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Kim SW, Kim B, Kim Y, Lee KA. Re-evaluation of a Fibrillin-1 Gene Variant of Uncertain Significance Using the ClinGen Guidelines. Ann Lab Med 2024; 44:271-278. [PMID: 37840311 PMCID: PMC10813823 DOI: 10.3343/alm.2023.0152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Background Marfan syndrome (MFS) is caused by fibrillin-1 gene (FBN1) variants. Mutational hotspots and/or well-established critical functional domains of FBN1 include cysteine residues, calcium-binding consensus sequences, and amino acids related to interdomain packaging. Previous guidelines for variant interpretation do not reflect the features of genes or related diseases. Using the Clinical Genome Resource (ClinGen) FBN1 variant curation expert panel (VCEP), we re-evaluated FBN1 germline variants reported as variants of uncertain significance (VUSs). Methods We re-evaluated 26 VUSs in FBN1 reported in 161 patients with MFS. We checked the variants in the Human Genome Mutation Database, ClinVar, and VarSome databases and assessed their allele frequencies using the gnomAD database. Patients' clinical information was reviewed. Results Four missense variants affecting cysteines (c.460T>C, c.1006T>C, c.5330G>C, and c.8020T>C) were reclassified as likely pathogenic and were assigned PM1_strong or PM1. Two intronic variants were reclassified as benign by granting BA1 (stand-alone). Four missense variants were reclassified as likely benign. BP5 criteria were applied in cases with an alternate molecular basis for disease, one of which (c.7231G>A) was discovered alongside a pathogenic de novo COL3A1 variant (c.1988G>T, p.Gly633Val). Conclusions Considering the high penetrance of FBN1 variants and clinical variability of MFS, the detection of pathogenic variants is important. The ClinGen FBN1 VCEP encompasses mutational hotspots and/or well-established critical functional domains and adjusts the criteria specifically for MFS; therefore, it is beneficial not only for identifying pathogenic FBN1 variants but also for distinguishing these variants from those that cause other connective tissue disorders with overlapping clinical features.
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Affiliation(s)
- Seo Wan Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Boyeon Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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2
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Powell NR, Geck RC, Lai D, Shugg T, Skaar TC, Dunham M. Functional Analysis of G6PD Variants Associated With Low G6PD Activity in the All of Us Research Program. medRxiv 2024:2024.04.12.24305393. [PMID: 38645242 PMCID: PMC11030488 DOI: 10.1101/2024.04.12.24305393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) protects red blood cells against oxidative damage through regeneration of NADPH. Individuals with G6PD polymorphisms (variants) that produce an impaired G6PD enzyme are usually asymptomatic, but at risk of hemolytic anemia from oxidative stressors, including certain drugs and foods. Prevention of G6PD deficiency-related hemolytic anemia is achievable through G6PD genetic testing or whole-genome sequencing (WGS) to identify affected individuals who should avoid hemolytic triggers. However, accurately predicting the clinical consequence of G6PD variants is limited by over 800 G6PD variants which remain of uncertain significance. There also remains significant variability in which deficiency-causing variants are included in pharmacogenomic testing arrays across institutions: many panels only include c.202G>A, even though dozens of other variants can also cause G6PD deficiency. Here, we seek to improve G6PD genotype interpretation using data available in the All of Us Research Program and using a yeast functional assay. We confirm that G6PD coding variants are the main contributor to decreased G6PD activity, and that 13% of individuals in the All of Us data with deficiency-causing variants would be missed if only the c.202G>A variant were tested for. We expand clinical interpretation for G6PD variants of uncertain significance; reporting that c.595A>G, known as G6PD Dagua or G6PD Açores, and the newly identified variant c.430C>G, reduce activity sufficiently to lead to G6PD deficiency. We also provide evidence that five missense variants of uncertain significance are unlikely to lead to G6PD deficiency, since they were seen in hemi- or homozygous individuals without a reduction in G6PD activity. We also applied the new WHO guidelines and were able to classify two synonymous variants as WHO class C. We anticipate these results will improve the accuracy, and prompt increased use, of G6PD genetic tests through a more complete clinical interpretation of G6PD variants. As the All of Us data increases from 245,000 to 1 million participants, and additional functional assays are carried out, we expect this research to serve as a template to enable complete characterization of G6PD deficiency genotypes. With an increased number of interpreted variants, genetic testing of G6PD will be more informative for preemptively identifying individuals at risk for drug- or food-induced hemolytic anemia.
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Affiliation(s)
- Nicholas R Powell
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis IN
| | - Renee C Geck
- University of Washington, Department of Genome Sciences, Seattle WA
| | - Dongbing Lai
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis IN
| | - Tyler Shugg
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis IN
| | - Todd C Skaar
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis IN
| | - Maitreya Dunham
- University of Washington, Department of Genome Sciences, Seattle WA
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3
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Cordova I, Blesson A, Savatt JM, Sveden A, Mahida S, Hazlett H, Rooney Riggs E, Chopra M. Expansion of the Genotypic and Phenotypic Spectrum of ASH1L-Related Syndromic Neurodevelopmental Disorder. Genes (Basel) 2024; 15:423. [PMID: 38674358 PMCID: PMC11049257 DOI: 10.3390/genes15040423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic ASH1L variants have been reported in probands with broad phenotypic presentations, including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, seizures, congenital anomalies, and other skeletal, muscular, and sleep differences. Here, we review previously published individuals with pathogenic ASH1L variants and report three further probands with novel ASH1L variants and previously unreported phenotypic features, including mixed receptive language disorder and gait disturbances. These novel data from the Brain Gene Registry, an accessible repository of clinically derived genotypic and phenotypic data, have allowed for the expansion of the phenotypic and genotypic spectrum of this condition.
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Affiliation(s)
- Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Alyssa Blesson
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Juliann M. Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Abigail Sveden
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Sonal Mahida
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC 27510, USA
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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4
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Spier I, Yin X, Richardson M, Pineda M, Laner A, Ritter D, Boyle J, Mur P, Hansen TVO, Shi X, Mahmood K, Plazzer JP, Ognedal E, Nordling M, Farrington SM, Yamamoto G, Baert-Desurmont S, Martins A, Borras E, Tops C, Webb E, Beshay V, Genuardi M, Pesaran T, Capellá G, Tavtigian SV, Latchford A, Frayling IM, Plon SE, Greenblatt M, Macrae FA, Aretz S. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genet Med 2024; 26:100992. [PMID: 37800450 PMCID: PMC10922469 DOI: 10.1016/j.gim.2023.100992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. METHODS Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. RESULTS The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). CONCLUSION The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
| | - Xiaoyu Yin
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | | | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | | | - Deborah Ritter
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Julie Boyle
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Australia; Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
| | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | | | | | | | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sean V Tavtigian
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Andrew Latchford
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | - Ian M Frayling
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, United Kingdom
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Marc Greenblatt
- Larner College of Medicine, University of Vermont, Burlington, VT
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
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5
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Flowers M, Dickson A, Miller MJ, Spector E, Enns GM, Baudet H, Pasquali M, Racacho L, Sadre-Bazzaz K, Wen T, Fogarty M, Fernandez R, Weaver MA, Feigenbaum A, Graham BH, Mao R. Specifications of the ACMG/AMP guidelines for ACADVL variant interpretation. Mol Genet Metab 2023; 140:107668. [PMID: 37549443 PMCID: PMC10811274 DOI: 10.1016/j.ymgme.2023.107668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023]
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) deficiency (VLCADD) is a relatively common inborn error of metabolism, but due to difficulty in accurately predicting affected status through newborn screening, molecular confirmation of the causative variants by sequencing of the ACADVL gene is necessary. Although the ACMG/AMP guidelines have helped standardize variant classification, ACADVL variant classification remains disparate due to a phenotype that can be nonspecific, the possibility of variants that produce late-onset disease, and relatively high carrier frequency, amongst other challenges. Therefore, an ACADVL-specific variant curation expert panel (VCEP) was created to facilitate the specification of the ACMG/AMP guidelines for VLCADD. We expect these guidelines to help streamline, increase concordance, and expedite the classification of ACADVL variants.
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Affiliation(s)
- May Flowers
- Invitae Corporation, San Francisco, CA 94103, USA
| | - Alexa Dickson
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Elaine Spector
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gregory Mark Enns
- Division of Medical Genetics, Department of Pediatrics, Lucile Packard Children's Hospital, Stanford University, Stanford, CA 94304, USA
| | - Heather Baudet
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Marzia Pasquali
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA
| | - Lemuel Racacho
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta T3B6A8, Canada
| | | | - Ting Wen
- ARUP Laboratories, Salt Lake City, UT 84108, USA
| | | | - Raquel Fernandez
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD 20814, USA
| | - Annette Feigenbaum
- Department of Pediatrics, Division of Genetics, Rady Children's Hospital and The University of California, San Diego, CA 92123, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA.
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6
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Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
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Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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7
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Griffin EL, Nees SN, Morton SU, Wynn J, Patel N, Jobanputra V, Robinson S, Kochav SM, Tao A, Andrews C, Cross N, Geva J, Lanzilotta K, Ritter A, Taillie E, Thompson A, Meyer C, Akers R, King EC, Cnota JF, Kim RW, Porter GA, Brueckner M, Seidman CE, Shen Y, Gelb BD, Goldmuntz E, Newburger JW, Roberts AE, Chung WK. Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circ Genom Precis Med 2023; 16:e003791. [PMID: 36803080 PMCID: PMC10121846 DOI: 10.1161/circgen.122.003791] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/28/2022] [Indexed: 02/23/2023]
Abstract
BACKGROUND Congenital heart disease (CHD) is the most common major congenital anomaly and causes significant morbidity and mortality. Epidemiologic evidence supports a role of genetics in the development of CHD. Genetic diagnoses can inform prognosis and clinical management. However, genetic testing is not standardized among individuals with CHD. We sought to develop a list of validated CHD genes using established methods and to evaluate the process of returning genetic results to research participants in a large genomic study. METHODS Two-hundred ninety-five candidate CHD genes were evaluated using a ClinGen framework. Sequence and copy number variants involving genes in the CHD gene list were analyzed in Pediatric Cardiac Genomics Consortium participants. Pathogenic/likely pathogenic results were confirmed on a new sample in a clinical laboratory improvement amendments-certified laboratory and disclosed to eligible participants. Adult probands and parents of probands who received results were asked to complete a post-disclosure survey. RESULTS A total of 99 genes had a strong or definitive clinical validity classification. Diagnostic yields for copy number variants and exome sequencing were 1.8% and 3.8%, respectively. Thirty-one probands completed clinical laboratory improvement amendments-confirmation and received results. Participants who completed postdisclosure surveys reported high personal utility and no decision regret after receiving genetic results. CONCLUSIONS The application of ClinGen criteria to CHD candidate genes yielded a list that can be used to interpret clinical genetic testing for CHD. Applying this gene list to one of the largest research cohorts of CHD participants provides a lower bound for the yield of genetic testing in CHD.
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Affiliation(s)
- Emily L. Griffin
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Shannon N. Nees
- Nemours Cardiac Center, Nemours Children’s Hospital, Delaware. Wilmington, DE
| | - Sarah U. Morton
- Division of Newborn Medicine, Dept of Medicine, Boston Children’s Hospital
- Dept of Pediatrics, Harvard Medical School, Boston, MA
| | - Julia Wynn
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nihir Patel
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Vaidehi Jobanputra
- Dept of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Scott Robinson
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Stephanie M. Kochav
- Division of Cardiology, Dept of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY
| | - Alice Tao
- Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Carli Andrews
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Nancy Cross
- Division of Pediatric Cardiology, Yale School of Medicine, New Haven, CT
| | - Judith Geva
- Dept of Cardiology, Boston Children’s Hospital
| | - Kristen Lanzilotta
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Alyssa Ritter
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
- Division of Human Genetics, Dept of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Eileen Taillie
- Dept of Pediatrics, Golisano Children’s Hospital, University of Rochester Medical Center, Rochester, NY
| | - Alexandra Thompson
- Division of Cardiothoracic Surgery, Children’s Hospital of Los Angeles, Los Angeles, CA
| | | | - Rachel Akers
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Eileen C. King
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - James F Cnota
- The Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Richard W. Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, CA
| | - George A. Porter
- Dept of Pediatrics, University of Rochester Medical Center, The School of Medicine & Dentistry, Rochester, NY
| | - Martina Brueckner
- Dept of Genetics & Pediatrics, Yale University School of Medicine, New Haven, CT
| | - Christine E. Seidman
- Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA
- Dept of Genetics, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Yufeng Shen
- Depts of Systems Biology & Biomedical Informatics, Columbia University, New York, NY
| | - Bruce D. Gelb
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY
- Depts of Pediatrics and Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children’s Hospital of Philadelphia, Dept of Pediatrics, Perelman School of Medicine, University of Pennsylvania
| | - Jane W. Newburger
- Dept of Pediatrics, Harvard Medical School, Boston, MA
- Dept of Cardiology, Boston Children’s Hospital
| | - Amy E. Roberts
- Dept of Cardiology, Boston Children’s Hospital
- Division of Genetics, Dept of Pediatrics, Boston Children’s Hospital
| | - Wendy K. Chung
- Dept of Pediatrics, Columbia University Irving Medical Center, New York, NY
- Dept of Medicine, Columbia University Irving Medical Center, New York, NY
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8
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Hatton JN, Frone MN, Cox HC, Crowley SB, Hiraki S, Yokoyama NN, Abul-Husn NS, Amatruda JF, Anderson MJ, Bofill-De Ros X, Carr AG, Chao EC, Chen KS, Gu S, Higgs C, Machado J, Ritter D, Schultz KA, Soper ER, Wu MK, Mester JL, Kim J, Foulkes WD, Witkowski L, Stewart DR. Specifications of the ACMG/AMP Variant Classification Guidelines for Germline DICER1 Variant Curation. Hum Mutat 2023; 2023:9537832. [PMID: 38084291 PMCID: PMC10713350 DOI: 10.1155/2023/9537832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Germline pathogenic variants in DICER1 predispose individuals to develop a variety of benign and malignant tumors. Accurate variant curation and classification is essential for reliable diagnosis of DICER1-related tumor predisposition and identification of individuals who may benefit from surveillance. Since 2015, most labs have followed the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) sequence variant classification guidelines for DICER1 germline variant curation. However, these general guidelines lack gene-specific nuances and leave room for subjectivity. Consequently, a group of DICER1 experts joined ClinGen to form the DICER1 and miRNA-Processing Genes Variant Curation Expert Panel (VCEP), to create DICER1- specific ACMG/AMP guidelines for germline variant curation. The VCEP followed the FDA-approved ClinGen protocol for adapting and piloting these guidelines. A diverse set of 40 DICER1 variants were selected for piloting, including 14 known Pathogenic/Likely Pathogenic (P/LP) variants, 12 known Benign/Likely Benign (B/LB) variants, and 14 variants classified as variants of uncertain significance (VUS) or with conflicting interpretations in ClinVar. Clinically meaningful classifications (i.e., P, LP, LB, or B) were achieved for 82.5% (33/40) of the pilot variants, with 100% concordance among the known P/LP and known B/LB variants. Half of the VUS or conflicting variants were resolved with four variants classified as LB and three as LP. These results demonstrate that the DICER1-specific guidelines for germline variant curation effectively classify known pathogenic and benign variants while reducing the frequency of uncertain classifications. Individuals and labs curating DICER1 variants should consider adopting this classification framework to encourage consistency and improve objectivity.
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Affiliation(s)
- Jessica N Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Hannah C Cox
- PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | | | | | | | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James F Amatruda
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Xavier Bofill-De Ros
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California, USA
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, California, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shuo Gu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Cecilia Higgs
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Jerry Machado
- Exact Sciences Laboratories, Madison, Wisconsin, USA
| | | | - Kris Ann Schultz
- Cancer and Blood Disorders, Children's Minnesota, International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, Minnesota, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mona K Wu
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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9
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Clause AR, Taylor JP, Rajkumar R, Bluske K, Bennett M, Amendola LM, Bentley DR, Taft RJ, Perry DL, Coffey AJ; ICSL Interpretation and Reporting Team. Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases. Cell Genom 2023; 3:100258. [PMID: 36819666 DOI: 10.1016/j.xgen.2023.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/13/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants. We describe our experience incorporating the ClinGen Gene-Disease Clinical Validity framework in our interpretation and reporting workflow for a clinical genome sequencing (cGS) test for individuals with rare and undiagnosed genetic diseases. This "reactive" gene curation is completed upon identification of candidate variants during active case analysis and within the test turn-around time by focusing on the most impactful evidence and taking advantage of the broad applicability of the framework to cover a wide range of disease areas. We demonstrate that reactive gene curation can be successfully implemented in support of cGS in a clinical laboratory environment, enabling robust clinical decision making and allowing all variants to be fully and appropriately considered and their clinical significance confidently interpreted.
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10
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Riggs ER, Bingaman TI, Barry CA, Behlmann A, Bluske K, Bostwick B, Bright A, Chen CA, Clause AR, Dharmadhikari AV, Ganapathi M, Gonzaga-Jauregui C, Grant AR, Hughes MY, Kim SR, Krause A, Liao J, Lumaka A, Mah M, Maloney CM, Mohan S, Osei-Owusu IA, Reble E, Rennie O, Savatt JM, Shimelis H, Siegert RK, Sneddon TP, Thaxton C, Toner KA, Tran KT, Webb R, Wilcox EH, Yin J, Zhuo X, Znidarsic M, Martin CL, Betancur C, Vorstman JAS, Miller DT, Schaaf CP. Clinical validity assessment of genes frequently tested on intellectual disability/autism sequencing panels. Genet Med 2022; 24:1899-1908. [PMID: 35616647 PMCID: PMC10200330 DOI: 10.1016/j.gim.2022.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and autism spectrum disorder (ASD), exhibit genetic and phenotypic heterogeneity, making them difficult to differentiate without a molecular diagnosis. The Clinical Genome Resource Intellectual Disability/Autism Gene Curation Expert Panel (GCEP) uses systematic curation to distinguish ID/ASD genes that are appropriate for clinical testing (ie, with substantial evidence supporting their relationship to disease) from those that are not. METHODS Using the Clinical Genome Resource gene-disease validity curation framework, the ID/Autism GCEP classified genes frequently included on clinical ID/ASD testing panels as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship. RESULTS As of September 2021, 156 gene-disease pairs have been evaluated. Although most (75%) were determined to have definitive roles in NDDs, 22 (14%) genes evaluated had either Limited or Disputed evidence. Such genes are currently not recommended for use in clinical testing owing to the limited ability to assess the effect of identified variants. CONCLUSION Our understanding of gene-disease relationships evolves over time; new relationships are discovered and previously-held conclusions may be questioned. Without periodic re-examination, inaccurate gene-disease claims may be perpetuated. The ID/Autism GCEP will continue to evaluate these claims to improve diagnosis and clinical care for NDDs.
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Affiliation(s)
| | | | | | | | | | - Bret Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | | | - Avinash V Dharmadhikari
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA; Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mythily Ganapathi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Claudia Gonzaga-Jauregui
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, Mexico
| | - Andrew R Grant
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; New York Medical College, Valhalla, NY
| | | | - Se Rin Kim
- National Human Genome Research Institute, Bethesda, MD
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jun Liao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Aimé Lumaka
- Laboratoire de Génétique Humaine, University of Liège, Liège, Belgium
| | - Michelle Mah
- Trillium Health Partners, Mississauga, Ontario, Canada
| | | | | | - Ikeoluwa A Osei-Owusu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emma Reble
- St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Olivia Rennie
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Hermela Shimelis
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Rebecca K Siegert
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tam P Sneddon
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Courtney Thaxton
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina, Chapel Hill, NC
| | - Kelly A Toner
- Drexel University College of Medicine, Philadelphia, PA
| | - Kien Trung Tran
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ryan Webb
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Emma H Wilcox
- The Warren Alpert Medical School of Brown University, Providence, RI
| | - Jiani Yin
- Department of Neurology, University of California Los Angeles, Los Angeles, CA
| | - Xinming Zhuo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Masa Znidarsic
- University Medical Center Ljubljana, Ljubljana, Slovenia
| | | | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
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Wyrwoll MJ, Köckerling N, Vockel M, Dicke AK, Rotte N, Pohl E, Emich J, Wöste M, Ruckert C, Wabschke R, Seggewiss J, Ledig S, Tewes AC, Stratis Y, Cremers JF, Wistuba J, Krallmann C, Kliesch S, Röpke A, Stallmeyer B, Friedrich C, Tüttelmann F. Genetic Architecture of Azoospermia-Time to Advance the Standard of Care. Eur Urol 2022; 83:452-462. [PMID: 35690514 DOI: 10.1016/j.eururo.2022.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Crypto- and azoospermia (very few/no sperm in the semen) are main contributors to male factor infertility. Genetic causes for spermatogenic failure (SPGF) include Klinefelter syndrome and Y-chromosomal azoospermia factor microdeletions, and CFTR mutations for obstructive azoospermia (OA). However, the majority of cases remain unexplained because monogenic causes are not analysed. OBJECTIVE To elucidate the monogenic contribution to azoospermia by prospective exome sequencing and strict application of recent clinical guidelines. DESIGN, SETTING, AND PARTICIPANTS Since January 2017, we studied crypto- and azoospermic men without chromosomal aberrations and Y-chromosomal microdeletions attending the Centre of Reproductive Medicine and Andrology, Münster. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We performed exome sequencing in 647 men, analysed 60 genes having at least previous limited clinical validity, and strictly assessed variants according to clinical guidelines. RESULTS AND LIMITATIONS Overall, 55 patients (8.5%) with diagnostic genetic variants were identified. Of these patients, 20 (3.1%) carried mutations in CFTR or ADGRG2, and were diagnosed with OA. In 35 patients (5.4%) with SPGF, mutations in 20 different genes were identified. According to ClinGen criteria, 19 of the SPGF genes now reach at least moderate clinical validity. As limitations, only one transcript per gene was considered, and the list of genes is increasing rapidly so cannot be exhaustive. CONCLUSIONS The number of diagnostic genes in crypto-/azoospermia was almost doubled to 21 using exome-based analyses and clinical guidelines. Application of this procedure in routine diagnostics will significantly improve the diagnostic yield and clinical workup as the results indicate the success rate of testicular sperm extraction. PATIENT SUMMARY When no sperm are found in the semen, a man cannot conceive naturally. The causes are often unknown, but genetics play a major role. We searched for genetic variants in a large group of patients and found causal mutations for one in 12 men; these predict the chances for fatherhood.
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Affiliation(s)
- Margot J Wyrwoll
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nils Köckerling
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Matthias Vockel
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Ann-Kristin Dicke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Nadja Rotte
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eva Pohl
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jana Emich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Marius Wöste
- Institute of Medical Informatics, University Hospital Münster, Münster, Germany
| | - Christian Ruckert
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Rebecca Wabschke
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Jochen Seggewiss
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Susanne Ledig
- Institute of Human Genetics, University of Münster, Münster, Germany
| | | | - Yvonne Stratis
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Jann F Cremers
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Joachim Wistuba
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Claudia Krallmann
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Sabine Kliesch
- Centre of Reproductive Medicine and Andrology (CeRA), University Hospital Münster, Münster, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Birgit Stallmeyer
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Corinna Friedrich
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany.
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12
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Wilcox EH, Sarmady M, Wulf B, Wright MW, Rehm HL, Biesecker LG, Abou Tayoun AN. Evaluating the impact of in silico predictors on clinical variant classification. Genet Med 2022; 24:924-930. [PMID: 34955381 PMCID: PMC9164215 DOI: 10.1016/j.gim.2021.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/29/2022] Open
Abstract
PURPOSE According to the American College of Medical Genetics and Genomics/Association of Medical Pathology (ACMG/AMP) guidelines, in silico evidence is applied at the supporting strength level for pathogenic (PP3) and benign (BP4) evidence. Although PP3 is commonly used, less is known about the effect of these criteria on variant classification outcomes. METHODS A total of 727 missense variants curated by Clinical Genome Resource expert groups were analyzed to determine how often PP3 and BP4 were applied and their impact on variant classification. The ACMG/AMP categorical system of variant classification was compared with a quantitative point-based system. The pathogenicity likelihood ratios of REVEL, VEST, FATHMM, and MPC were calibrated using a gold standard set of 237 pathogenic and benign variants (classified independent of the PP3/BP4 criteria). RESULTS The PP3 and BP4 criteria were applied by Variant Curation Expert Panels to 55% of missense variants. Application of those criteria changed the classification of 15% of missense variants for which either criterion was applied. The point-based system resolved borderline classifications. REVEL and VEST performed best at a strength level consistent with moderate evidence. CONCLUSION We show that in silico criteria are commonly applied and often affect the final variant classifications. When appropriate thresholds for in silico predictors are established, our results show that PP3 and BP4 can be used at a moderate strength.
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Affiliation(s)
- Emma H Wilcox
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Bryan Wulf
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Matt W Wright
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Leslie G Biesecker
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Ahmad N Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates; Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
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13
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Chora JR, Iacocca MA, Tichý L, Wand H, Kurtz CL, Zimmermann H, Leon A, Williams M, Humphries SE, Hooper AJ, Trinder M, Brunham LR, Costa Pereira A, Jannes CE, Chen M, Chonis J, Wang J, Kim S, Johnston T, Soucek P, Kramarek M, Leigh SE, Carrié A, Sijbrands EJ, Hegele RA, Freiberger T, Knowles JW, Bourbon M. The Clinical Genome Resource ( ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification. Genet Med 2021; 24:293-306. [PMID: 34906454 DOI: 10.1016/j.gim.2021.09.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/06/2021] [Accepted: 09/15/2021] [Indexed: 01/02/2023] Open
Abstract
PURPOSE In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published consensus standardized guidelines for sequence-level variant classification in Mendelian disorders. To increase accuracy and consistency, the Clinical Genome Resource Familial Hypercholesterolemia (FH) Variant Curation Expert Panel was tasked with optimizing the existing ACMG/AMP framework for disease-specific classification in FH. In this study, we provide consensus recommendations for the most common FH-associated gene, LDLR, where >2300 unique FH-associated variants have been identified. METHODS The multidisciplinary FH Variant Curation Expert Panel met in person and through frequent emails and conference calls to develop LDLR-specific modifications of ACMG/AMP guidelines. Through iteration, pilot testing, debate, and commentary, consensus among experts was reached. RESULTS The consensus LDLR variant modifications to existing ACMG/AMP guidelines include (1) alteration of population frequency thresholds, (2) delineation of loss-of-function variant types, (3) functional study criteria specifications, (4) cosegregation criteria specifications, and (5) specific use and thresholds for in silico prediction tools, among others. CONCLUSION Establishment of these guidelines as the new standard in the clinical laboratory setting will result in a more evidence-based, harmonized method for LDLR variant classification worldwide, thereby improving the care of patients with FH.
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Affiliation(s)
- Joana R Chora
- Department of Health Promotion and Prevention of Noncommunicable Diseases, Nacional Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; BioISI - BioSystems & Integrative Sciences Institute, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Michael A Iacocca
- Departments of Biomedical Data Science and Pathology, School of Medicine, Stanford University, Stanford, CA; Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto Ontario, Canada
| | - Lukáš Tichý
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno, Brno, Czech Republic
| | - Hannah Wand
- Departments of Biomedical Data Science and Pathology, School of Medicine, Stanford University, Stanford, CA; Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford University, Stanford, CA
| | - C Lisa Kurtz
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, United Kingdom
| | - Steve E Humphries
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Amanda J Hooper
- Department of Clinical Biochemistry, PathWest Laboratory Medicine WA, Royal Perth Hospital and Fiona Stanley Hospital Network, University of Western Australia, Perth, Western Australia, Australia
| | - Mark Trinder
- Department of Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam R Brunham
- Department of Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Institute of the Hearth (InCor), Faculty of Medicine, São Paulo University, São Paulo, Brazil
| | - Cinthia E Jannes
- Laboratory of Genetics and Molecular Cardiology, Institute of the Hearth (InCor), Faculty of Medicine, São Paulo University, São Paulo, Brazil
| | | | | | - Jian Wang
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | | | | | - Premysl Soucek
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Kramarek
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Alain Carrié
- University Hospitals Pitié-Salpêtrière/Charles-Foix, Molecular and Chromosomal Genetics Center, Obesity and Dyslipidemia Genetics Unit, Sorbonne University, Paris, France
| | - Eric J Sijbrands
- Academic Medical Center, Erasmus University, Rotterdam, Netherlands
| | - Robert A Hegele
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic; Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Joshua W Knowles
- Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Prevention Research Center, and Diabetes Research Center, School of Medicine, Stanford University, Stanford, CA; FH Foundation, Pasadena, CA
| | - Mafalda Bourbon
- Department of Health Promotion and Prevention of Noncommunicable Diseases, Nacional Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; BioISI - BioSystems & Integrative Sciences Institute, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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14
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Popejoy AB, Crooks KR, Fullerton SM, Hindorff LA, Hooker GW, Koenig BA, Pino N, Ramos EM, Ritter DI, Wand H, Wright MW, Yudell M, Zou JY, Plon SE, Bustamante CD, Ormond KE. Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures. Am J Hum Genet 2020; 107:72-82. [PMID: 32504544 PMCID: PMC7332657 DOI: 10.1016/j.ajhg.2020.05.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/06/2020] [Indexed: 02/05/2023] Open
Abstract
Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.
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Affiliation(s)
- Alice B Popejoy
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Kristy R Crooks
- Department of Pathology, University of Colorado, Aurora, CO 80045, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Barbara A Koenig
- Program in Bioethics, University of California San Francisco Laurel Heights, San Francisco, CA 94118, USA
| | - Natalie Pino
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin M Ramos
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Deborah I Ritter
- Department of Pediatrics, Oncology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hannah Wand
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Cardiology, Stanford Healthcare, Stanford, CA 94305, USA
| | - Matt W Wright
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Yudell
- Department of Community Health and Prevention, Dornsife School of Public Health, Drexel University, Philadelphia, PA 19104, USA
| | - James Y Zou
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon E Plon
- Department of Pediatrics, Oncology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carlos D Bustamante
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelly E Ormond
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
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15
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Xiang J, Peng J, Baxter S, Peng Z. AutoPVS1: An automatic classification tool for PVS1 interpretation of null variants. Hum Mutat 2020; 41:1488-1498. [PMID: 32442321 DOI: 10.1002/humu.24051] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 11/12/2022]
Abstract
Null variants are prevalent within the human genome, and their accurate interpretation is critical for clinical management. In 2018, the ClinGen Sequence Variant Interpretation (SVI) Working Group refined the only criterion with a very strong pathogenicity rating (PVS1). To streamline PVS1 interpretation, we have developed an automatic classification tool with a graphical user interface called AutoPVS1. The performance of AutoPVS1 was assessed using 56 variants manually curated by the ClinGen's SVI Working Group; it achieved an interpretation concordance of 93% (52/56). A further analysis of 28,586 putative loss-of-function variants by AutoPVS1 demonstrated that at least 27.7% of them do not reach a very strong strength level, 17.5% because of variant-specific issues and 10.2% due to disease mechanism considerations. Notably, 41.0% (1,936/4,717) of splicing variants were assigned a decreased preliminary PVS1 strength level, a significantly greater fraction than in frameshift variants (13.2%) and nonsense variants (10.8%). Our results reinforce the necessity of considering variant-specific issues and disease mechanisms in variant interpretation and demonstrate that AutoPVS1 meets an urgent need by enabling biocurators to easily assign accurate, reliable and reproducible PVS1 strength levels in the process of variant interpretation. AutoPVS1 is publicly available at http://autopvs1.genetics.bgi.com/.
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Affiliation(s)
| | | | - Samantha Baxter
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
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16
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Abstract
Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.
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Affiliation(s)
- Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yanyi Yao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Haixian He
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, China
| | - Jun Shen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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17
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Adler A, Novelli V, Amin AS, Abiusi E, Care M, Nannenberg EA, Feilotter H, Amenta S, Mazza D, Bikker H, Sturm AC, Garcia J, Ackerman MJ, Hershberger RE, Perez MV, Zareba W, Ware JS, Wilde AAM, Gollob MH. An International, Multicentered, Evidence-Based Reappraisal of Genes Reported to Cause Congenital Long QT Syndrome. Circulation 2020; 141:418-428. [PMID: 31983240 PMCID: PMC7017940 DOI: 10.1161/circulationaha.119.043132] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Supplemental Digital Content is available in the text. Background: Long QT syndrome (LQTS) is the first described and most common inherited arrhythmia. Over the last 25 years, multiple genes have been reported to cause this condition and are routinely tested in patients. Because of dramatic changes in our understanding of human genetic variation, reappraisal of reported genetic causes for LQTS is required. Methods: Utilizing an evidence-based framework, 3 gene curation teams blinded to each other’s work scored the level of evidence for 17 genes reported to cause LQTS. A Clinical Domain Channelopathy Working Group provided a final classification of these genes for causation of LQTS after assessment of the evidence scored by the independent curation teams. Results: Of 17 genes reported as being causative for LQTS, 9 (AKAP9, ANK2, CAV3, KCNE1, KCNE2, KCNJ2, KCNJ5, SCN4B, SNTA1) were classified as having limited or disputed evidence as LQTS-causative genes. Only 3 genes (KCNQ1, KCNH2, SCN5A) were curated as definitive genes for typical LQTS. Another 4 genes (CALM1, CALM2, CALM3, TRDN) were found to have strong or definitive evidence for causality in LQTS with atypical features, including neonatal atrioventricular block. The remaining gene (CACNA1C) had moderate level evidence for causing LQTS. Conclusions: More than half of the genes reported as causing LQTS have limited or disputed evidence to support their disease causation. Genetic variants in these genes should not be used for clinical decision-making, unless accompanied by new and sufficient genetic evidence. The findings of insufficient evidence to support gene-disease associations may extend to other disciplines of medicine and warrants a contemporary evidence-based evaluation for previously reported disease-causing genes to ensure their appropriate use in precision medicine.
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Affiliation(s)
- Arnon Adler
- Division of Cardiology, Toronto General Hospital and University of Toronto, Canada (A.A, M.C., M.H.G.)
| | - Valeria Novelli
- Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, and Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy (V.N., E.A., S.A., D.M.)
| | - Ahmad S Amin
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences (A.S.A., A.A.M.W.), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Emanuela Abiusi
- Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, and Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy (V.N., E.A., S.A., D.M.)
| | - Melanie Care
- Division of Cardiology, Toronto General Hospital and University of Toronto, Canada (A.A, M.C., M.H.G.)
| | - Eline A Nannenberg
- Department of Clinical Genetics (E.A.N., H.B.), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada (H.F.)
| | - Simona Amenta
- Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, and Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy (V.N., E.A., S.A., D.M.)
| | - Daniela Mazza
- Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, and Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy (V.N., E.A., S.A., D.M.)
| | - Hennie Bikker
- Department of Clinical Genetics (E.A.N., H.B.), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands
| | - Amy C Sturm
- Geisinger Genomic Medicine Institute, Danville, PA (A.C.S.)
| | - John Garcia
- Invitae Corporation, San Francisco, CA (J.G.)
| | - Michael J Ackerman
- Departments of Cardiovascular Diseases, Pediatrics, and Molecular Pharmacology and Experimental Therapeutics, Divisions of Heart Rhythm Services and Pediatric Cardiology, Windland Smith Rice Sudden Death Genomics Laboratory, Rochester, MN (M.J.A.)
| | - Raymond E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine in the Department of Internal Medicine, Ohio State University, Columbus (R.E.H.)
| | - Marco V Perez
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, CA (M.V.P.)
| | - Wojciech Zareba
- Cardiology Unit of the Department of Medicine, University of Rochester Medical Center, NY (W.Z.)
| | - James S Ware
- National Heart and Lung Institute and Medical Research Council London Institute of Medical Sciences, Imperial College London, UK (J.S.W.).,Royal Brompton and Harefield Hospitals National Health Service Trust, London, UK (J.S.W.)
| | - Arthur A M Wilde
- Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences (A.S.A., A.A.M.W.), Amsterdam University Medical Centers, University of Amsterdam, The Netherlands.,Columbia University Irving Medical Center, New York (A.A.M.W.)
| | - Michael H Gollob
- Division of Cardiology, Toronto General Hospital and University of Toronto, Canada (A.A, M.C., M.H.G.).,Department of Physiology, University of Toronto, and The Toronto General Hospital Research Institute, University Health Network, University of Toronto, Canada (M.H.G.)
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18
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Abstract
Historically, both pretest and posttest genetic counseling has been standard of care for genetic testing. This model should be adapted for primary care providers (PCPs) willing to learn critical information about the test and key concepts that patients need to make an informed testing decision. It is helpful for PCPs to discuss a few initial patients with a genetic counselor to prepare for the key concepts of pretest and posttest counseling. This article provides guidance about the recommended level of involvement of PCPs based on the test indication, test complexity, disorder management, and the potential for psychosocial sequela.
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Affiliation(s)
- W Andrew Faucett
- Office of the Chief Scientific Officer, Geisinger, MC 30-42, 100 North Academy Avenue, Danville, PA 17822, USA.
| | - Holly Peay
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, 3040 East Institute Drive, Research Triangle Park, NC 27709, USA
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, East 17th Avenue, Aurora, CO 80045, USA
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19
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Shen J, Oza AM, Del Castillo I, Duzkale H, Matsunaga T, Pandya A, Kang HP, Mar-Heyming R, Guha S, Moyer K, Lo C, Kenna M, Alexander JJ, Zhang Y, Hirsch Y, Luo M, Cao Y, Wai Choy K, Cheng YF, Avraham KB, Hu X, Garrido G, Moreno-Pelayo MA, Greinwald J, Zhang K, Zeng Y, Brownstein Z, Basel-Salmon L, Davidov B, Frydman M, Weiden T, Nagan N, Willis A, Hemphill SE, Grant AR, Siegert RK, DiStefano MT, Amr SS, Rehm HL, Abou Tayoun AN. Consensus interpretation of the p.Met34Thr and p.Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel. Genet Med 2019; 21:2442-2452. [PMID: 31160754 PMCID: PMC7235630 DOI: 10.1038/s41436-019-0535-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 04/24/2019] [Indexed: 12/02/2022] Open
Abstract
PURPOSE 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.
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Affiliation(s)
- Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA.
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA.
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ignacio Del Castillo
- Servicio de Genetica, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Hatice Duzkale
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Tatsuo Matsunaga
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Arti Pandya
- University of North Carolina, Chapel Hill, NC, USA
| | | | | | - Saurav Guha
- Counsyl, South San Francisco, CA, USA
- New York Genome Center, New York, NY, 10013, USA
| | | | | | - Margaret Kenna
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - John J Alexander
- EGL Genetics/Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- ConsulGene, LLC, Jacksonville, FL, USA
| | - Yan Zhang
- Certer for Medical Genetics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Brooklyn, NY, USA
| | - Minjie Luo
- The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ye Cao
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterinary Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Karen B Avraham
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Xinhua Hu
- Department of Biostatistics, Fairbanks School of Public Health and School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Gema Garrido
- Servicio de Genetica, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Miguel A Moreno-Pelayo
- Servicio de Genetica, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - John Greinwald
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kejian Zhang
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yukun Zeng
- Certer for Medical Genetics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Zippora Brownstein
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
- Pediatric Genetics Clinic, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Bella Davidov
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
| | - Moshe Frydman
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petach Tikva, Israel
- Danek Gartner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Tzvi Weiden
- Dor Yeshorim, Committee for Prevention of Jewish Genetic Diseases, Jerusalem, Israel
| | - Narasimhan Nagan
- Integrated Genetics, Laboratory Corporation of America® Holdings, Westborough, MA, USA
| | - Alecia Willis
- Integrated Genetics, Laboratory Corporation of America® Holdings, Research Triangle Park, NC, USA
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Sami S Amr
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Heidi L Rehm
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Medical School Center for Hereditary Deafness, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
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20
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Renard M, Francis C, Ghosh R, Scott AF, Witmer PD, Adès LC, Andelfinger GU, Arnaud P, Boileau C, Callewaert BL, Guo D, Hanna N, Lindsay ME, Morisaki H, Morisaki T, Pachter N, Robert L, Van Laer L, Dietz HC, Loeys BL, Milewicz DM, De Backer J. Clinical Validity of Genes for Heritable Thoracic Aortic Aneurysm and Dissection. J Am Coll Cardiol 2018; 72:605-15. [PMID: 30071989 DOI: 10.1016/j.jacc.2018.04.089] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Thoracic aortic aneurysms progressively enlarge and predispose to acute aortic dissections. Up to 25% of individuals with thoracic aortic disease harbor an underlying Mendelian pathogenic variant. An evidence-based strategy for selection of genes to test in hereditary thoracic aortic aneurysm and dissection (HTAAD) helps inform family screening and intervention to prevent life-threatening thoracic aortic events. OBJECTIVES The purpose of this study was to accurately identify genes that predispose to HTAAD using the Clinical Genome Resource (ClinGen) framework. METHODS We applied the semiquantitative ClinGen framework to assess presumed gene-disease relationships between 53 candidate genes and HTAAD. Genes were classified as causative for HTAAD if they were associated with isolated thoracic aortic disease and were clinically actionable, triggering routine aortic surveillance, intervention, and family cascade screening. All gene-disease assertions were evaluated by a pre-defined curator-expert pair and subsequently discussed with an expert panel. RESULTS Genes were classified based on the strength of association with HTAAD into 5 categories: definitive (n = 9), strong (n = 2), moderate (n = 4), limited (n = 15), and no reported evidence (n = 23). They were further categorized by severity of associated aortic disease and risk of progression. Eleven genes in the definitive and strong groups were designated as "HTAAD genes" (category A). Eight genes were classified as unlikely to be progressive (category B) and 4 as low risk (category C). The remaining genes were recent genes with an uncertain classification or genes with no evidence of association with HTAAD. CONCLUSIONS The ClinGen framework is useful to semiquantitatively assess the strength of gene-disease relationships for HTAAD. Gene categories resulting from the curation may inform clinical laboratories in the development, interpretation, and subsequent clinical implications of genetic testing for patients with aortic disease.
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21
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Riggs ER, Nelson T, Merz A, Ackley T, Bunke B, Collins CD, Collinson MN, Fan YS, Goodenberger ML, Golden DM, Haglund-Hazy L, Krgovic D, Lamb AN, Lewis Z, Li G, Liu Y, Meck J, Neufeld-Kaiser W, Runke CK, Sanmann JN, Stavropoulos DJ, Strong E, Su M, Tayeh MK, Kokalj Vokac N, Thorland EC, Andersen E, Martin CL. Copy number variant discrepancy resolution using the ClinGen dosage sensitivity map results in updated clinical interpretations in ClinVar. Hum Mutat 2019; 39:1650-1659. [PMID: 30095202 DOI: 10.1002/humu.23610] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 11/07/2022]
Abstract
Conflict resolution in genomic variant interpretation is a critical step toward improving patient care. Evaluating interpretation discrepancies in copy number variants (CNVs) typically involves assessing overlapping genomic content with focus on genes/regions that may be subject to dosage sensitivity (haploinsufficiency (HI) and/or triplosensitivity (TS)). CNVs containing dosage sensitive genes/regions are generally interpreted as "likely pathogenic" (LP) or "pathogenic" (P), and CNVs involving the same known dosage sensitive gene(s) should receive the same clinical interpretation. We compared the Clinical Genome Resource (ClinGen) Dosage Map, a publicly available resource documenting known HI and TS genes/regions, against germline, clinical CNV interpretations within the ClinVar database. We identified 251 CNVs overlapping known dosage sensitive genes/regions but not classified as LP or P; these were sent back to their original submitting laboratories for re-evaluation. Of 246 CNVs re-evaluated, an updated clinical classification was warranted in 157 cases (63.8%); no change was made to the current classification in 79 cases (32.1%); and 10 cases (4.1%) resulted in other types of updates to ClinVar records. This effort will add curated interpretation data into the public domain and allow laboratories to focus attention on more complex discrepancies.
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Affiliation(s)
- Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Tristan Nelson
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Andrew Merz
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Todd Ackley
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | | | | | - Morag N Collinson
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire, UK
| | - Yao-Shan Fan
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - McKinsey L Goodenberger
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Denae M Golden
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Linda Haglund-Hazy
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Danijela Krgovic
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Allen N Lamb
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Zoe Lewis
- ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Yajuan Liu
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Whitney Neufeld-Kaiser
- Clinical Cytogenomics Laboratory, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer N Sanmann
- Human Genetics Laboratory, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Emma Strong
- Genome Diagnostics, The Hospital for Sick Children, University of Toronto, Canada
| | - Meng Su
- University of Miami Miller School of Medicine, Miami, FL, USA
| | - Marwan K Tayeh
- Michigan Medical Genetics Laboratories (MMGL), University of Michigan, Ann Arbor, MI, USA
| | - Nadja Kokalj Vokac
- University Medical Centre Maribor, Laboratory of Medical Genetics, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Erica Andersen
- ARUP Laboratories, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
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22
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Mester JL, Ghosh R, Pesaran T, Huether R, Karam R, Hruska KS, Costa HA, Lachlan K, Ngeow J, Barnholtz-Sloan J, Sesock K, Hernandez F, Zhang L, Milko L, Plon SE, Hegde M, Eng C. Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel. Hum Mutat 2019; 39:1581-1592. [PMID: 30311380 PMCID: PMC6329583 DOI: 10.1002/humu.23636] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/27/2018] [Accepted: 08/28/2018] [Indexed: 01/07/2023]
Abstract
The ClinGen PTEN Expert Panel was organized by the ClinGen Hereditary Cancer Clinical Domain Working Group to assemble clinicians, researchers, and molecular diagnosticians with PTEN expertise to develop specifications to the 2015 ACMG/AMP Sequence Variant Interpretation Guidelines for PTEN variant interpretation. We describe finalized PTEN-specific variant classification criteria and outcomes from pilot testing of 42 variants with benign/likely benign (BEN/LBEN), pathogenic/likely pathogenic (PATH/LPATH), uncertain significance (VUS), and conflicting (CONF) ClinVar assertions. Utilizing these rules, classifications concordant with ClinVar assertions were achieved for 14/15 (93.3%) BEN/LBEN and 16/16 (100%) PATH/LPATH ClinVar consensus variants for an overall concordance of 96.8% (30/31). The variant where agreement was not reached was a synonymous variant near a splice donor with noncanonical sequence for which in silico models cannot predict the native site. Applying these rules to six VUS and five CONF variants, adding shared internal laboratory data enabled one VUS to be classified as LBEN and two CONF variants to be as classified as PATH and LPATH. This study highlights the benefit of gene-specific criteria and the value of sharing internal laboratory data for variant interpretation. Our PTEN-specific criteria and expertly reviewed assertions should prove helpful for laboratories and others curating PTEN variants.
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Affiliation(s)
| | | | | | | | | | | | - Helio A Costa
- Stanford University School of Medicine, Stanford, California
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospitals Southampton, Southampton, UK.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Jill Barnholtz-Sloan
- Case Comprehensive Cancer Center, Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Milko
- University of North Carolina, Chapel Hill, North Carolina
| | | | - Madhuri Hegde
- Emory University, Atlanta, Georgia.,PerkinElmer Genetics, Pittsburgh, Pennsylvania
| | - Charis Eng
- Case Comprehensive Cancer Center, Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio.,Cleveland Clinic Genomic Medicine Institute, Cleveland, Ohio
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23
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Grant AR, Cushman BJ, Cavé H, Dillon MW, Gelb BD, Gripp KW, Lee JA, Mason-Suares H, Rauen KA, Tartaglia M, Vincent LM, Zenker M. Assessing the gene-disease association of 19 genes with the RASopathies using the ClinGen gene curation framework. Hum Mutat 2019; 39:1485-1493. [PMID: 30311384 DOI: 10.1002/humu.23624] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/05/2018] [Accepted: 08/23/2018] [Indexed: 11/10/2022]
Abstract
The RASopathies are a complex group of conditions regarding phenotype and genetic etiology. The ClinGen RASopathy Expert Panel (RAS EP) assessed published and other publicly available evidence supporting the association of 19 genes with RASopathy conditions. Using the semiquantitative literature curation method developed by the ClinGen Gene Curation Working Group, evidence for each gene was curated and scored for Noonan syndrome (NS), Costello syndrome, cardiofaciocutaneous syndrome, NS with multiple lentigines, and Noonan-like syndrome with loose anagen hair. The curated evidence supporting each gene-disease relationship was then discussed and approved by the ClinGen RASopathy Expert Panel. Each association's strength was classified as definitive, strong, moderate, limited, disputed, or no evidence. Eleven genes were classified as definitively associated with at least one RASopathy condition. Two genes classified as strong for association with at least one RASopathy condition while one gene was moderate and three were limited. The RAS EP also disputed the association of two genes for all RASopathy conditions. Overall, our results provide a greater understanding of the different gene-disease relationships within the RASopathies and can help in guiding and directing clinicians, patients, and researchers who are identifying variants in individuals with a suspected RASopathy.
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Affiliation(s)
- Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Hélène Cavé
- Département de Génétique, Hôpital Robert Debré and Institut Universitaire d'Hématologie, Université Paris Diderot, Paris-Sorbonne-Cité, Paris, France
| | - Mitchell W Dillon
- Molecular Genetic Testing Laboratory, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Bruce D Gelb
- Departments of Pediatrics and Genetic and Genomic Sciences, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Karen W Gripp
- Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Jennifer A Lee
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Katherine A Rauen
- Department of Pediatrics, UC Davis Children's Hospital, Sacramento, California
| | | | | | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
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24
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Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss. Hum Mutat 2019; 39:1593-1613. [PMID: 30311386 DOI: 10.1002/humu.23630] [Citation(s) in RCA: 271] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/23/2018] [Accepted: 08/25/2018] [Indexed: 12/23/2022]
Abstract
Due to the high genetic heterogeneity of hearing loss (HL), current clinical testing includes sequencing large numbers of genes, which often yields a significant number of novel variants. Therefore, the standardization of variant interpretation is crucial to provide consistent and accurate diagnoses. The Hearing Loss Variant Curation Expert Panel was created within the Clinical Genome Resource to provide expert guidance for standardized genomic interpretation in the context of HL. As one of its major tasks, our Expert Panel has adapted the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for the interpretation of sequence variants in HL genes. Here, we provide a comprehensive illustration of the newly specified ACMG/AMP HL rules. Three rules remained unchanged, four rules were removed, and the remaining 21 rules were specified. These rules were further validated and refined using a pilot set of 51 variants assessed by curators and disease experts. Of the 51 variants evaluated in the pilot, 37% (19/51) changed category based upon application of the expert panel specified rules and/or aggregation of evidence across laboratories. These HL-specific ACMG/AMP rules will help standardize variant interpretation, ultimately leading to better care for individuals with HL.
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Affiliation(s)
- Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts
| | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Jun Shen
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | | | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Schimmenti
- Department of Otorhinolaryngology, Clinical Genomics and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jaclyn B Murry
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa.,The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa
| | - Andrew Griffith
- Audiology Unit, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hannie Kremer
- Department of Otorhinolaryngology and Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | - Ahmad N Abou Tayoun
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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25
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Savatt JM, Azzariti DR, Faucett WA, Harrison S, Hart J, Kattman B, Landrum MJ, Ledbetter DH, Miller VR, Palen E, Rehm HL, Rhode J, Turner S, Vidal JA, Wain KE, Riggs ER, Martin CL. ClinGen's GenomeConnect registry enables patient-centered data sharing. Hum Mutat 2019; 39:1668-1676. [PMID: 30311371 DOI: 10.1002/humu.23633] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 08/23/2018] [Indexed: 01/09/2023]
Abstract
GenomeConnect, the NIH-funded Clinical Genome Resource (ClinGen) patient registry, engages patients in data sharing to support the goal of creating a genomic knowledge base to inform clinical care and research. Participant self-reported health information and genomic variants from genetic testing reports are curated and shared with public databases, such as ClinVar. There are four primary benefits of GenomeConnect: (1) sharing novel genomic data-47.9% of variants were new to ClinVar, highlighting patients as a genomic data source; (2) contributing additional phenotypic information-of the 52.1% of variants already in ClinVar, GenomeConnect provided enhanced case-level data; (3) providing a way for patients to receive variant classification updates if the reporting laboratory submits to ClinVar-97.3% of responding participants opted to receive such information and 13 updates have been identified; and (4) supporting connections with others, including other participants, clinicians, and researchers to enable the exchange of information and support-60.4% of participants have opted to partake in participant matching. Moving forward, ClinGen plans to increase patient-centric data sharing by partnering with other existing patient groups. By engaging patients, more information is contributed to the public knowledge base, benefiting both patients and the genomics community.
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Affiliation(s)
- Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts
| | - W Andrew Faucett
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Steven Harrison
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer Hart
- National Center for Biotechnology Information, Bethesda, Maryland
| | - Brandi Kattman
- National Center for Biotechnology Information, Bethesda, Maryland
| | | | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Emily Palen
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Stefanie Turner
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan
| | | | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
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26
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Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R. Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene. Hum Mutat 2019; 39:1569-1580. [PMID: 30311390 DOI: 10.1002/humu.23649] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/28/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022]
Abstract
The ClinGen Inborn Errors of Metabolism Working Group was tasked with creating a comprehensive, standardized knowledge base of genes and variants for metabolic diseases. Phenylalanine hydroxylase (PAH) deficiency was chosen to pilot development of the Working Group's standards and guidelines. A PAH variant curation expert panel (VCEP) was created to facilitate this process. Following ACMG-AMP variant interpretation guidelines, we present the development of these standards in the context of PAH variant curation and interpretation. Existing ACMG-AMP rules were adjusted based on disease (6) or strength (5) or both (2). Disease adjustments include allele frequency thresholds, functional assay thresholds, and phenotype-specific guidelines. Our validation of PAH-specific variant interpretation guidelines is presented using 85 variants. The PAH VCEP interpretations were concordant with existing interpretations in ClinVar for 69 variants (81%). Development of biocurator tools and standards are also described. Using the PAH-specific ACMG-AMP guidelines, 714 PAH variants have been curated and will be submitted to ClinVar. We also discuss strategies and challenges in applying ACMG-AMP guidelines to autosomal recessive metabolic disease, and the curation of variants in these genes.
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Affiliation(s)
- Diane B Zastrow
- Palo Alto Medical Foundation, Palo Alto, California.,Stanford University, Stanford, California
| | - Heather Baudet
- University of North Carolina, Chapel Hill, North Carolina
| | - Wei Shen
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Amanda Thomas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Yue Si
- GeneDx, Gaithersburg, Maryland
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Angela M Lager
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jixia Liu
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | | | | | | | | | | | - Annette Feigenbaum
- Rady Children's Hospital and University of California, San Diego, California
| | - Uta Lichter-Konecki
- Children's Hospital of Pittsburg of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elaine Lyon
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Marzia Pasquali
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Michael Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Nenad Blau
- Dietmar-Hopp Metabolic Center, University Children's Hospital, Department of General Pediatrics, Heidelberg, Germany
| | - Robert D Steiner
- Marshfield Clinic Research Institute, Marshfield, Wisconsin.,University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
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27
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McGlaughon JL, Goldstein JL, Thaxton C, Hemphill SE, Berg JS. The progression of the ClinGen gene clinical validity classification over time. Hum Mutat 2019; 39:1494-1504. [PMID: 30311372 PMCID: PMC6190678 DOI: 10.1002/humu.23604] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/06/2018] [Accepted: 08/02/2018] [Indexed: 01/18/2023]
Abstract
In order for ClinGen to maintain up-to-date gene-disease clinical validity classifications for use by clinicians and clinical laboratories, an appropriate timeline for reevaluating curated gene-disease associations will need to be determined. To provide guidance on how often a gene-disease association should be recurated, a retrospective analysis of 30 gene curations was performed. Curations were simulated at one-year intervals starting with the year of the first publication to assert disease-causing variants in the gene to observe trends in the classification over time, as well as factors that influenced changes in classification. On average, gene-disease associations spent the least amount of time in the "Moderate" classification before progressing to "Strong" or "Definitive." In contrast, gene-disease associations that spent five or more years in the "Limited" classification were most likely to remain "Limited" or become "Disputed/Refuted." Large population datasets contributed to the reclassification of several gene-disease associations from "Limited" to "Disputed/Refuted." Finally, recent advancements in sequencing technology correlated with an increase in the quantity of case-level evidence that was curated per paper. This study provided a number of key points to consider when determining how often to recurate a gene-disease association.
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Affiliation(s)
- Jennifer L McGlaughon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer L Goldstein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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28
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Rivera-Muñoz EA, Milko LV, Harrison SM, Azzariti DR, Kurtz CL, Lee K, Mester JL, Weaver MA, Currey E, Craigen W, Eng C, Funke B, Hegde M, Hershberger RE, Mao R, Steiner RD, Vincent LM, Martin CL, Plon SE, Ramos E, Rehm HL, Watson M, Berg JS. ClinGen Variant Curation Expert Panel experiences and standardized processes for disease and gene-level specification of the ACMG/AMP guidelines for sequence variant interpretation. Hum Mutat 2019; 39:1614-1622. [PMID: 30311389 DOI: 10.1002/humu.23645] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/09/2018] [Accepted: 08/30/2018] [Indexed: 01/09/2023]
Abstract
Genome-scale sequencing creates vast amounts of genomic data, increasing the challenge of clinical sequence variant interpretation. The demand for high-quality interpretation requires multiple specialties to join forces to accelerate the interpretation of sequence variant pathogenicity. With over 600 international members including clinicians, researchers, and laboratory diagnosticians, the Clinical Genome Resource (ClinGen), funded by the National Institutes of Health, is forming expert groups to systematically evaluate variants in clinically relevant genes. Here, we describe the first ClinGen variant curation expert panels (VCEPs), development of consistent and streamlined processes for establishing new VCEPs, and creation of standard operating procedures for VCEPs to define application of the ACMG/AMP guidelines for sequence variant interpretation in specific genes or diseases. Additionally, ClinGen has created user interfaces to enhance reliability of curation and a Sequence Variant Interpretation Working Group (SVI WG) to harmonize guideline specifications and ensure consistency between groups. The expansion of VCEPs represents the primary mechanism by which curation of a substantial fraction of genomic variants can be accelerated and ultimately undertaken systematically and comprehensively. We welcome groups to utilize our resources and become involved in our effort to create a publicly accessible, centralized resource for clinically relevant genes and variants.
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Affiliation(s)
- Edgar A Rivera-Muñoz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Laura V Milko
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Steven M Harrison
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Danielle R Azzariti
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | | | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Erin Currey
- Division of Genomic Medicine, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland
| | - William Craigen
- Baylor College of Medicine, Departments of Molecular and Human Genetics, and Pediatrics, Houston, Texas
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Birgit Funke
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts.,Veritas Genetics, Danvers, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Madhuri Hegde
- PerkinElmer, Global Laboratory Services, Waltham, Massachusetts.,Emory University, Department of Human Genetics, Atlanta, Georgia
| | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah.,Department of Molecular Genetics and Genomics, ARUP Laboratories, Salt Lake City, Utah
| | - Robert D Steiner
- Departments of Pediatrics and Genetics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.,Prevention Genetics, Marshfield, Wisconsin
| | | | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA
| | - Sharon E Plon
- Baylor College of Medicine, Departments of Molecular and Human Genetics, and Pediatrics, Houston, Texas
| | - Erin Ramos
- Division of Genomic Medicine, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland
| | - Heidi L Rehm
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
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29
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Lee K, Seifert BA, Shimelis H, Ghosh R, Crowley SB, Carter NJ, Doonanco K, Foreman AK, Ritter DI, Jimenez S, Trapp M, Offit K, Plon SE, Couch FJ. Clinical validity assessment of genes frequently tested on hereditary breast and ovarian cancer susceptibility sequencing panels. Genet Med 2019; 21:1497-1506. [PMID: 30504931 PMCID: PMC6579711 DOI: 10.1038/s41436-018-0361-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/01/2018] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Several genes on hereditary breast and ovarian cancer susceptibility test panels have not been systematically examined for strength of association with disease. We employed the Clinical Genome Resource (ClinGen) clinical validity framework to assess the strength of evidence between selected genes and breast or ovarian cancer. METHODS Thirty-one genes offered on cancer panel testing were selected for evaluation. The strength of gene-disease relationship was systematically evaluated and a clinical validity classification of either Definitive, Strong, Moderate, Limited, Refuted, Disputed, or No Reported Evidence was assigned. RESULTS Definitive clinical validity classifications were made for 10/31 and 10/32 gene-disease pairs for breast and ovarian cancer respectively. Two genes had a Moderate classification whereas, 6/31 and 6/32 genes had Limited classifications for breast and ovarian cancer respectively. Contradictory evidence resulted in Disputed or Refuted assertions for 9/31 genes for breast and 4/32 genes for ovarian cancer. No Reported Evidence of disease association was asserted for 5/31 genes for breast and 11/32 for ovarian cancer. CONCLUSION Evaluation of gene-disease association using the ClinGen clinical validity framework revealed a wide range of classifications. This information should aid laboratories in tailoring appropriate gene panels and assist health-care providers in interpreting results from panel testing.
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Affiliation(s)
- Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - A Katherine Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Sharisse Jimenez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mackenzie Trapp
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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30
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DiStefano MT, Hemphill SE, Oza AM, Siegert RK, Grant AR, Hughes MY, Cushman BJ, Azaiez H, Booth KT, Chapin A, Duzkale H, Matsunaga T, Shen J, Zhang W, Kenna M, Schimmenti LA, Tekin M, Rehm HL, Tayoun ANA, Amr SS; ClinGen Hearing Loss Clinical Domain Working Group. ClinGen expert clinical validity curation of 164 hearing loss gene-disease pairs. Genet Med 2019; 21:2239-47. [PMID: 30894701 DOI: 10.1038/s41436-019-0487-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/01/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Proper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semiquantitative framework to assign clinical validity to gene-disease relationships. METHODS The ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss. RESULTS The final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website ( https://search.clinicalgenome.org/kb/gene-validity ). CONCLUSION This gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.
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Seifert BA, McGlaughon JL, Jackson SA, Ritter DI, Roberts ME, Schmidt RJ, Thompson BA, Jimenez S, Trapp M, Lee K, Plon SE, Offit K, Stadler ZK, Zhang L, Greenblatt MS, Ferber MJ. Determining the clinical validity of hereditary colorectal cancer and polyposis susceptibility genes using the Clinical Genome Resource Clinical Validity Framework. Genet Med. 2019;21:1507-1516. [PMID: 30523343 PMCID: PMC6579719 DOI: 10.1038/s41436-018-0373-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/07/2018] [Indexed: 12/23/2022] Open
Abstract
Purpose: Gene-disease associations implicated in hereditary colorectal cancer and polyposis susceptibility were evaluated using the ClinGen Clinical Validity framework. Methods: Forty-two gene-disease pairs were assessed for strength of evidence supporting an association with hereditary colorectal cancer and/or polyposis. Genetic and experimental evidence supporting each gene-disease relationship was curated independently by two trained biocurators. Evidence was reviewed with experts and assigned a final clinical validity classification. Results: Of all gene-disease pairs evaluated, 14/42 (33.3%) were Definitive, 1/42 (2.4%) were Strong, 6/42 (14.3%) were Moderate, 18/42 (42.9%) were Limited, and 3/42 (7.1%) were either No Reported Evidence, Disputed, or Refuted. Of panels in the NIH Genetic Testing Registry, 4/26 (~15.4%) contain genes with Limited clinical evidence. Conclusion: Clinicians and laboratory diagnosticians should note that <60% of the genes on clinically available panels have Strong or Definitive evidence of association with hereditary colon cancer or polyposis, and >40% have only Moderate, Limited, Disputed, or Refuted evidence. Continuing to expand the structured assessment of the clinical relevance of genes listed on hereditary cancer testing panels will help clinicians and diagnostic laboratories focus the communication of genetic testing results on clinically significant genes.
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Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Hum Mutat 2018; 39:1721-1732. [PMID: 30311370 PMCID: PMC6282863 DOI: 10.1002/humu.23651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 12/19/2022]
Abstract
Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant-associated knowledge are central problems that arise with increased usage of clinical next-generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open-source platform supporting crowdsourced and expert-moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field-by-field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group-level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.
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Affiliation(s)
- Arpad M. Danos
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | | | - Alex H. Wagner
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Kilannin Krysiak
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and DiagnosisNational Cancer InstituteRockvilleMaryland
| | | | - Matthew McCoy
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Shruti Rao
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Gordana Raca
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Simina M. Boca
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | | | - Erica K. Barnell
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Joshua F. McMichael
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Susanna Kiwala
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Adam C. Coffman
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Lynzey Kujan
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Shashikant Kulkarni
- Baylor College of MedicineHoustonTexas
- Baylor GeneticsHoustonTexas
- Dan L. Duncan Cancer CenterHoustonTexas
| | - Malachi Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Subha Madhavan
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Obi L. Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
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Lee K, Krempely K, Roberts ME, Anderson MJ, Carneiro F, Chao E, Dixon K, Figueiredo J, Ghosh R, Huntsman D, Kaurah P, Kesserwan C, Landrith T, Li S, Mensenkamp AR, Oliveira C, Pardo C, Pesaran T, Richardson M, Slavin TP, Spurdle AB, Trapp M, Witkowski L, Yi CS, Zhang L, Plon SE, Schrader KA, Karam R. Specifications of the ACMG/AMP variant curation guidelines for the analysis of germline CDH1 sequence variants. Hum Mutat 2018; 39:1553-1568. [PMID: 30311375 PMCID: PMC6188664 DOI: 10.1002/humu.23650] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/30/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022]
Abstract
The variant curation guidelines published in 2015 by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) provided the genetics community with a framework to assess variant pathogenicity; however, these rules are not gene specific. Germline pathogenic variants in the CDH1 gene cause hereditary diffuse gastric cancer and lobular breast cancer, a clinically challenging cancer predisposition syndrome that often requires a multidisciplinary team of experts to be properly managed. Given this challenge, the Clinical Genome Resource (ClinGen) Hereditary Cancer Domain prioritized the development of the CDH1 variant curation expert panel (VCEP) to develop and implement rules for CDH1 variant classifications. Here, we describe the CDH1 specifications of the ACMG/AMP guidelines, which were developed and validated after a systematic evaluation of variants obtained from a cohort of clinical laboratory data encompassing ∼827,000 CDH1 sequenced alleles. Comparing previously reported germline variants that were classified using the 2015 ACMG/AMP guidelines to the CDH1 VCEP recommendations resulted in reduced variants of uncertain significance and facilitated resolution of variants with conflicted assertions in ClinVar. The ClinGen CDH1 VCEP recommends the use of these CDH1-specific guidelines for the assessment and classification of variants identified in this clinically actionable gene.
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Affiliation(s)
- Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Fatima Carneiro
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA, USA
- University of California Irvine, Irvine, CA, USA
| | | | - Joana Figueiredo
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | | | | | | | | | | | - Shuwei Li
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Carla Oliveira
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
| | | | | | | | - Thomas P. Slavin
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | | | - Mackenzie Trapp
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leora Witkowski
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA
| | | | | | | | - Kasmintan A. Schrader
- Institute for Research and Innovation in Health of the University of Porto, Instituto de Investigação e Inovação em Saúde – (i3S), Faculty of Medicine – University of Porto, Porto, PRT
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Abou Tayoun AN, Pesaran T, DiStefano MT, Oza A, Rehm HL, Biesecker LG, Harrison SM. Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion. Hum Mutat 2018; 39:1517-1524. [PMID: 30192042 DOI: 10.1002/humu.23626] [Citation(s) in RCA: 427] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/15/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022]
Abstract
The 2015 ACMG/AMP sequence variant interpretation guideline provided a framework for classifying variants based on several benign and pathogenic evidence criteria, including a pathogenic criterion (PVS1) for predicted loss of function variants. However, the guideline did not elaborate on specific considerations for the different types of loss of function variants, nor did it provide decision-making pathways assimilating information about variant type, its location, or any additional evidence for the likelihood of a true null effect. Furthermore, this guideline did not take into account the relative strengths for each evidence type and the final outcome of their combinations with respect to PVS1 strength. Finally, criteria specifying the genes for which PVS1 can be applied are still missing. Here, as part of the ClinGen Sequence Variant Interpretation (SVI) Workgroup's goal of refining ACMG/AMP criteria, we provide recommendations for applying the PVS1 criterion using detailed guidance addressing the above-mentioned gaps. Evaluation of the refined criterion by seven disease-specific groups using heterogeneous types of loss of function variants (n = 56) showed 89% agreement with the new recommendation, while discrepancies in six variants (11%) were appropriately due to disease-specific refinements. Our recommendations will facilitate consistent and accurate interpretation of predicted loss of function variants.
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Affiliation(s)
- Ahmad N Abou Tayoun
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrea Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven M Harrison
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
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Milko LV, Funke BH, Hershberger RE, Azzariti DR, Lee K, Riggs ER, Rivera-Munoz EA, Weaver MA, Niehaus A, Currey EL, Craigen WJ, Mao R, Offit K, Steiner RD, Martin CL, Rehm HL, Watson MS, Ramos EM, Plon SE, Berg JS. Development of Clinical Domain Working Groups for the Clinical Genome Resource ( ClinGen): lessons learned and plans for the future. Genet Med 2018; 21:987-993. [PMID: 30181607 PMCID: PMC6401338 DOI: 10.1038/s41436-018-0267-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/31/2018] [Indexed: 11/09/2022] Open
Abstract
The Clinical Genome Resource (ClinGen) is supported by the National Institutes of Health (NIH) to develop expertly curated and freely accessible resources defining the clinical relevance of genes and variants for use in precision medicine and research. To facilitate expert input, ClinGen has formed Clinical Domain Working Groups (CDWGs) to leverage the collective knowledge of clinicians, laboratory diagnosticians, and researchers. In the initial phase of ClinGen, CDWGs were launched in the cardiovascular, hereditary cancer, and inborn errors of metabolism clinical fields. These early CDWGs established the infrastructure necessary to implement standardized processes developed or adopted by ClinGen working groups for the interpretation of gene-disease associations and variant pathogenicity, and provided a sustainable model for the formation of future disease-focused curation groups. The establishment of CDWGs requires recruitment of international experts to broadly represent the interests of their field and ensure that assertions made are reliable and widely accepted. Building on the successes, challenges, and trade-offs made in establishing the original CDWGs, ClinGen has developed standard operating procedures for the development of CDWGs in new clinical domains, while maximizing efforts to scale up curation and facilitate involvement of external groups who wish to utilize ClinGen methods and infrastructure for expert curation.
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Affiliation(s)
- Laura V Milko
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Birgit H Funke
- Veritas Genetics, Danvers, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Danielle R Azzariti
- Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA
| | - Kristy Lee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Edgar A Rivera-Munoz
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland, USA
| | - Annie Niehaus
- Medical University of South Carolina, Charleston, South Carolina, USA
| | - Erin L Currey
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | | | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,Molecular Genetics and Genomics in ARUP Laboratories, Salt Lake City, Utah, USA
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert D Steiner
- Departments of Pediatrics and Genetics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Heidi L Rehm
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.,Partners HealthCare Laboratory for Molecular Medicine, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S Watson
- Autism & Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Erin M Ramos
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Sharon E Plon
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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36
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Williams JL, Chung WK, Fedotov A, Kiryluk K, Weng C, Connolly JJ, Harr M, Hakonarson H, Leppig KA, Larson EB, Jarvik GP, Veenstra DL, Hoell C, Smith ME, Holm IA, Peterson JF, Williams MS. Harmonizing Outcomes for Genomic Medicine: Comparison of eMERGE Outcomes to ClinGen Outcome/Intervention Pairs. Healthcare (Basel) 2018; 6:healthcare6030083. [PMID: 30011878 PMCID: PMC6164315 DOI: 10.3390/healthcare6030083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 11/16/2022] Open
Abstract
Genomic medicine is moving from research to the clinic. There is a lack of evidence about the impact of genomic medicine interventions on health outcomes. This is due in part to a lack of standardized outcome measures that can be used across different programs to evaluate the impact of interventions targeted to specific genetic conditions. The eMERGE Outcomes working group (OWG) developed measures to collect information on outcomes following the return of genomic results to participants for several genetic disorders. These outcomes were compared to outcome intervention pairs for genetic disorders developed independently by the ClinGen Actionability working group (AWG). In general, there was concordance between the defined outcomes between the two groups. The ClinGen outcomes tended to be from a higher level and the AWG scored outcomes represented a subset of outcomes referenced in the accompanying AWG evidence review. eMERGE OWG outcomes were more detailed and discrete, facilitating a collection of relevant information from the health records. This paper demonstrates that common outcomes for genomic medicine interventions can be identified. Further work is needed to standardize outcomes across genomic medicine implementation projects and to make these publicly available to enhance dissemination and assist in making precision public health a reality.
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Affiliation(s)
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10025, USA.
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10025, USA.
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10025, USA.
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10025, USA.
| | - John J Connolly
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Hakon Hakonarson
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kathleen A Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, WA 98101, USA.
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, USA.
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - David L Veenstra
- Department Pharmacy, University of Washington, Seattle, WA 98195, USA.
| | - Christin Hoell
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Josh F Peterson
- Departments of Biomedical Informatics and Medicine, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA.
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Riggs ER, Azzariti DR, Niehaus A, Goehringer SR, Ramos EM, Rodriguez LL, Knoppers B, Rehm HL, Martin CL. Development of a consent resource for genomic data sharing in the clinical setting. Genet Med 2018; 21:81-88. [PMID: 29899502 PMCID: PMC6292744 DOI: 10.1038/s41436-018-0017-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Data sharing between clinicians, laboratories, and patients is essential for improvements in genomic medicine, but obtaining consent for individual-level data sharing is often hindered by a lack of time and resources. To address this issue, the Clinical Genome Resource (ClinGen) developed tools to facilitate consent, including a one-page consent form and online supplemental video with information on key topics, such as risks and benefits of data sharing. METHODS To determine whether the consent form and video accurately conveyed key data sharing concepts, we surveyed 5,162 members of the general public. We measured comprehension at baseline, after reading the form and watching the video. Additionally, we assessed participants' attitudes toward genomic data sharing. RESULTS Participants' performance on comprehension questions significantly improved over baseline after reading the form and continued to improve after watching the video. CONCLUSION Results suggest reading the form alone provided participants with important knowledge regarding broad data sharing, and watching the video allowed for broader comprehension. These materials are now available at http://www.clinicalgenome.org/share . These resources will provide patients a straightforward way to share their genetic and health information, and improve the scientific community's access to data generated through routine healthcare.
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Affiliation(s)
- Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA.
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Annie Niehaus
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Scott R Goehringer
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Rockville, MD, USA
| | - Bartha Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
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38
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Gelb BD, Cavé H, Dillon MW, Gripp KW, Lee JA, Mason-Suares H, Rauen KA, Williams B, Zenker M, Vincent LM. ClinGen's RASopathy Expert Panel consensus methods for variant interpretation. Genet Med 2018; 20:1334-1345. [PMID: 29493581 PMCID: PMC6119537 DOI: 10.1038/gim.2018.3] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/02/2018] [Indexed: 01/06/2023] Open
Abstract
Purpose Standardized and accurate variant assessment is essential for effective medical care. To that end, Clinical Genome (ClinGen) Resource clinical domain working groups (CDWG) are systematically reviewing disease-associated genes for sufficient evidence to support disease causality and creating disease-specific specifications of ACMG-AMP guidelines for consistent and accurate variant classification. Methods The ClinGen RASopathy CDWG established an expert panel (EP) to curate gene information and generate gene and disease-specific specifications to ACMG-AMP variant classification framework. These specifications were tested by classifying 37 exemplar pathogenic variants plus an additional 66 variants in ClinVar distributed across nine RASopathy genes. Results RASopathy-related specifications were applied to sixteen ACMG-AMP criteria, with five also having adjustable strength with availability of additional evidence. Another five criteria were deemed not applicable. Key adjustments to minor allele frequency thresholds, multiple de novo occurrence events and/or segregation, and strength adjustments impacted 60% of variant classifications. Unpublished case-level data from participating laboratories impacted 45% of classifications supporting the need for data sharing. Conclusions RAS-specific ACMG-AMP specifications optimized the utility of available clinical evidence and Ras/MAPK pathway-specific characteristics to consistently classify RASopathy-associated variants. These specifications highlight how grouping genes by shared features promotes rapid multi-genic variant assessment without sacrificing specificity and accuracy.
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Affiliation(s)
- Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hélène Cavé
- Département de Génétique, Hôpital Robert Debré and Institut Universitaire d'Hématologie, Université Paris Diderot, Paris-Sorbonne-Cité, Paris, France
| | - Mitchell W Dillon
- Icahn School of Medicine at Mount Sinai, Molecular Genetic Testing Laboratory, New York, New York, USA
| | - Karen W Gripp
- Division of Medical Genetics, A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Jennifer A Lee
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners Healthcare, Cambridge, Massachusetts, USA
| | - Katherine A Rauen
- Department of Pediatrics, University of California Davis, UC Davis MIND Institute, Sacramento, California, USA
| | | | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
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Ghouse J, Skov MW, Bigseth RS, Ahlberg G, Kanters JK, Olesen MS. Distinguishing pathogenic mutations from background genetic noise in cardiology: The use of large genome databases for genetic interpretation. Clin Genet 2017; 93:459-466. [PMID: 28589536 DOI: 10.1111/cge.13066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
Advances in clinical genetic testing have led to increased insight into the human genome, including how challenging it is to interpret rare genetic variation. In some cases, the ability to detect genetic mutations exceeds the ability to understand their clinical impact, limiting the advantage of these technologies. Obstacles in genomic medicine are many and include: understanding the level of certainty/uncertainty behind pathogenicity determination, the numerous different variant interpretation-guidelines used by clinical laboratories, delivering the certain or uncertain result to the patient, helping patients evaluate medical decisions in light of uncertainty regarding the consequence of the findings. Through publication of large publicly available exome/genome databases, researchers and physicians are now able to highlight dubious variants previously associated with different cardiac traits. Also, continuous efforts through data sharing, international collaborative efforts to develop disease-gene-specific guidelines, and computational analyses using large data, will indubitably assist in better variant interpretation and classification. This article discusses the current, and quickly changing, state of variant interpretation resources within cardiovascular genetic research, e.g., publicly available databases and ways of how cardiovascular genetic counselors and geneticists can aid in improving variant interpretation in cardiology.
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Affiliation(s)
- J Ghouse
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - M W Skov
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - R S Bigseth
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - G Ahlberg
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M S Olesen
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Patel RY, Shah N, Jackson AR, Ghosh R, Pawliczek P, Paithankar S, Baker A, Riehle K, Chen H, Milosavljevic S, Bizon C, Rynearson S, Nelson T, Jarvik GP, Rehm HL, Harrison SM, Azzariti D, Powell B, Babb L, Plon SE, Milosavljevic A. ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants. Genome Med 2017; 9:3. [PMID: 28081714 PMCID: PMC5228115 DOI: 10.1186/s13073-016-0391-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through practice guidelines, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have published standards and guidelines for the interpretation of sequence variants. However, manual application of the guidelines is tedious and prone to human error. Web-based tools and software systems may not only address this problem but also document reasoning and supporting evidence, thus enabling transparency of evidence-based reasoning and resolution of discordant interpretations. RESULTS In this report, we describe the design, implementation, and initial testing of the Clinical Genome Resource (ClinGen) Pathogenicity Calculator, a configurable system and web service for the assessment of pathogenicity of Mendelian germline sequence variants. The system allows users to enter the applicable ACMG/AMP-style evidence tags for a specific allele with links to supporting data for each tag and generate guideline-based pathogenicity assessment for the allele. Through automation and comprehensive documentation of evidence codes, the system facilitates more accurate application of the ACMG/AMP guidelines, improves standardization in variant classification, and facilitates collaborative resolution of discordances. The rules of reasoning are configurable with gene-specific or disease-specific guideline variations (e.g. cardiomyopathy-specific frequency thresholds and functional assays). The software is modular, equipped with robust application program interfaces (APIs), and available under a free open source license and as a cloud-hosted web service, thus facilitating both stand-alone use and integration with existing variant curation and interpretation systems. The Pathogenicity Calculator is accessible at http://calculator.clinicalgenome.org . CONCLUSIONS By enabling evidence-based reasoning about the pathogenicity of genetic variants and by documenting supporting evidence, the Calculator contributes toward the creation of a knowledge commons and more accurate interpretation of sequence variants in research and clinical care.
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Affiliation(s)
- Ronak Y Patel
- Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Neethu Shah
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | | | - Aaron Baker
- Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin Riehle
- Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hailin Chen
- Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Chris Bizon
- The Renaissance Computing Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27517, USA
| | - Shawn Rynearson
- University of Utah Hospitals and Clinics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Tristan Nelson
- Geisinger autism and developmental medicine, Lewisburg, PA, 17837, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA.,Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Steven M Harrison
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
| | - Danielle Azzariti
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, 02139, USA
| | - Bradford Powell
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Larry Babb
- GeneInsight, Sunquest Information System, Boston, MA, 02210, USA
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