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Browsing by Author "Rehm, Heidi L."
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Item Consensus interpretation of the p.Met34Thr and p.Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel(Springer Nature, 2019-11) Shen, Jun; Oza, Andrea M.; Del Castillo, Ignacio; Duzkale, Hatice; Matsunaga, Tatsuo; Pandya, Arti; Kang, Hyunseok P.; Mar-Heyming, Rebecca; Guha, Saurav; Moyer, Krista; Lo, Christine; Kenna, Margaret; Alexander, John J.; Zhang, Yan; Hirsch, Yoel; Luo, Minjie; Cao, Ye; Choy, Kwong Wai; Cheng, Yen-Fu; Avraham, Karen B.; Hu, Xinhua; Garrido, Gema; Moreno-Pelayo, Miguel A.; Greinwald, John; Zhang, Kejian; Zeng, Yukun; Brownstein, Zippora; Basel-Salmon, Lina; Davidov, Bella; Frydman, Moshe; Weiden, Tzvi; Nagan, Narasimhan; Willis, Alecia; Hemphill, Sarah E.; Grant, Andrew R.; Siegert, Rebecca K.; DiStefano, Marina T.; Amr, Sami S.; Rehm, Heidi L.; Abou Tayoun, Ahmad N.; Clin Gen Hearing Loss Working Group; Biostatistics, School of Public HealthPurpose: Pathogenic variants in GJB2 are the most common cause of autosomal recessive sensorineural hearing loss. The classification of c.101T>C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants. Methods: The ClinGen Hearing Loss Expert Panel collected published data and shared unpublished information from contributing laboratories and clinics regarding the two variants. Functional, computational, allelic, and segregation data were also obtained. Case-control statistical analyses were performed. Results: The panel reviewed the synthesized information, and classified the p.Met34Thr and p.Val37Ile variants utilizing professional variant interpretation guidelines and professional judgment. We found that p.Met34Thr and p.Val37Ile are significantly overrepresented in hearing loss patients, compared with population controls. Individuals homozygous or compound heterozygous for p.Met34Thr or p.Val37Ile typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for these two variants. Conclusion: Resolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification guidelines, review evidence, and reach a consensus. We concluded that p.Met34Thr and p.Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and incomplete penetrance.Item FAVOR: functional annotation of variants online resource and annotator for variation across the human genome(Oxford University Press, 2023) Zhou, Hufeng; Arapoglou, Theodore; Li, Xihao; Li, Zilin; Zheng, Xiuwen; Moore, Jill; Asok, Abhijith; Kumar, Sushant; Blue, Elizabeth E.; Buyske, Steven; Cox, Nancy; Felsenfeld, Adam; Gerstein, Mark; Kenny, Eimear; Li, Bingshan; Matise, Tara; Philippakis, Anthony; Rehm, Heidi L.; Sofia, Heidi J.; Snyder, Grace; NHGRI Genome Sequencing Program Variant Functional Annotation Working Group; Weng, Zhiping; Neale, Benjamin; Sunyaev, Shamil R.; Lin, Xihong; Biostatistics, School of Public HealthLarge biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https://favor.genohub.org.Item Genetic Architecture of Dilated Cardiomyopathy in Individuals of African and European Ancestry(American Medical Association, 2023) Jordan, Elizabeth; Kinnamon, Daniel D.; Haas, Garrie J.; Hofmeyer, Mark; Kransdorf, Evan; Ewald, Gregory A.; Morris, Alanna A.; Owens, Anjali; Lowes, Brian; Stoller, Douglas; Tang, W. H. Wilson; Garg, Sonia; Trachtenberg, Barry H.; Shah, Palak; Pamboukian, Salpy V.; Sweitzer, Nancy K.; Wheeler, Matthew T.; Wilcox, Jane E.; Katz, Stuart; Pan, Stephen; Jimenez, Javier; Fishbein, Daniel P.; Smart, Frank; Wang, Jessica; Gottlieb, Stephen S.; Judge, Daniel P.; Moore, Charles K.; Mead, Jonathan O.; Hurst, Natalie; Cao, Jinwen; Huggins, Gordon S.; Cowan, Jason; Ni, Hanyu; Rehm, Heidi L.; Jarvik, Gail P.; Vatta, Matteo; Burke, Wylie; Hershberger, Ray E.; DCM Precision Medicine Study of the DCM Consortium; Medical and Molecular Genetics, School of MedicineImportance: Black patients with dilated cardiomyopathy (DCM) have increased familial risk and worse outcomes than White patients, but most DCM genetic data are from White patients. Objective: To compare the rare variant genetic architecture of DCM by genomic ancestry within a diverse population of patients with DCM. Design: Cross-sectional study enrolling patients with DCM who self-identified as non-Hispanic Black, Hispanic, or non-Hispanic White from June 7, 2016, to March 15, 2020, at 25 US advanced heart failure programs. Variants in 36 DCM genes were adjudicated as pathogenic, likely pathogenic, or of uncertain significance. Exposure: Presence of DCM. Main outcomes and measures: Variants in DCM genes classified as pathogenic/likely pathogenic/uncertain significance and clinically actionable (pathogenic/likely pathogenic). Results: A total of 505, 667, and 26 patients with DCM of predominantly African, European, or Native American genomic ancestry, respectively, were included. Compared with patients of European ancestry, a lower percentage of patients of African ancestry had clinically actionable variants (8.2% [95% CI, 5.2%-11.1%] vs 25.5% [95% CI, 21.3%-29.6%]), reflecting the lower odds of a clinically actionable variant for those with any pathogenic variant/likely pathogenic variant/variant of uncertain significance (odds ratio, 0.25 [95% CI, 0.17-0.37]). On average, patients of African ancestry had fewer clinically actionable variants in TTN (difference, -0.09 [95% CI, -0.14 to -0.05]) and other genes with predicted loss of function as a disease-causing mechanism (difference, -0.06 [95% CI, -0.11 to -0.02]). However, the number of pathogenic variants/likely pathogenic variants/variants of uncertain significance was more comparable between ancestry groups (difference, -0.07 [95% CI, -0.22 to 0.09]) due to a larger number of non-TTN non-predicted loss of function variants of uncertain significance, mostly missense, in patients of African ancestry (difference, 0.15 [95% CI, 0.00-0.30]). Published clinical case-based evidence supporting pathogenicity was less available for variants found only in patients of African ancestry (P < .001). Conclusion and relevance: Patients of African ancestry with DCM were less likely to have clinically actionable variants in DCM genes than those of European ancestry due to differences in genetic architecture and a lack of representation of African ancestry in clinical data sets.Item Research Directions in the Clinical Implementation of Pharmacogenomics: An Overview of US Programs and Projects(Wiley, 2018-05) Volpi, Simona; Bult, Carol J.; Chisholm, Rex L.; Deverka, Patricia A.; Ginsburg, Geoffrey S.; Jacob, Howard J.; Kasapi, Melpomeni; McLeod, Howard L.; Roden, Dan M.; Williams, Marc S.; Green, Eric D.; Rodriguez, Laura Lyman; Aronson, Samuel; Cavallari, Larisa H.; Denny, Joshua C.; Dressler, Lynn G.; Johnson, Julie A.; Klein, Teri E.; Leeder, J. Steven; Piquette-Miller, Micheline; Perera, Minoli; Rasmussen-Torvik, Laura J.; Rehm, Heidi L.; Ritchie, Marylyn D.; Skaar, Todd C.; Wagle, Nikhil; Weinshilboum, Richard; Weitzel, Kristin W.; Wildin, Robert; Wilson, John; Manolio, Teri A.; Relling, Mary V.; Pharmacology and Toxicology, School of MedicineResponse to a drug often differs widely among individual patients. This variability is frequently observed not only with respect to effective responses but also with adverse drug reactions. Matching patients to the drugs that are most likely to be effective and least likely to cause harm is the goal of effective therapeutics. Pharmacogenomics (PGx) holds the promise of precision medicine through elucidating the genetic determinants responsible for pharmacological outcomes and using them to guide drug selection and dosing. Here we survey the US landscape of research programs in PGx implementation, review current advances and clinical applications of PGx, summarize the obstacles that have hindered PGx implementation, and identify the critical knowledge gaps and possible studies needed to help to address them.Item The Responsibility to Recontact Research Participants after Reinterpretation of Genetic and Genomic Research Results(Elsevier, 2019-04-04) Bombard, Yvonne; Brothers, Kyle B.; Fitzgerald-Butt, Sara; Garrison, Nanibaa’ A.; Jamal, Leila; James, Cynthia A.; Jarvik, Gail P.; McCormick, Jennifer B.; Nelson, Tanya N.; Ormond, Kelly E.; Rehm, Heidi L.; Richer, Julie; Souzeau, Emmanuelle; Vassy, Jason L.; Wagner, Jennifer K.; Levy, Howard P.; Medical and Molecular Genetics, School of MedicineThe evidence base supporting genetic and genomic sequence-variant interpretations is continuously evolving. An inherent consequence is that a variant's clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis. There has been discussion concerning the extent of this obligation in the context of both research and clinical care. Although clinical recommendations have begun to emerge, guidance is lacking on the responsibilities of researchers to inform participants of reinterpreted results. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in November 2018. The workgroup included representatives from the National Society of Genetic Counselors, the Canadian College of Medical Genetics, and the Canadian Association of Genetic Counsellors. The final statement includes twelve position statements that were endorsed or supported by the following organizations: Genetic Alliance, European Society of Human Genetics, Canadian Association of Genetic Counsellors, American Association of Anthropological Genetics, Executive Committee of the American Association of Physical Anthropologists, Canadian College of Medical Genetics, Human Genetics Society of Australasia, and National Society of Genetic CounselorsItem Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies(Elsevier, 2023) Lowther, Chelsea; Valkanas, Elise; Giordano, Jessica L.; Wang, Harold Z.; Currall, Benjamin B.; O'Keefe, Kathryn; Pierce-Hoffman, Emma; Kurtas, Nehir E.; Whelan, Christopher W.; Hao, Stephanie P.; Weisburd, Ben; Jalili, Vahid; Fu, Jack; Wong, Isaac; Collins, Ryan L.; Zhao, Xuefang; Austin-Tse, Christina A.; Evangelista, Emily; Lemire, Gabrielle; Aggarwal, Vimla S.; Lucente, Diane; Gauthier, Laura D.; Tolonen, Charlotte; Sahakian, Nareh; Stevens, Christine; An, Joon-Yong; Dong, Shan; Norton, Mary E.; MacKenzie, Tippi C.; Devlin, Bernie; Gilmore, Kelly; Powell, Bradford C.; Brandt, Alicia; Vetrini, Francesco; DiVito, Michelle; Sanders, Stephan J.; MacArthur, Daniel G.; Hodge, Jennelle C.; O'Donnell-Luria, Anne; Rehm, Heidi L.; Vora, Neeta L.; Levy, Brynn; Brand, Harrison; Wapner, Ronald J.; Talkowski, Michael E.; Medical and Molecular Genetics, School of MedicineShort-read genome sequencing (GS) holds the promise of becoming the primary diagnostic approach for the assessment of autism spectrum disorder (ASD) and fetal structural anomalies (FSAs). However, few studies have comprehensively evaluated its performance against current standard-of-care diagnostic tests: karyotype, chromosomal microarray (CMA), and exome sequencing (ES). To assess the clinical utility of GS, we compared its diagnostic yield against these three tests in 1,612 quartet families including an individual with ASD and in 295 prenatal families. Our GS analytic framework identified a diagnostic variant in 7.8% of ASD probands, almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However, when we systematically captured copy-number variants (CNVs) from the exome data, the diagnostic yield of ES (7.4%) was brought much closer to, but did not surpass, GS. Similarly, we estimated that GS could achieve an overall diagnostic yield of 46.1% in unselected FSAs, representing a 17.2% increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV calling or 36.1% increase without CNV discovery. Overall, GS provided an added diagnostic yield of 0.4% and 0.8% beyond the combination of all three standard-of-care tests in ASD and FSAs, respectively. This corresponded to nine GS unique diagnostic variants, including sequence variants in exons not captured by ES, structural variants (SVs) inaccessible to existing standard-of-care tests, and SVs where the resolution of GS changed variant classification. Overall, this large-scale evaluation demonstrated that GS significantly outperforms each individual standard-of-care test while also outperforming the combination of all three tests, thus warranting consideration as the first-tier diagnostic approach for the assessment of ASD and FSAs.