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Zukin E, Culver JO, Liu Y, Yang Y, Ricker CN, Hodan R, Sturgeon D, Kingham K, Chun NM, Rowe-Teeter C, Singh K, Zell JA, Ladabaum U, McDonnell KJ, Ford JM, Parmigiani G, Braun D, Kurian AW, Gruber SB, Idos GE. Clinical implications of conflicting variant interpretations in the cancer genetics clinic. Genet Med 2023; 25:100837. [PMID: 37057674 PMCID: PMC10416421 DOI: 10.1016/j.gim.2023.100837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE The aim of this study was to describe the clinical impact of commercial laboratories issuing conflicting classifications of genetic variants. METHODS Results from 2000 patients undergoing a multigene hereditary cancer panel by a single laboratory were analyzed. Clinically significant discrepancies between the laboratory-provided test reports and other major commercial laboratories were identified, including differences between pathogenic/likely pathogenic and variant of uncertain significance (VUS) classifications, via review of ClinVar archives. For patients carrying a VUS, clinical documentation was assessed for evidence of provider awareness of the conflict. RESULTS Fifty of 975 (5.1%) patients with non-negative results carried a variant with a clinically significant conflict, 19 with a pathogenic/likely pathogenic variant reported in APC or MUTYH, and 31 with a VUS reported in CDKN2A, CHEK2, MLH1, MSH2, MUTYH, RAD51C, or TP53. Only 10 of 28 (36%) patients with a VUS with a clinically significant conflict had a documented discussion by a provider about the conflict. Discrepant counseling strategies were used for different patients with the same variant. Among patients with a CDKN2A variant or a monoallelic MUTYH variant, providers were significantly more likely to make recommendations based on the laboratory-reported classification. CONCLUSION Our findings highlight the frequency of variant interpretation discrepancies and importance of clinician awareness. Guidance is needed on managing patients with discrepant variants to support accurate risk assessment.
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Affiliation(s)
- Elyssa Zukin
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA; University of California, Irvine, Irvine, CA
| | - Julie O Culver
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Yuxi Liu
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yunqi Yang
- Dana-Farber Cancer Institute, Boston, MA
| | - Charité N Ricker
- University of Southern California, Keck School of Medicine, Los Angeles, CA
| | - Rachel Hodan
- Stanford University School of Medicine, Stanford, CA
| | - Duveen Sturgeon
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Kerry Kingham
- Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | - Uri Ladabaum
- Stanford University School of Medicine, Stanford, CA
| | - Kevin J McDonnell
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - James M Ford
- Stanford University School of Medicine, Stanford, CA
| | - Giovanni Parmigiani
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Danielle Braun
- Dana-Farber Cancer Institute, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Stephen B Gruber
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA
| | - Gregory E Idos
- City of Hope National Medical Center, Center for Precision Medicine, Duarte, CA.
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2
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Giles HH, Hegde MR, Lyon E, Stanley CM, Kerr ID, Garlapow ME, Eggington JM. The Science and Art of Clinical Genetic Variant Classification and Its Impact on Test Accuracy. Annu Rev Genomics Hum Genet 2021; 22:285-307. [PMID: 33900788 DOI: 10.1146/annurev-genom-121620-082709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clinical genetic variant classification science is a growing subspecialty of clinical genetics and genomics. The field's continued improvement is essential for the success of precision medicine in both germline (hereditary) and somatic (oncology) contexts. This review focuses on variant classification for DNA next-generation sequencing tests. We first summarize current limitations in variant discovery and definition, and then describe the current five- and four-tier classification systems outlined in dominant standards and guideline publications for germline and somatic tests, respectively. We then discuss measures of variant classification discordance and the field's bias for positive results, as well as considerations for panel size and population screening in the context of estimates of positive predictive value thatincorporate estimated variant classification imperfections. Finally, we share opinions on the current state of variant classification from some of the authors of the most widely used standards and guideline publications and from other domain experts.
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Affiliation(s)
- Hunter H Giles
- Center for Genomic Interpretation, Sandy, Utah 84092, USA; , ,
| | - Madhuri R Hegde
- PerkinElmer Genomics, Waltham, Massachusetts 02450, USA; .,Department of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Elaine Lyon
- HudsonAlpha Clinical Services Lab, Huntsville, Alabama 35806, USA;
| | - Christine M Stanley
- C2i Genomics, Cambridge, Massachusetts 02139, USA.,Variantyx, Framingham, Massachusetts 01701, USA;
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3
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Harrison SM, Dolinksy JS, Chen W, Collins CD, Das S, Deignan JL, Garber KB, Garcia J, Jarinova O, Knight Johnson AE, Koskenvuo JW, Lee H, Mao R, Mar-Heyming R, McFaddin AS, Moyer K, Nagan N, Rentas S, Santani AB, Seppälä EH, Shirts BH, Tidwell T, Topper S, Vincent LM, Vinette K, Rehm HL. Scaling resolution of variant classification differences in ClinVar between 41 clinical laboratories through an outlier approach. Hum Mutat 2019; 39:1641-1649. [PMID: 30311378 DOI: 10.1002/humu.23643] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 11/09/2022]
Abstract
ClinVar provides open access to variant classifications shared from many clinical laboratories. Although most classifications are consistent across laboratories, classification differences exist. To facilitate resolution of classification differences on a large scale, clinical laboratories were encouraged to reassess outlier classifications of variants with medically significant differences (MSDs). Outliers were identified by first comparing ClinVar submissions from 41 clinical laboratories to detect variants with MSDs between the laboratories (650 variants). Next, MSDs were filtered for variants with ≥3 classifications (244 variants), of which 87.6% (213 variants) had a majority consensus in ClinVar, thus allowing for identification of outlier classifications in need of reassessment. Laboratories with outlier classifications were sent a custom report and encouraged to reassess variants. Results were returned for 204 (96%) variants, of which 62.3% (127) were resolved. Of those 127, 64.6% (82) were resolved due to reassessment prompted by this study and 35.4% (45) resolved by a previously completed reassessment. This study demonstrates a scalable approach to classification resolution and capitalizes on the value of data sharing within ClinVar. These activities will help the community move toward more consistent variant classifications, which will improve the care of patients with, or at risk for, genetic disorders.
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Affiliation(s)
- Steven M Harrison
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Wenjie Chen
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
| | - Christin D Collins
- EGL Genetics, Tucker, Georgia.,Global Laboratory Services, PerkinElmer Genomics, Branford, Connecticut
| | - Soma Das
- Department of Human Genetics, The University of Chicago, Chicago, Illinois
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | | | - John Garcia
- Invitae Corporation, San Francisco, California
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | | | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - Andrew S McFaddin
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Narasimhan Nagan
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
| | - Stefan Rentas
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Avni B Santani
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | | | - Scott Topper
- Invitae Corporation, San Francisco, California.,Color Genomics, South San Francisco, California
| | | | - Kathy Vinette
- Molecular Diagnostics Laboratory, A. I. duPont Hospital for Children, Wilmington, Delaware
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston
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4
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Balmaña J, Nathanson K, Offit K, Robson M, Domchek S. Reply to R.L. Nussbaum et al and J.S. Dolinsky et al. J Clin Oncol 2017; 35:1262-1263. [PMID: 28135137 DOI: 10.1200/jco.2016.71.3859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Judith Balmaña
- Judith Balmaña, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, and Vall d'Hebron Institute of Oncology, Barcelona, Spain; Katherine Nathanson, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Kenneth Offit and Mark Robson, Memorial Sloan Kettering Cancer Center, New York, NY; and Susan Domchek, Perelman School of Medicine at the University of Pennsylvania and Basser Center for BRCA, Philadelphia, PA
| | - Katherine Nathanson
- Judith Balmaña, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, and Vall d'Hebron Institute of Oncology, Barcelona, Spain; Katherine Nathanson, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Kenneth Offit and Mark Robson, Memorial Sloan Kettering Cancer Center, New York, NY; and Susan Domchek, Perelman School of Medicine at the University of Pennsylvania and Basser Center for BRCA, Philadelphia, PA
| | - Kenneth Offit
- Judith Balmaña, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, and Vall d'Hebron Institute of Oncology, Barcelona, Spain; Katherine Nathanson, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Kenneth Offit and Mark Robson, Memorial Sloan Kettering Cancer Center, New York, NY; and Susan Domchek, Perelman School of Medicine at the University of Pennsylvania and Basser Center for BRCA, Philadelphia, PA
| | - Mark Robson
- Judith Balmaña, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, and Vall d'Hebron Institute of Oncology, Barcelona, Spain; Katherine Nathanson, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Kenneth Offit and Mark Robson, Memorial Sloan Kettering Cancer Center, New York, NY; and Susan Domchek, Perelman School of Medicine at the University of Pennsylvania and Basser Center for BRCA, Philadelphia, PA
| | - Susan Domchek
- Judith Balmaña, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, and Vall d'Hebron Institute of Oncology, Barcelona, Spain; Katherine Nathanson, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA; Kenneth Offit and Mark Robson, Memorial Sloan Kettering Cancer Center, New York, NY; and Susan Domchek, Perelman School of Medicine at the University of Pennsylvania and Basser Center for BRCA, Philadelphia, PA
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