRB2 associated with intellectual disability and epilepsy. American journal of medical genetics. Part A Srivastava, S., Cohen, J., Pevsner, J., Aradhya, S., McKnight, D., Butler, E., Johnston, M., Fatemi, A. 2014; 164A (11): 2914-21

  Abstract

  The γ-aminobutyric acid type A (GABAA ) receptor is one of the three main classes of receptors activated by GABA, the principal inhibitory neurotransmitter in the central nervous system. Mutations in genes encoding various subunits of this receptor (GABRA1, GABRA2, GABRA4, GABRA5, GABRA6, GABRB1, GABRB3, GABRG1, GABRG2, GABRG3, and GABRD) are implicated in a number of neurological and developmental disorders, including epilepsy and autism. To date, no human genetics studies have implicated mutations in GABRB2, encoding the β2 subunit of the GABAA receptor, with neurodevelopmental disorders. Here we present a 12-year-old girl with intellectual disability and epilepsy, who was discovered by whole exome sequencing to have a de novo heterozygous missense variant in exon 4 of GABRB2 (c.236T>C; p.M79T). This variant is likely pathogenic, based on in silico analyses, as well as the fact that it results in the non-conservative substitution of a non-polar amino acid with a polar amino acid at a position that is evolutionarily conserved across multiple species. Our findings underscore the need for further investigation into the mechanisms by which mutations in GABRB2 contribute to neurological and developmental dysfunction.

  View details for DOI 10.1002/ajmg.a.36714

  View details for PubMedID 25124326

  View details for PubMedCentralID PMC4205182

• Development of a genomic DNA reference material panel for Rett syndrome (MECP2-related disorders) genetic testing. The Journal of molecular diagnostics : JMD Kalman, L. V., Tarleton, J. C., Percy, A. K., Aradhya, S., Bale, S., Barker, S. D., Bayrak-Toydemir, P., Bridges, C., Buller-Burckle, A. M., Das, S., Iyer, R. K., Vo, T. D., Zvereff, V. V., Toji, L. H. 2014; 16 (2): 273-9

  Abstract

  Rett syndrome is a dominant X-linked disorder caused by point mutations (approximately 80%) or by deletions or insertions (approximately 15% to 18%) in the MECP2 gene. It is most common in females but lethal in males, with a distinctly different phenotype. Rett syndrome patients have severe neurological and behavioral problems. Clinical genetic testing laboratories commonly use characterized genomic DNA reference materials to assure the quality of the testing process; however, none are commercially available for MECP2 genetic testing. The Centers for Disease Control and Prevention's Genetic Testing Reference Material Coordination Program, in collaboration with the genetic testing community and the Coriell Cell Repositories, established 27 new cell lines and characterized the MECP2 mutations in these and in 8 previously available cell lines. DNA samples from the 35 cell lines were tested by eight clinical genetic testing laboratories using DNA sequence analysis and methods to assess copy number (multiplex ligation-dependent probe amplification, semiquantitative PCR, or array-based comparative genomic hybridization). The eight common point mutations known to cause approximately 60% of Rett syndrome cases were identified, as were other MECP2 variants, including deletions, duplications, and frame shift and splice-site mutations. Two of the 35 samples were from males with MECP2 duplications. These MECP2 and other characterized genomic DNA samples are publicly available from the NIGMS Repository at the Coriell Cell Repositories.

  View details for DOI 10.1016/j.jmoldx.2013.11.004

  View details for PubMedID 24508304

  View details for PubMedCentralID PMC3937532

• Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder. European journal of human genetics : EJHG Mullegama, S. V., Rosenfeld, J. A., Orellana, C., van Bon, B. W., Halbach, S., Repnikova, E. A., Brick, L., Li, C., Dupuis, L., Rosello, M., Aradhya, S., Stavropoulos, D. J., Manickam, K., Mitchell, E., Hodge, J. C., Talkowski, M. E., Gusella, J. F., Keller, K., Zonana, J., Schwartz, S., Pyatt, R. E., Waggoner, D. J., Shaffer, L. G., Lin, A. E., de Vries, B. B., Mendoza-Londono, R., Elsea, S. H. 2014; 22 (1): 57-63

  Abstract

  Copy number variations associated with abnormal gene dosage have an important role in the genetic etiology of many neurodevelopmental disorders, including intellectual disability (ID) and autism. We hypothesize that the chromosome 2q23.1 region encompassing MBD5 is a dosage-dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome. The observed phenotype includes ID, language impairments, infantile hypotonia and gross motor delay, behavioral problems, autistic features, dysmorphic facial features (pinnae anomalies, arched eyebrows, prominent nose, small chin, thin upper lip), and minor digital anomalies (fifth finger clinodactyly and large broad first toe). The microduplication size varies among all cases and ranges from 68 kb to 53.7 Mb, encompassing a region that includes MBD5, an important factor in methylation patterning and epigenetic regulation. We previously reported that haploinsufficiency of MBD5 is the primary causal factor in 2q23.1 microdeletion syndrome and that mutations in MBD5 are associated with autism. In this study, we demonstrate that MBD5 is the only gene in common among all duplication cases and that overexpression of MBD5 is likely responsible for the core clinical features present in 2q23.1 microduplication syndrome. Phenotypic analyses suggest that 2q23.1 duplication results in a slightly less severe phenotype than the reciprocal deletion. The features associated with a deletion, mutation or duplication of MBD5 and the gene expression changes observed support MBD5 as a dosage-sensitive gene critical for normal development.

  View details for DOI 10.1038/ejhg.2013.67

  View details for PubMedID 23632792

  View details for PubMedCentralID PMC3865402

• Adrenal hypoplasia congenita with phenotypic features suggestive of neurofibromatosis type 1 among three African-American brothers. American journal of medical genetics. Part A Balikcioglu, P. G., Gómez, R., Vargas, A., Aradhya, S., Messiaen, L. M., Lacassie, Y. 2013; 161A (8): 2105-7

  View details for DOI 10.1002/ajmg.a.36031

  View details for PubMedID 23824603

• The duplication 17p13.3 phenotype: analysis of 21 families delineates developmental, behavioral and brain abnormalities, and rare variant phenotypes. American journal of medical genetics. Part A Curry, C. J., Rosenfeld, J. A., Grant, E., Gripp, K. W., Anderson, C., Aylsworth, A. S., Saad, T. B., Chizhikov, V. V., Dybose, G., Fagerberg, C., Falco, M., Fels, C., Fichera, M., Graakjaer, J., Greco, D., Hair, J., Hopkins, E., Huggins, M., Ladda, R., Li, C., Moeschler, J., Nowaczyk, M. J., Ozmore, J. R., Reitano, S., Romano, C., Roos, L., Schnur, R. E., Sell, S., Suwannarat, P., Svaneby, D., Szybowska, M., Tarnopolsky, M., Tervo, R., Tsai, A. C., Tucker, M., Vallee, S., Wheeler, F. C., Zand, D. J., Barkovich, A. J., Aradhya, S., Shaffer, L. G., Dobyns, W. B. 2013; 161A (8): 1833-52

  Abstract

  Chromosome 17p13.3 is a gene rich region that when deleted is associated with the well-known Miller-Dieker syndrome. A recently described duplication syndrome involving this region has been associated with intellectual impairment, autism and occasional brain MRI abnormalities. We report 34 additional patients from 21 families to further delineate the clinical, neurological, behavioral, and brain imaging findings. We found a highly diverse phenotype with inter- and intrafamilial variability, especially in cognitive development. The most specific phenotype occurred in individuals with large duplications that include both the YWHAE and LIS1 genes. These patients had a relatively distinct facial phenotype and frequent structural brain abnormalities involving the corpus callosum, cerebellar vermis, and cranial base. Autism spectrum disorders were seen in a third of duplication probands, most commonly in those with duplications of YWHAE and flanking genes such as CRK. The typical neurobehavioral phenotype was usually seen in those with the larger duplications. We did not confirm the association of early overgrowth with involvement of YWHAE and CRK, or growth failure with duplications of LIS1. Older patients were often overweight. Three variant phenotypes included cleft lip/palate (CLP), split hand/foot with long bone deficiency (SHFLD), and a connective tissue phenotype resembling Marfan syndrome. The duplications in patients with clefts appear to disrupt ABR, while the SHFLD phenotype was associated with duplication of BHLHA9 as noted in two recent reports. The connective tissue phenotype did not have a convincing critical region. Our experience with this large cohort expands knowledge of this diverse duplication syndrome.

  View details for DOI 10.1002/ajmg.a.35996

  View details for PubMedID 23813913

  View details for PubMedCentralID PMC5517092

• Partial deletion of ANKRD11 results in the KBG phenotype distinct from the 16q24.3 microdeletion syndrome. American journal of medical genetics. Part A Khalifa, M., Stein, J., Grau, L., Nelson, V., Meck, J., Aradhya, S., Duby, J. 2013; 161A (4): 835-40

  Abstract

  KBG syndrome (OMIM 148050) is a very rare genetic disorder characterized by macrodontia, distinctive craniofacial abnormalities, short stature, intellectual disability, skeletal, and neurologic involvement. Approximately 60 patients have been reported since it was first described in 1975. Recently mutations in ANKRD11 have been documented in patients with KBG syndrome, and it has been proposed that haploinsufficiency of ANKRD11 is the cause of this syndrome. In addition, copy number variation in the 16q24.3 region that includes ANKRD11 results in a variable phenotype that overlaps with KBG syndrome and also includes autism spectrum disorders and other dysmorphic facial features. In this report we present a 2½-year-old African American male with features highly suggestive of KBG syndrome. Genomic microarray identified an intragenic 154 kb deletion at 16q24.3 within ANKRD11. This child's mother was mosaic for the same deletion (present in approximately 38% of cells) and exhibited a milder phenotype including macrodontia, short stature and brachydactyly. This family provides additional evidence that ANKRD11 causes KBG syndrome, and the mild phenotype in the mosaic form suggests that KBG phenotypes might be dose dependent, differentiating it from the more variable 16q24.3 microdeletion syndrome. This family has additional features that might expand the phenotype of KBG syndrome.

  View details for DOI 10.1002/ajmg.a.35739

  View details for PubMedID 23494856

• RUNX2 quadruplication: additional evidence toward a new form of syndromic craniosynostosis. The Journal of craniofacial surgery Greives, M. R., Odessey, E. A., Waggoner, D. J., Shenaq, D. S., Aradhya, S., Mitchell, A., Whitcomb, E., Warshawsky, N., He, T. C., Reid, R. R. 2013; 24 (1): 126-9

  Abstract

  The RUNX2 transcription factor regulates osteoblast differentiation. Its absence, as with cleidocranial dysplasia, results in deficient bone formation. However, its excess seems to follow a dose response of over ossification. RUNX2 duplications (3 copies) are exceedingly rare but have been reported to cause craniosynostosis. There are no existing reports of quadruplications (4 copies). We present a case study of a boy with an atypical skull deformity with pan-craniosynostosis whose microarray analysis revealed 4 copies of a 1.24-Mb region from 6p12.3 to 6p21.1 containing the RUNX2 gene. Further characterization of this osteogenic pathway may aid in our understanding of the pathogenesis and subsequent prevention and treatment of syndromic craniosynostosis.

  View details for DOI 10.1097/SCS.0b013e31826686d3

  View details for PubMedID 23348268

• A systematic analysis of small supernumerary marker chromosomes using array CGH exposes unexpected complexity. Genetics in medicine : official journal of the American College of Medical Genetics Reddy, K. S., Aradhya, S., Meck, J., Tiller, G., Abboy, S., Bass, H. 2013; 15 (1): 3-13

  Abstract

  A small supernumerary marker chromosome is often seen in patients with developmental disorders. Prior to array-based comparative genomic hybridization markers were rarely genotyped end to end. In this study, a valid genotype-to-phenotype correlation was possible because the supernumerary marker chromosomes were fully characterized by array-based comparative genomic hybridization in a genome-wide analysis.Ten consecutive de novo small supernumerary marker chromosome cases were systematically genotyped using G-banding, C-banding, AgNOR staining, whole-genome array-based comparative genomic hybridization, and fluorescence in situ hybridization.Among 10 small supernumerary marker chromosome cases studied, 4 (40%) were not identified by array-based comparative genomic hybridization because of low-level mosaicism or because they lacked euchromatin. One case (10%) was a simple pericentromeric marker extending from 5p13.3 to 5q11.2. Five (50%) markers showed unexpected complexity. Two cases had markers that were derivative acrocentric (AgNOR+) chromosomes with the euchromatin from chromosomes 18p or 19p. Each of the other three cases with complex markers had unusual characteristics including a marker from noncontiguous segments of chromosome 19q, a highly complex rearrangement involving a chromosome 20 homolog as well as the small supernumerary marker chromosome, and a mosaic duplication of a proximal 8p marker.Small supernumerary marker chromosomes are frequently complex on the basis of our small sample. Whole-genome array-based comparative genomic hybridization characterization of the small supernumerary marker chromosome provided informed genetic counseling.

  View details for DOI 10.1038/gim.2012.78

  View details for PubMedID 22935720

• Nablus mask-like facial syndrome: deletion of chromosome 8q22.1 is necessary but not sufficient to cause the phenotype. American journal of medical genetics. Part A Allanson, J., Smith, A., Hare, H., Albrecht, B., Bijlsma, E., Dallapiccola, B., Donti, E., Fitzpatrick, D., Isidor, B., Lachlan, K., Le Caignec, C., Prontera, P., Raas-Rothschild, A., Rogaia, D., van Bon, B., Aradhya, S., Crocker, S. F., Jarinova, O., McGowan-Jordan, J., Boycott, K., Bulman, D., Fagerberg, C. R. 2012; 158A (9): 2091-9

  Abstract

  Nablus mask-like facial syndrome (NMLFS) has many distinctive phenotypic features, particularly tight glistening skin with reduced facial expression, blepharophimosis, telecanthus, bulky nasal tip, abnormal external ear architecture, upswept frontal hairline, and sparse eyebrows. Over the last few years, several individuals with NMLFS have been reported to have a microdeletion of 8q21.3q22.1, demonstrated by microarray analysis. The minimal overlapping region is 93.98-96.22 Mb (hg19). Here we present clinical and microarray data from five singletons and two mother-child pairs who have heterozygous deletions significantly overlapping the region associated with NMLFS. Notably, while one mother and child were said to have mild tightening of facial skin, none of these individuals exhibited reduced facial expression or the classical facial phenotype of NMLFS. These findings indicate that deletion of the 8q21.3q22.1 region is necessary but not sufficient for development of the NMLFS. We discuss possible genetic mechanisms underlying the complex pattern of inheritance for this condition.

  View details for DOI 10.1002/ajmg.a.35446

  View details for PubMedID 22821852

• Deletion of filamin A in two female patients with periventricular nodular heterotopia. American journal of medical genetics. Part A Chardon, J. W., Mignot, C., Aradhya, S., Keren, B., Afenjar, A., Kaminska, A., Beldjord, C., Héron, D., Boycott, K. M. 2012; 158A (6): 1512-6

  View details for DOI 10.1002/ajmg.a.35409

  View details for PubMedID 22522697

• Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders. Genetics in medicine : official journal of the American College of Medical Genetics Aradhya, S., Lewis, R., Bonaga, T., Nwokekeh, N., Stafford, A., Boggs, B., Hruska, K., Smaoui, N., Compton, J. G., Richard, G., Suchy, S. 2012; 14 (6): 594-603

  Abstract

  Mendelian disorders are most commonly caused by mutations identifiable by DNA sequencing. Exonic deletions and duplications can go undetected by sequencing, and their frequency in most Mendelian disorders is unknown.We designed an array comparative genomic hybridization (CGH) test with probes in exonic regions of 589 genes. Targeted testing was performed for 219 genes in 3,018 patients. We demonstrate for the first time the utility of exon-level array CGH in a large clinical cohort by testing for 136 autosomal dominant, 53 autosomal recessive, and 30 X-linked disorders.Overall, 98 deletions and two duplications were identified in 53 genes, corresponding to a detection rate of 3.3%. Approximately 40% of positive findings were deletions of only one or two exons. A high frequency of deletions was observed for several autosomal dominant disorders, with a detection rate of 2.9%. For autosomal recessive disorders, array CGH was usually performed after a single mutation was identified by sequencing. Among 138 individuals tested for recessive disorders, 10.1% had intragenic deletions. For X-linked disorders, 3.5% of 313 patients carried a deletion or duplication.Our results demonstrate that exon-level array CGH provides a robust option for intragenic copy number analysis and should routinely supplement sequence analysis for Mendelian disorders.

  View details for DOI 10.1038/gim.2011.65

  View details for PubMedID 22382802

• A de novo 1.13 Mb microdeletion in 12q13.13 associated with congenital distal arthrogryposis, intellectual disability and mild dysmorphism. European journal of medical genetics Jonsson, D. I., Ludvigsson, P., Aradhya, S., Sigurdardottir, S., Steinarsdottir, M., Hauksdottir, H., Jonsson, J. J. 2012; 55 (6-7): 437-40

  Abstract

  A girl presented with congenital arthrogryposis, intellectual disability and mild bone-related dysmorphism. Molecular workup including the NimbleGen Human CGH 2.1M platform revealed a 1.13 Mb de novo microdeletion on chromosome 12q13.13 of paternal origin. The deletion contains 33 genes, including AAAS, AMRH2, and RARG genes as well as the HOXC gene cluster. At least one gene, CSAD, is expressed in fetal brain. The deletion partially overlaps number of reported benign CNVs and pathogenic duplications. This case appears to represent a previously unknown microdeletion syndrome and possibly the first description in humans of a disease phenotype associated with copy loss of HOXC genes.

  View details for DOI 10.1016/j.ejmg.2012.03.001

  View details for PubMedID 22534424

• Towards an evidence-based process for the clinical interpretation of copy number variation. Clinical genetics Riggs, E. R., Church, D. M., Hanson, K., Horner, V. L., Kaminsky, E. B., Kuhn, R. M., Wain, K. E., Williams, E. S., Aradhya, S., Kearney, H. M., Ledbetter, D. H., South, S. T., Thorland, E. C., Martin, C. L. 2012; 81 (5): 403-12

  Abstract

  The evidence-based review (EBR) process has been widely used to develop standards for medical decision-making and to explore complex clinical questions. This approach can be applied to genetic tests, such as chromosomal microarrays, in order to assist in the clinical interpretation of certain copy number variants (CNVs), particularly those that are rare, and guide array design for optimal clinical utility. To address these issues, the International Standards for Cytogenomic Arrays Consortium has established an EBR Work Group charged with building a framework to systematically assess the potential clinical relevance of CNVs throughout the genome. This group has developed a rating system enumerating the evidence supporting or refuting dosage sensitivity for individual genes and regions that considers the following criteria: number of causative mutations reported; patterns of inheritance; consistency of phenotype; evidence from large-scale case-control studies; mutational mechanisms; data from public genome variation databases; and expert consensus opinion. The system is designed to be dynamic in nature, with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected will be displayed within a publically available database, and can be used in part to inform clinical laboratory CNV interpretations as well as to guide array design.

  View details for DOI 10.1111/j.1399-0004.2011.01818.x

  View details for PubMedID 22097934

  View details for PubMedCentralID PMC5008023

• Severe intellectual disability and autistic features associated with microduplication 2q23.1. European journal of human genetics : EJHG Chung, B. H., Mullegama, S., Marshall, C. R., Lionel, A. C., Weksberg, R., Dupuis, L., Brick, L., Li, C., Scherer, S. W., Aradhya, S., Stavropoulos, D. J., Elsea, S. H., Mendoza-Londono, R. 2012; 20 (4): 398-403

  Abstract

  We report on two patients with developmental delay, hypotonia, and autistic features associated with duplications of chromosome region 2q23.1-2q23.2 detected by chromosome microarray analysis. The duplications include one OMIM Morbid Map gene, MBD5, as well as seven known RefSeq genes (ACVR2A, ORC4L, EPC2, KIF5C, MIR1978, LYPD6B, and LYPD6). MBD5 lies in the minimum area of overlap of the 2q23.1 microdeletion syndrome. This report provides the first detailed clinical examination of two individuals with a duplication of this region and suggests that brain development and cognitive function may be affected by an increased dosage of the genes involved.

  View details for DOI 10.1038/ejhg.2011.199

  View details for PubMedID 22085900

  View details for PubMedCentralID PMC3306850

• Microdeletion 9q22.3 syndrome includes metopic craniosynostosis, hydrocephalus, macrosomia, and developmental delay AMERICAN JOURNAL OF MEDICAL GENETICS PART A Muller, E. A., Aradhya, S., Atkin, J. F., Carmany, E. P., Elliott, A. M., Chudley, A. E., Clark, R. D., Everman, D. B., Garner, S., Hall, B. D., Herman, G. E., Kivuva, E., Ramanathan, S., Stevenson, D. A., Stockton, D. W., Hudgins, L. 2012; 158A (2): 391-399

  Abstract

  Basal cell nevus syndrome (BCNS), also known as Gorlin syndrome (OMIM #109400) is a well-described rare autosomal dominant condition due to haploinsufficiency of PTCH1. With the availability of comparative genomic hybridization arrays, increasing numbers of individuals with microdeletions involving this locus are being identified. We present 10 previously unreported individuals with 9q22.3 deletions that include PTCH1. While 7 of the 10 patients (7 females, 3 males) did not meet strict clinical criteria for BCNS at the time of molecular diagnosis, almost all of the patients were too young to exhibit many of the diagnostic features. A number of the patients exhibited metopic craniosynostosis, severe obstructive hydrocephalus, and macrosomia, which are not typically observed in BCNS. All individuals older than a few months of age also had developmental delays and/or intellectual disability. Only facial features typical of BCNS, except in those with prominent midforeheads secondary to metopic craniosynostosis, were shared among the 10 patients. The deletions in these individuals ranged from 352  kb to 20.5  Mb in size, the largest spanning 9q21.33 through 9q31.2. There was significant overlap of the deleted segments among most of the patients. The smallest common regions shared among the deletions were identified in order to localize putative candidate genes that are potentially responsible for each of the non-BCNS features. These were a 929  kb region for metopic craniosynostosis, a 1.08  Mb region for obstructive hydrocephalus, and a 1.84  Mb region for macrosomia. Additional studies are needed to further characterize the candidate genes within these regions.

  View details for DOI 10.1002/ajmg.a.34216

  View details for PubMedID 22190277

• A de novo 2.1-Mb deletion of 13q12.11 in a child with developmental delay and minor dysmorphic features. American journal of medical genetics. Part A Der Kaloustian, V. M., Russell, L., Aradhya, S., Richard, G., Rosenblatt, B., Melançon, S. 2011; 155A (10): 2538-42

  Abstract

  We report on a patient with an interstitial deletion at 13q12.11. He had mild developmental delay, craniofacial dysmorphism, a pectus excavatum, narrow shoulders, malformed toes, and café-au-lait spots. Array CGH analysis disclosed a de novo deletion spanning 2.1 Mb,within cytogenetic band 13q12.11.The deletion produces hemizygozity for 16 known genes, among which GJA3, GJB2, GJB6, IFT88, LATS2, and FGF9 have potential clinical significance. The observed phenotype may be due to mutation in one of the 16 genes, or to a combination of deletion and/or mutation in a number of them.

  View details for DOI 10.1002/ajmg.a.34198

  View details for PubMedID 22043489

• An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genetics in medicine : official journal of the American College of Medical Genetics Kaminsky, E. B., Kaul, V., Paschall, J., Church, D. M., Bunke, B., Kunig, D., Moreno-De-Luca, D., Moreno-De-Luca, A., Mulle, J. G., Warren, S. T., Richard, G., Compton, J. G., Fuller, A. E., Gliem, T. J., Huang, S., Collinson, M. N., Beal, S. J., Ackley, T., Pickering, D. L., Golden, D. M., Aston, E., Whitby, H., Shetty, S., Rossi, M. R., Rudd, M. K., South, S. T., Brothman, A. R., Sanger, W. G., Iyer, R. K., Crolla, J. A., Thorland, E. C., Aradhya, S., Ledbetter, D. H., Martin, C. L. 2011; 13 (9): 777-84

  Abstract

  Copy number variants have emerged as a major cause of human disease such as autism and intellectual disabilities. Because copy number variants are common in normal individuals, determining the functional and clinical significance of rare copy number variants in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain large copy number variant datasets generated through routine patient care.A consortium of diagnostic laboratories was established (the International Standards for Cytogenomic Arrays consortium) to share copy number variant and phenotypic data in a central, public database. We present the largest copy number variant case-control study to date comprising 15,749 International Standards for Cytogenomic Arrays cases and 10,118 published controls, focusing our initial analysis on recurrent deletions and duplications involving 14 copy number variant regions.Compared with controls, 14 deletions and seven duplications were significantly overrepresented in cases, providing a clinical diagnosis as pathogenic.Given the rapid expansion of clinical chromosomal microarray analysis testing, very large datasets will be available to determine the functional significance of increasingly rare copy number variants. This data will provide an evidence-based guide to clinicians across many disciplines involved in the diagnosis, management, and care of these patients and their families.

  View details for DOI 10.1097/GIM.0b013e31822c79f9

  View details for PubMedID 21844811

  View details for PubMedCentralID PMC3661946

• The phenotype of recurrent 10q22q23 deletions and duplications. European journal of human genetics : EJHG van Bon, B. W., Balciuniene, J., Fruhman, G., Nagamani, S. C., Broome, D. L., Cameron, E., Martinet, D., Roulet, E., Jacquemont, S., Beckmann, J. S., Irons, M., Potocki, L., Lee, B., Cheung, S. W., Patel, A., Bellini, M., Selicorni, A., Ciccone, R., Silengo, M., Vetro, A., Knoers, N. V., de Leeuw, N., Pfundt, R., Wolf, B., Jira, P., Aradhya, S., Stankiewicz, P., Brunner, H. G., Zuffardi, O., Selleck, S. B., Lupski, J. R., de Vries, B. B. 2011; 19 (4): 400-8

  Abstract

  The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.

  View details for DOI 10.1038/ejhg.2010.211

  View details for PubMedID 21248748

  View details for PubMedCentralID PMC3060324

• De novo duplication 11p13 involving the PAX6 gene in a patient with neonatal seizures, hypotonia, microcephaly, developmental disability and minor ocular manifestations. American journal of medical genetics. Part A Aradhya, S., Smaoui, N., Marble, M., Lacassie, Y. 2011; 155A (2): 442-4

  View details for DOI 10.1002/ajmg.a.33814

  View details for PubMedID 21271670

• Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia. American journal of human genetics Moreno-De-Luca, D., Mulle, J. G., Kaminsky, E. B., Sanders, S. J., Myers, S. M., Adam, M. P., Pakula, A. T., Eisenhauer, N. J., Uhas, K., Weik, L., Guy, L., Care, M. E., Morel, C. F., Boni, C., Salbert, B. A., Chandrareddy, A., Demmer, L. A., Chow, E. W., Surti, U., Aradhya, S., Pickering, D. L., Golden, D. M., Sanger, W. G., Aston, E., Brothman, A. R., Gliem, T. J., Thorland, E. C., Ackley, T., Iyer, R., Huang, S., Barber, J. C., Crolla, J. A., Warren, S. T., Martin, C. L., Ledbetter, D. H. 2010; 87 (5): 618-30

  Abstract

  Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻⁵). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.

  View details for DOI 10.1016/j.ajhg.2010.10.004

  View details for PubMedID 21055719

  View details for PubMedCentralID PMC2978962

• Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. American journal of human genetics Miller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., Church, D. M., Crolla, J. A., Eichler, E. E., Epstein, C. J., Faucett, W. A., Feuk, L., Friedman, J. M., Hamosh, A., Jackson, L., Kaminsky, E. B., Kok, K., Krantz, I. D., Kuhn, R. M., Lee, C., Ostell, J. M., Rosenberg, C., Scherer, S. W., Spinner, N. B., Stavropoulos, D. J., Tepperberg, J. H., Thorland, E. C., Vermeesch, J. R., Waggoner, D. J., Watson, M. S., Martin, C. L., Ledbetter, D. H. 2010; 86 (5): 749-64

  Abstract

  Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.

  View details for DOI 10.1016/j.ajhg.2010.04.006

  View details for PubMedID 20466091

  View details for PubMedCentralID PMC2869000

• Variability in interpreting and reporting copy number changes detected by array-based technology in clinical laboratories. Genetics in medicine : official journal of the American College of Medical Genetics Tsuchiya, K. D., Shaffer, L. G., Aradhya, S., Gastier-Foster, J. M., Patel, A., Rudd, M. K., Biggerstaff, J. S., Sanger, W. G., Schwartz, S., Tepperberg, J. H., Thorland, E. C., Torchia, B. A., Brothman, A. R. 2009; 11 (12): 866-73

  Abstract

  : The purpose of this study was to assess the variability in interpretation and reporting of copy number changes that are detected by array-based technology in the clinical laboratory.: Thirteen different copy number changes, detected by array comparative genomic hybridization, that have not been associated with an abnormal phenotype in the literature were evaluated by directors from 11 different clinical laboratories to determine how they would interpret and report the findings.: For none of the thirteen copy number changes was there complete agreement in the interpretation of the clinical significance of the deletion or duplication. For some cases, the interpretations ranged from normal to abnormal.: There is a need for more specific guidelines for interpreting and reporting copy number changes detected by array-based technology to clearly and more consistently communicate the clinical significance of these findings to ordering providers.

  View details for DOI 10.1097/GIM.0b013e3181c0c3b0

  View details for PubMedID 19904209

• Mutations in the calcium-related gene IL1RAPL1 are associated with autism. Human molecular genetics Piton, A., Michaud, J. L., Peng, H., Aradhya, S., Gauthier, J., Mottron, L., Champagne, N., Lafrenière, R. G., Hamdan, F. F., Joober, R., Fombonne, E., Marineau, C., Cossette, P., Dubé, M. P., Haghighi, P., Drapeau, P., Barker, P. A., Carbonetto, S., Rouleau, G. A. 2008; 17 (24): 3965-74

  Abstract

  In a systematic sequencing screen of synaptic genes on the X chromosome, we have identified an autistic female without mental retardation (MR) who carries a de novo frameshift Ile367SerfsX6 mutation in Interleukin-1 Receptor Accessory Protein-Like 1 (IL1RAPL1), a gene implicated in calcium-regulated vesicle release and dendrite differentiation. We showed that the function of the resulting truncated IL1RAPL1 protein is severely altered in hippocampal neurons, by measuring its effect on neurite outgrowth activity. We also sequenced the coding region of the close related member IL1RAPL2 and of NCS-1/FREQ, which physically interacts with IL1RAPL1, in a cohort of subjects with autism. The screening failed to identify non-synonymous variant in IL1RAPL2, whereas a rare missense (R102Q) in NCS-1/FREQ was identified in one autistic patient. Furthermore, we identified by comparative genomic hybridization a large intragenic deletion of exons 3-7 of IL1RAPL1 in three brothers with autism and/or MR. This deletion causes a frameshift and the introduction of a premature stop codon, Ala28GlufsX15, at the very beginning of the protein. All together, our results indicate that mutations in IL1RAPL1 cause a spectrum of neurological impairments ranging from MR to high functioning autism.

  View details for DOI 10.1093/hmg/ddn300

  View details for PubMedID 18801879

• Clinical and molecular delineation of the 17q21.31 microdeletion syndrome JOURNAL OF MEDICAL GENETICS Koolen, D. A., Sharp, A. J., Hurst, J. A., Firth, H. V., Knight, S. J., Goldenberg, A., Saugier-Veber, P., Pfundt, R., Vissers, L. E., Destree, A., Grisart, B., Rooms, L., Van der Aa, N., Field, M., Hackett, A., Bell, K., Nowaczyk, M. J., Mancini, G. M., Poddighe, P. J., Schwartz, C. E., Rossi, E., De Gregori, M., Antonacci-Fulton, L. L., McLellan, M. D., Garrett, J. M., Wiechert, M. A., Miner, T. L., Crosby, S., Ciccone, R., Willatt, L., Rauch, A., Zenker, M., Aradhya, S., Manning, M. A., Strom, T. M., Wagenstaller, J., Krepischi-Santos, A. C., Vianna-Morgante, A. M., Rosenberg, C., Price, S. M., Stewart, H., Shaw-Smith, C., Brunner, H. G., Wilkie, A. O., Veltman, J. A., Zuffardi, O., Eichler, E. E., de Vries, B. B. 2008; 45 (11): 710-720

  Abstract

  The chromosome 17q21.31 microdeletion syndrome is a novel genomic disorder that has originally been identified using high resolution genome analyses in patients with unexplained mental retardation.We report the molecular and/or clinical characterisation of 22 individuals with the 17q21.31 microdeletion syndrome.We estimate the prevalence of the syndrome to be 1 in 16,000 and show that it is highly underdiagnosed. Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features. Other clinically important features include epilepsy, heart defects and kidney/urologic anomalies. Using high resolution oligonucleotide arrays we narrow the 17q21.31 critical region to a 424 kb genomic segment (chr17: 41046729-41470954, hg17) encompassing at least six genes, among which is the gene encoding microtubule associated protein tau (MAPT). Mutation screening of MAPT in 122 individuals with a phenotype suggestive of 17q21.31 deletion carriers, but who do not carry the recurrent deletion, failed to identify any disease associated variants. In five deletion carriers we identify a <500 bp rearrangement hotspot at the proximal breakpoint contained within an L2 LINE motif and show that in every case examined the parent originating the deletion carries a common 900 kb 17q21.31 inversion polymorphism, indicating that this inversion is a necessary factor for deletion to occur (p<10(-5)).Our data establish the 17q21.31 microdeletion syndrome as a clinically and molecularly well recognisable genomic disorder.

  View details for DOI 10.1136/jmg.2008.058701

  View details for Web of Science ID 000260535600004

  View details for PubMedID 18628315

  View details for PubMedCentralID PMC3071570

• Genetic analysis of attractin homologs GENESIS Walker, W. P., Aradhya, S., Hu, C., Shen, S., Zhang, W., Azarani, A., Lu, X., Barsh, G. S., Gunn, T. M. 2007; 45 (12): 744-756

  Abstract

  Attractin (ATRN) and Attractin-like 1 (ATRNL1) are highly similar type I transmembrane proteins. Atrn null mutant mice have a pleiotropic phenotype including dark fur, juvenile-onset spongiform neurodegeneration, hypomyelination, tremor, and reduced body weight and adiposity, implicating ATRN in numerous biological processes. Bioinformatic analysis indicated that Atrn and Atrnl1 arose from a common ancestral gene early in vertebrate evolution. To investigate the genetics of the ATRN system and explore potential redundancy between Atrn and Atrnl1, we generated and characterized Atrnl1 loss- and gain-of-function mutations in mice. Atrnl1 mutant mice were grossly normal with no alterations of pigmentation, central nervous system pathology or body weight. Atrn null mutant mice carrying a beta-actin promoter-driven Atrnl1 transgene had normal, agouti-banded hairs and significantly delayed onset of spongiform neurodegeneration, indicating that over-expression of ATRNL1 compensates for loss of ATRN. Thus, the two genes are redundant from the perspective of gain-of-function but not loss-of-function mutations.

  View details for DOI 10.1002/dvg.20351

  View details for Web of Science ID 000252307200003

  View details for PubMedID 18064672

• Array-based comparative genomic hybridization: clinical contexts for targeted and whole-genome designs GENETICS IN MEDICINE Aradhya, S., Cherry, A. M. 2007; 9 (9): 553-559

  Abstract

  Array-based comparative genomic hybridization is ushering in a new standard for analyzing the genome, overcoming the limits of resolution associated with conventional G-banded karyotyping. The first genomic arrays were based on bacterial artificial chromosome clones mapped during the initial phases of the Human Genome Project. These arrays essentially represented multiple fluorescence in situ hybridization assays performed simultaneously. The first arrays featured a targeted design, consisting of hundreds of bacterial artificial chromosome clones limited mostly to genomic regions of known medical significance. Then came whole-genome arrays, which contained bacterial artificial chromosome clones from across the entire genome. More recently, alternative designs based on oligonucleotide probes have been developed, and all these are high-density whole-genome arrays with resolutions between 3 and 35 kb. Certain clinical circumstances are well suited for investigation by targeted arrays, and there are others in which high-resolution whole-genome arrays are necessary. Here we review the differences between the two types of arrays and the clinical contexts for which they are best suited. As array-based comparative genomic hybridization is integrated into diagnostic laboratories and different array designs are used in appropriate clinical contexts, this novel technology will invariably alter the testing paradigm in medical genetics and will lead to the discovery of novel genetic conditions caused by chromosomal anomalies.

  View details for DOI 10.1097/GIM.0b013e318149e354

  View details for Web of Science ID 000249640800001

  View details for PubMedID 17873642

• Whole-genome array-CGH identifies novel contiguous gene deletions and duplications associated with developmental delay, mental retardation, and dysmorphic features AMERICAN JOURNAL OF MEDICAL GENETICS PART A Aradhya, S., Manning, M. A., Splendore, A., Cherry, A. M. 2007; 143A (13): 1431-1441

  Abstract

  Cytogenetic imbalances are the most frequently identified cause of developmental delay or mental retardation, which affect 1-3% of children and are often seen in conjunction with growth retardation, dysmorphic features, and various congenital anomalies. A substantial number of patients with developmental delay or mental retardation are predicted to have cytogenetic imbalances, but conventional methods for identifying these imbalances yield positive results in only a small fraction of these patients. We used microarray-based comparative genomic hybridization (aCGH) to study a panel of 20 patients predicted to have chromosomal aberrations based on clinical presentation of developmental delay or mental retardation, growth delay, dysmorphic features, and/or congenital anomalies. Previous G-banded karyotypes and fluorescence in situ hybridization results were normal for all of these patients. Using both oligonucleotide-based and bacterial artificial chromosome (BAC)-based arrays on the same panel of patients, we identified 10 unique deletions and duplications ranging in size from 280 kb to 8.3 Mb. The whole-genome oligonucleotide arrays identified nearly twice as many imbalances as did the lower-resolution whole-genome BAC arrays. This has implications for using aCGH in a clinical setting. Analysis of parental DNA samples indicated that most of the imbalances had occurred de novo. Moreover, seven of the 10 imbalances represented novel disorders, adding to an increasing number of conditions caused by large-scale deletions or duplications. These results underscore the strength of high-resolution genomic arrays in diagnosing cases of unknown genetic etiology and suggest that contiguous genomic alterations are the underlying pathogenic cause of a significant number of cases of developmental delay.

  View details for DOI 10.1002/ajmg.a.31773

  View details for Web of Science ID 000247760600005

  View details for PubMedID 17568414

• Novel cytogenetic alterations detected by array CGH in patients with developmental delay, dysmorphology, and mental retardation Aradhya, S., Shieh, J., Hoyme, E., Manning, M., Cherry, A. M. KARGER. 2007

  View details for Web of Science ID 000245885400029

• Nablus mask-like facial syndrome is caused by a microdeletion of 8q detected by array-based comparative genomic hybridization. American journal of medical genetics. Part A Shieh, J. T., Aradhya, S., Novelli, A., Manning, M. A., Cherry, A. M., Brumblay, J., Salpietro, C. D., Bernardini, L., Dallapiccola, B., Hoyme, H. E. 2006; 140 (12): 1267-1273

  Abstract

  In 2000, Teebi reported on a 4-year-old boy with a distinctive pattern of malformation, which he termed the "Nablus mask-like facial syndrome" (OMIM# 608156). Characterization of this syndrome has been difficult because of the paucity of patients described in the medical literature and its unknown etiology and pathogenesis. We present two patients with Nablus mask-like facial syndrome who both display a microdeletion in the 8q21-8q22 region detected by array-based comparative genomic hybridization. Patient 1, a boy, has a distinct facial appearance characterized by severe blepharophimosis, tight-appearing glistening facial skin, sparse and unruly hair, a flat and broad nose, and distinctive ears that are triangular in shape with prominent antihelices. He also demonstrates camptodactyly, contractures, unusual dentition, cryptorchidism, mild developmental delay, and a happy demeanor. Patient 2, a girl with a strikingly similar phenotype, was previously described in a report by Salpietro et al. 2003. She has distinctive ears, dental anomalies, and developmental delay. The etiology of her pattern of malformation was not identified at that time. Although high-resolution chromosome and subtelomeric FISH analyses were normal, array-based comparative genomic hybridization revealed an approximately 4 Mb deletion involving the 8q21.3-8q22.1 region in both patients. This region encompasses a number of genes that may contribute to this unique phenotype. These results demonstrate a chromosomal microdeletion as the etiology of Nablus mask-like facial syndrome and emphasize the diagnostic utility of array-based comparative genomic hybridization in the evaluation of multiple malformation syndromes of previously unrecognized causation.

  View details for PubMedID 16691576

• A mouse keratin 1 mutation causes dark skin and epidermolytic hyperkeratosis JOURNAL OF INVESTIGATIVE DERMATOLOGY McGowan, K. A., Aradhya, S., Fuchs, H., de Angelis, M. H., Barsh, G. S. 2006; 126 (5): 1013-1016

  Abstract

  Chemical mutagenesis in the mouse has increased the utility of phenotype-driven genetics as a means for studying different organ systems, developmental pathways, and pathologic processes. From a large-scale screen for dominant phenotypes in mice, a novel class of pigmentation mutants was identified by dark skin (Dsk). We describe a Dsk mutant, Dsk12, which models the human disease, epidermolytic hyperkeratosis (EHK). At 2 days of age, mutant animals exhibit intraepidermal blisters and erosions at sites of trauma, and by 2 weeks of age develop significant hyperkeratosis. We identified a missense mutation in mutant animals that predicts an S194P amino acid substitution in the 1A domain of Keratin 1, a known target for human mutations that cause EHK. Dsk12 recapitulates the gross pathologic, histologic, and genetic aspects of the human disorder, EHK.

  View details for DOI 10.1038/sj.jid.5700241

  View details for Web of Science ID 000238968700016

  View details for PubMedID 16528356

• Nablus mask-like facial syndrome is caused by deletion in 8q21-8q22 detected by array-based comparative genomic hybridiztion. Shieh, J. T., Aradhya, S., Manning, M. A., Cherry, A. M., Dallapiccola, B., Hoyme, H. E. B C DECKER INC. 2006: S138

  View details for Web of Science ID 000235301500352

• Dark skin mouse mutants reveal new genes involved in pigmentation 66th Annual Meeting of the Society-for-Investigative-Dermatology McGowan, K., Aradhya, S., Fuchs, H., de Angelis, M. H., Barsh, G. NATURE PUBLISHING GROUP. 2005: A151–A151

  View details for Web of Science ID 000228179901442

• The DNA sequence of the human X chromosome NATURE Ross, M. T., Grafham, D. V., Coffey, A. J., Scherer, S., McLay, K., Muzny, D., Platzer, M., Howell, G. R., Burrows, C., Bird, C. P., Frankish, A., Lovell, F. L., Howe, K. L., Ashurst, J. L., Fulton, R. S., Sudbrak, R., Wen, G. P., Jones, M. C., Hurles, M. E., Andrews, T. D., Scott, C. E., Searle, S., Ramser, J., Whittaker, A., Deadman, R., Carter, N. P., Hunt, S. E., Chen, R., Cree, A., Gunaratne, P., Havlak, P., Hodgson, A., Metzker, M. L., Richards, S., Scott, G., Steffen, D., Sodergren, E., Wheeler, D. A., Worley, K. C., Ainscough, R., Ambrose, K. D., Ansari-Lari, M. A., Aradhya, S., Ashwell, R. I., Babbage, A. K., Bagguley, C. L., Ballabio, A., Banerjee, R., Barker, G. E., Barlow, K. F., Barrett, I. P., Bates, K. N., Beare, D. M., Beasley, H., Beasley, O., Beck, A., Bethel, G., Blechschmidt, K., Brady, N., Bray-Allen, S., Bridgeman, A. M., Brown, A. J., Brown, M. J., Bonnin, D., Bruford, E. A., Buhay, C., Burch, P., Burford, D., Burgess, J., Burrill, W., Burton, J., Bye, J. M., Carder, C., Carrel, L., Chako, J., Chapman, J. C., Chavez, D., Chen, E., Chen, G., Chen, Y., Chen, Z. J., Chinault, C., Ciccodicola, A., Clark, S. Y., Clarke, G., Clee, C. M., CLEGG, S., Clerc-Blankenburg, K., Clifford, K., Cobley, V., Cole, C. G., Conquer, J. S., Corby, N., Connor, R. E., David, R., DAVIES, J., Davis, C., Davis, J., Delgado, O., DeShazo, D., Dhami, P., Ding, Y., Dinh, H., Dodsworth, S., Draper, H., Dugan-Rocha, S., Dunham, A., Dunn, M., Durbin, K. J., Dutta, I., Eades, T., Ellwood, M., Emery-Cohen, A., Errington, H., Evans, K. L., Faulkner, L., Francis, F., Frankland, J., Fraser, A. E., Galgoczy, P., Gilbert, J., Gill, R., Glockner, G., Gregory, S. G., Gribble, S., Griffiths, C., Grocock, R., Gu, Y. H., Gwilliam, R., Hamilton, C., Hart, E. A., Hawes, A., Heath, P. D., Heitmann, K., Hennig, S., Hernandez, J., Hinzmann, B., Ho, S., Hoffs, M., Howden, P. J., Huckle, E. J., Hume, J., Hunt, P. J., Hunt, A. R., Isherwood, J., Jacob, L., Johnson, D., Jones, S., de Jong, P. J., Joseph, S. S., Keenan, S., Kelly, S., Kershaw, J. K., Khan, Z., Kioschis, P., Klages, S., Knights, A. J., Kosiura, A., Kovar-Smith, C., Laird, G. K., Langford, C., Lawlor, S., Leversha, M., Lewis, L., Liu, W., LLOYD, C., Lloyd, D. M., Loulseged, H., Loveland, J. E., Lovell, J. D., Lozado, R., Lu, J., Lyne, R., Ma, J., Maheshwari, M., Matthews, L. H., McDowall, J., McLaren, S., McMurray, A., Meidl, P., Meitinger, T., Milne, S., Miner, G., Mistry, S. L., Morgan, M., Morris, S., Muller, I., Mullikin, J. C., Nguyen, N., Nordsiek, G., Nyakatura, G., O'Dell, C. N., Okwuonu, G., Palmer, S., Pandian, R., Parker, D., Parrish, J., Pasternak, S., Patel, D., Pearce, A. V., Pearson, D. M., Pelan, S. E., Perez, L., Porter, K. M., Ramsey, Y., Reichwald, K., Rhodes, S., Ridler, K. A., Schlessinger, D., Schueler, M. G., Sehra, H. K., Shaw-Smith, C., Shen, H., Sheridan, E. M., Shownkeen, R., Skuce, C. D., Smith, M. L., Sotheran, E. C., Steingruber, H. E., Steward, C. A., Storey, R., Swann, R. M., Swarbreck, D., Tabor, P. E., Taudien, S., Taylor, T., Teague, B., Thomas, K., Thorpe, A., Timms, K., Tracey, A., Trevanion, S., Tromans, A. C., D'Urso, M., Verduzco, D., Villasana, D., Waldron, L., Wall, M., Wang, Q. Y., Warren, J., Warry, G. L., Wei, X. H., West, A., Whitehead, S. L., Whiteley, M. N., Wilkinson, J. E., Willey, D. L., Williams, G., Williams, L., Williamson, A., Williamson, H., Wilming, L., Woodmansey, R. L., Wray, P. W., Yen, J., Zhang, J. K., Zhou, J. L., Zoghbi, H., Zorilla, S., Buck, D., Reinhardt, R., Poustka, A., Rosenthal, A., Lehrach, H., Meindl, A., Minx, P. J., Hillier, L. W., WILLARD, H. F., Wilson, R. K., Waterston, R. H., Rice, C. M., Vaudin, M., Coulson, A., Nelson, D. L., Weinstock, G., Sulston, J. E., Durbin, R., Hubbard, T., Gibbs, R. A., Beck, S., Rogers, J., Bentley, D. R. 2005; 434 (7031): 325-337

  Abstract

  The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

  View details for DOI 10.1038/nature03440

  View details for Web of Science ID 000227715100040

  View details for PubMedID 15772651

• The role of accessory proteins in melanocortin receptor signaling Barsh, G., Candille, S., He, L., Aradhya, S., Kerns, J. BLACKWELL MUNKSGAARD. 2004: 569

  View details for Web of Science ID 000223590800015

• The human secretin gene: fine structure in 11p15.5 and sequence variation in patients with autism. Genomics Yamagata, T., Aradhya, S., Mori, M., Inoue, K., Momoi, M. Y., Nelson, D. L. 2002; 80 (2): 185-94

  Abstract

  Secretin is a peptide hormone involved in digestion that has been studied as a potential therapeutic agent in patients with autism. We characterized the human secretin locus to determine whether mutations in this gene might play a role in a fraction of autism patients. While the secretin gene (SCT) was not found to be mutated in the majority of autistic patients, rare heterozygous sequence variants were identified in three patients. We also investigated length variation in a variable number of tandem repeats (VNTR) immediately upstream of SCT and found no significant differences in length between patients with autism and normal controls. SCT is located on 11p15.5, adjacent to DRD4 and HRAS. This region has been reported to be associated with both autism and attention deficit hyperactivity disorder (ADHD). Although imprinting is a characteristic of some genes in the vicinity, we could find no evidence for methylation of SCT in lymphoblast cells from patients or control individuals.

  View details for DOI 10.1006/geno.2002.6814

  View details for PubMedID 12160732

• Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28. Genomics Aradhya, S., Woffendin, H., Bonnen, P., Heiss, N. S., Yamagata, T., Esposito, T., Bardaro, T., Poustka, A., D'Urso, M., Kenwrick, S., Nelson, D. L. 2002; 79 (1): 31-40

  Abstract

  A large portion of human Xq28 has been completely characterized but the interval between G6PD and Xqter has remained poorly understood. Because of a lack of stable, high-density clone coverage in this region, we constructed a 1.6-Mb bacterial and P1 artificial chromosome (BAC and PAC, respectively) contig to expedite mapping, structural and evolutionary analysis, and sequencing. The contig helped to reposition previously mismapped genes and to characterize the XAP135 pseudogene near the int22h-2 repeat. BAC clones containing the distal int22h repeats also demonstrated spontaneous rearrangements and sparse coverage, which suggested that they were unstable. Because the int22h repeats are involved in genetic diseases, we examined them in great apes to see if they have always been unstable. Differences in copy number among the apes, due to duplications and deletions, indicated that they have been unstable throughout their evolution. Taking another approach toward understanding the genomic nature of distal Xq28, we examined the homologous mouse region and found an evolutionary junction near the distal int22h loci that separated the human distal Xq28 region into two segments on the mouse X chromosome. Finally, haplotype analysis showed that a segment within Xq28 has resisted excessive interchromosomal exchange through great ape evolution, potentially accounting for the linkage disequilibrium recently reported in this region. Collectively, these data highlight some interesting features of the genomic sequence in Xq28 and will be useful for positional cloning efforts, mouse mutagenesis studies, and further evolutionary analyses.

  View details for DOI 10.1006/geno.2001.6680

  View details for PubMedID 11827455

• Survival of male patients with incontinentia pigmenti carrying a lethal mutation can be explained by somatic mosaicism or Klinefelter syndrome. American journal of human genetics Kenwrick, S., Woffendin, H., Jakins, T., Shuttleworth, S. G., Mayer, E., Greenhalgh, L., Whittaker, J., Rugolotto, S., Bardaro, T., Esposito, T., D'Urso, M., Soli, F., Turco, A., Smahi, A., Hamel-Teillac, D., Lyonnet, S., Bonnefont, J. P., Munnich, A., Aradhya, S., Kashork, C. D., Shaffer, L. G., Nelson, D. L., Levy, M., Lewis, R. A. 2001; 69 (6): 1210-7

  Abstract

  Incontinentia pigmenti (IP), or "Bloch-Sulzberger syndrome," is an X-linked dominant disorder characterized by abnormalities of skin, teeth, hair, and eyes; skewed X-inactivation; and recurrent miscarriages of male fetuses. IP results from mutations in the gene for NF-kappaB essential modulator (NEMO), with deletion of exons 4-10 of NEMO accounting for >80% of new mutations. Male fetuses inheriting this mutation and other "null" mutations of NEMO usually die in utero. Less deleterious mutations can result in survival of males subjects, but with ectodermal dysplasia and immunodeficiency. Male patients with skin, dental, and ocular abnormalities typical of those seen in female patients with IP (without immunodeficiency) are rare. We investigated four male patients with clinical hallmarks of IP. All four were found to carry the deletion normally associated with male lethality in utero. Survival in one patient is explained by a 47,XXY karyotype and skewed X inactivation. Three other patients possess a normal 46,XY karyotype. We demonstrate that these patients have both wild-type and deleted copies of the NEMO gene and are therefore mosaic for the common mutation. Therefore, the repeat-mediated rearrangement leading to the common deletion does not require meiotic division. Hypomorphic alleles, a 47,XXY karyotype, and somatic mosaicism therefore represent three mechanisms for survival of males carrying a NEMO mutation.

  View details for DOI 10.1086/324591

  View details for PubMedID 11673821

  View details for PubMedCentralID PMC1235532

• Multiple pathogenic and benign genomic rearrangements occur at a 35 kb duplication involving the NEMO and LAGE2 genes. Human molecular genetics Aradhya, S., Bardaro, T., Galgóczy, P., Yamagata, T., Esposito, T., Patlan, H., Ciccodicola, A., Munnich, A., Kenwrick, S., Platzer, M., D'Urso, M., Nelson, D. L. 2001; 10 (22): 2557-67

  Abstract

  The X-linked dominant and male-lethal disorder incontinentia pigmenti (IP) is caused by mutations in a gene called NEMO (IKK-gamma). We recently reported the structure of NEMO and demonstrated that most IP patients carry an identical deletion that arises due to misalignment between repeats. Affected male abortuses with the IP deletion had provided clues that a second, incomplete copy of NEMO was present in the genome. We have now identified clones containing this truncated copy (Delta NEMO) and incorporated them into a previously constructed physical contig in distal Xq28. Delta NEMO maps 22 kb distal to NEMO and only contains exons 3-10, confirming our proposed model. A sequence of 26 kb 3' of the NEMO coding sequence is also present in the same position relative to the Delta NEMO locus, bringing the total length of the duplication to 35.5 kb. The LAGE2 gene is also located within this duplicated region, and a similar but unique LAGE1 gene is located just distal to the duplicated loci. Mapping and sequence information indicated that the duplicated regions are in opposite orientation. Analysis of the great apes suggested that the NEMO/LAGE2 duplication occurred after divergence of the lineage leading to present day humans, chimpanzees and gorillas, approximately 10-15 million years ago. Intriguingly, despite this substantial evolutionary history, only 22 single nucleotide differences exist between the two copies over the entire 35.5 kb, making the duplications >99% identical. This high sequence identity and the inverted orientations of the two copies, along with duplications of smaller internal sections within each copy, predispose this region to various genomic alterations. We detected four rearrangements that involved NEMO, Delta NEMO or LAGE1 and LAGE2. The high sequence similarity between the two NEMO/LAGE2 copies may be due to frequent gene conversion, as we have detected evidence of sequence transfer between them. Together, these data describe an unusual and complex genomic region that is susceptible to various types of pathogenic and polymorphic rearrangements, including the recurrent lethal deletion associated with IP.

  View details for DOI 10.1093/hmg/10.22.2557

  View details for PubMedID 11709543

• A recurrent deletion in the ubiquitously expressed NEMO (IKK-gamma) gene accounts for the vast majority of incontinentia pigmenti mutations. Human molecular genetics Aradhya, S., Woffendin, H., Jakins, T., Bardaro, T., Esposito, T., Smahi, A., Shaw, C., Levy, M., Munnich, A., D'Urso, M., Lewis, R. A., Kenwrick, S., Nelson, D. L. 2001; 10 (19): 2171-9

  Abstract

  Incontinentia pigmenti (IP) is an X-linked dominant disorder characterized by abnormal skin pigmentation, retinal detachment, anodontia, alopecia, nail dystrophy and central nervous system defects. This disorder segregates as a male lethal disorder and causes skewed X-inactivation in female patients. IP is caused by mutations in a gene called NEMO, which encodes a regulatory component of the IkappaB kinase complex required to activate the NF-kappaB pathway. Here we report the identification of 277 mutations in 357 unrelated IP patients. An identical genomic deletion within NEMO accounted for 90% of the identified mutations. The remaining mutations were small duplications, substitutions and deletions. Nearly all NEMO mutations caused frameshift and premature protein truncation, which are predicted to eliminate NEMO function and cause cell lethality. Examination of families transmitting the recurrent deletion revealed that the rearrangement occurred in the paternal germline in most cases, indicating that it arises predominantly by intrachromosomal misalignment during meiosis. Expression analysis of human and mouse NEMO/Nemo showed that the gene becomes active early during embryogenesis and is expressed ubiquitously. These data confirm the involvement of NEMO in IP and will help elucidate the mechanism underlying the manifestation of this disorder and the in vivo function of NEMO. Based on these and other recent findings, we propose a model to explain the pathogenesis of this complex disorder.

  View details for DOI 10.1093/hmg/10.19.2171

  View details for PubMedID 11590134

• NF-kappaB signaling and human disease. Current opinion in genetics & development Aradhya, S., Nelson, D. L. 2001; 11 (3): 300-6

  Abstract

  Despite substantial progress in understanding the NF-kappaB signaling pathway, the connections between this pathway and human disease are only now being elucidated. Genes that function within or upstream of the NF-kappaB pathway have been found to cause four distinct disorders and two allelic conditions. Investigation of these genes and disorders has brought significant insight into the role of NF-kappaB in various aspects of physiological development.

  View details for DOI 10.1016/s0959-437x(00)00194-5

  View details for PubMedID 11377967

• Atypical forms of incontinentia pigmenti in male individuals result from mutations of a cytosine tract in exon 10 of NEMO (IKK-gamma). American journal of human genetics Aradhya, S., Courtois, G., Rajkovic, A., Lewis, R. A., Levy, M., Israël, A., Nelson, D. L. 2001; 68 (3): 765-71

  Abstract

  Familial incontinentia pigmenti (IP [MIM 308310]), or Bloch-Sulzberger syndrome, is an X-linked dominant and male-lethal disorder. We recently demonstrated that mutations in NEMO (IKK-gamma), which encodes a critical component of the NF-kappaB signaling pathway, were responsible for IP. Virtually all mutations eliminate the production of NEMO, causing the typical skewing of X inactivation in female individuals and lethality in male individuals, possibly through enhanced sensitivity to apoptosis. Most mutations also give rise to classic signs of IP, but, in this report, we describe two mutations in families with atypical phenotypes. Remarkably, each family included a male individual with unusual signs, including postnatal survival and either immune dysfunction or hematopoietic disturbance. We found two duplication mutations in these families, at a cytosine tract in exon 10 of NEMO, both of which remove the zinc (Zn) finger at the C-terminus of the protein. Two deletion mutations were also identified in the same tract in additional families. However, only the duplication mutations allowed male individuals to survive, and affected female individuals with duplication mutations demonstrated random or slight skewing of X inactivation. Similarly, NF-kappaB activation was diminished in the presence of duplication mutations and was completely absent in cells with deletion mutations. These results strongly indicate that male individuals can also suffer from IP caused by NEMO mutations, and we therefore urge a reevaluation of the diagnostic criteria.

  View details for DOI 10.1086/318806

  View details for PubMedID 11179023

  View details for PubMedCentralID PMC1274488

• Filamin (FLN1), plexin (SEX), major palmitoylated protein p55 (MPP1), and von-Hippel Lindau binding protein (VBP1) are not involved in incontinentia pigmenti type 2. American journal of medical genetics Aradhya, S., Ahobila, P., Lewis, R. A., Nelson, D. L., Esposito, T., Ciccodicola, A., Bardaro, T., D'Urso, M., Woffendin, H., Kenwrick, S., Smahi, A., Heuertz, S., Munnich, A., Heiss, N. S., Poustka, A., Chishti, A. H. 2000; 94 (1): 79-84

  View details for DOI 10.1002/1096-8628(20000904)94:1<79::aid-ajmg17>3.0.co;2-m

  View details for PubMedID 10982489

• Genomic rearrangement in NEMO impairs NF-kappaB activation and is a cause of incontinentia pigmenti. The International Incontinentia Pigmenti (IP) Consortium. Nature Smahi, A., Courtois, G., Vabres, P., Yamaoka, S., Heuertz, S., Munnich, A., Israël, A., Heiss, N. S., Klauck, S. M., Kioschis, P., Wiemann, S., Poustka, A., Esposito, T., Bardaro, T., Gianfrancesco, F., Ciccodicola, A., D'Urso, M., Woffendin, H., Jakins, T., Donnai, D., Stewart, H., Kenwrick, S. J., Aradhya, S., Yamagata, T., Levy, M., Lewis, R. A., Nelson, D. L. 2000; 405 (6785): 466-72

  Abstract

  Familial incontinentia pigmenti (IP; MIM 308310) is a genodermatosis that segregates as an X-linked dominant disorder and is usually lethal prenatally in males. In affected females it causes highly variable abnormalities of the skin, hair, nails, teeth, eyes and central nervous system. The prominent skin signs occur in four classic cutaneous stages: perinatal inflammatory vesicles, verrucous patches, a distinctive pattern of hyperpigmentation and dermal scarring. Cells expressing the mutated X chromosome are eliminated selectively around the time of birth, so females with IP exhibit extremely skewed X-inactivation. The reasons for cell death in females and in utero lethality in males are unknown. The locus for IP has been linked genetically to the factor VIII gene in Xq28 (ref. 3). The gene for NEMO (NF-kappaB essential modulator)/IKKgamma (IkappaB kinase-gamma) has been mapped to a position 200 kilobases proximal to the factor VIII locus. NEMO is required for the activation of the transcription factor NF-kappaB and is therefore central to many immune, inflammatory and apoptotic pathways. Here we show that most cases of IP are due to mutations of this locus and that a new genomic rearrangement accounts for 80% of new mutations. As a consequence, NF-kappaB activation is defective in IP cells.

  View details for DOI 10.1038/35013114

  View details for PubMedID 10839543

• Human homologue of the murine bare patches/striated gene is not mutated in incontinentia pigmenti type 2. American journal of medical genetics Aradhya, S., Nelson, D. L., Heiss, N. S., Poustka, A., Woffendin, H., Kenwrick, S., Esposito, T., Ciccodicola, A., Bardaro, T., D'Urso, M., Smahi, A., Munnich, A., Herman, G. E., Lewis, R. A. 2000; 91 (3): 241-4

  View details for DOI 10.1002/(sici)1096-8628(20000320)91:3<241::aid-ajmg19>3.0.co;2-j

  View details for PubMedID 10756353

• Mutation analysis of the DKC1 gene in incontinentia pigmenti. Journal of medical genetics Heiss, N. S., Poustka, A., Knight, S. W., Aradhya, S., Nelson, D. L., Lewis, R. A., Esposito, T., Ciccodicola, A., D'Urso, M., Smahi, A., Heuertz, S., Munnich, A., Vabres, P., Woffendin, H., Kenwrick, S. 1999; 36 (11): 860-2

  View details for PubMedID 10636732

  View details for PubMedCentralID PMC1734257

• Validation studies of SNRPN methylation as a diagnostic test for Prader-Willi syndrome. American journal of medical genetics Kubota, T., Sutcliffe, J. S., Aradhya, S., Gillessen-Kaesbach, G., Christian, S. L., Horsthemke, B., Beaudet, A. L., Ledbetter, D. H. 1996; 66 (1): 77-80

  Abstract

  Prader-Willi syndrome (PWS) is caused by absence of a paternal contribution of the chromosome region 15q11-q13, resulting from paternal deletions, maternal uniparental disomy, or rare imprinting mutations. Laboratory diagnosis is currently performed using fluorescence in situ hybridization (FISH), DNA polymorphism (microsatellite) analysis, or DNA methylation analysis at locus PW71 (D15S63). We examined another parent-of-origin-specific DNA methylation assay at exon alpha of the small nuclear ribonucleoprotein-associated polypeptide N gene (SNRPN) in patients referred with clinical suspicion of PWS or Angelman syndrome (AS). These included 30 PWS and 17 AS patients with known deletion or uniparental disomy status, and a larger cohort of patients (n = 512) suspected of PWS who had been analyzed previously for their methylation status at the PW71 locus. Results of SNRPN methylation were consistent with known deletion or uniparental disomy (UPD) status as determined by other molecular methods in all 47 cases of PWS and AS. In the larger cohort of possible PWS patients, SNRPN results were consistent with clinical diagnosis by examination and with PW71 methylation results in all cases. These data provide support for the use of SNRPN methylation as a diagnostic method. Because methylation analysis can detect all three major classes of genetic defects associated with PWS (deletion, UPD, or imprinting mutations), methylation analysis with either PW71 or SNRPN is an efficient primary screening test to rule out a diagnosis of PWS. Only patients with an abnormal methylation result require further diagnostic investigation by FISH or DNA polymorphism analysis to distinguish among the three classes for accurate genetic counseling and recurrence-risk assessment.

  View details for DOI 10.1002/(SICI)1096-8628(19961202)66:1<77::AID-AJMG18>3.0.CO;2-N

  View details for PubMedID 8957518

• Analysis of parent of origin specific DNA methylation at SNRPN and PW71 in tissues: implication for prenatal diagnosis. Journal of medical genetics Kubota, T., Aradhya, S., Macha, M., Smith, A. C., Surh, L. C., Satish, J., Verp, M. S., Nee, H. L., Johnson, A., Christan, S. L., Ledbetter, D. H. 1996; 33 (12): 1011-4

  Abstract

  Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct developmental disorders caused by absence of paternal or maternal contributions of the chromosome region 15q11-q13, resulting from deletions, uniparental disomy (UPD), or rare imprinting mutations. Molecular cytogenetic diagnosis is currently performed using a combination of fluorescence in situ hybridisation (FISH), DNA polymorphism analysis, and DNA methylation analysis. Only methylation analysis will detect all three categories of PWS abnormalities, but its reliability in tissues other than peripheral blood has not been examined extensively. Therefore, we examined the methylation status at the CpG island of the small nuclear ribonucleoprotein associated polypeptide N (SNRPN) gene and at the PW71 locus using normal and abnormal lymphoblast (LB) cell lines (n = 48), amniotic fluid (AF) cell cultures (n = 25), cultured chorionic villus samples (CVS, n = 17), and fetal tissues (n = 18) by Southern blot analysis with methylation sensitive enzymes. Of these samples, 20 LB cell lines, three AF cultures, one CVS, and 15 fetal tissues had been previously diagnosed as having deletions or UPD by other molecular methods. Methylation status at SNRPN showed consistent results when compared with FISH or DNA polymorphism analysis using all cell types tested. However, the methylation pattern for PW71 was inconsistent when compared with other tests and should therefore not be used on tissues other than peripheral blood. We conclude that SNRPN, but not PW71, methylation analysis may be useful for diagnosis of PWS/AS on LB cell lines, cultured amniotic fluid, or chorionic villus samples and will allow, for the first time, prenatal diagnosis for families known to carry imprinting centre defects.

  View details for DOI 10.1136/jmg.33.12.1011

  View details for PubMedID 9004133

  View details for PubMedCentralID PMC1050812