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Pastò B, Buzzatti G, Schettino C, Malapelle U, Bergamini A, De Angelis C, Musacchio L, Dieci MV, Kuhn E, Lambertini M, Passarelli A, Toss A, Farolfi A, Roncato R, Capoluongo E, Vida R, Pignata S, Callari M, Baldassarre G, Bartoletti M, Gerratana L, Puglisi F. Unlocking the potential of Molecular Tumor Boards: from cutting-edge data interpretation to innovative clinical pathways. Crit Rev Oncol Hematol 2024; 199:104379. [PMID: 38718940 DOI: 10.1016/j.critrevonc.2024.104379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/02/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The emerging era of precision medicine is characterized by an increasing availability of targeted anticancer therapies and by the parallel development of techniques to obtain more refined molecular data, whose interpretation may not always be straightforward. Molecular tumor boards gather various professional figures, in order to leverage the analysis of molecular data and provide prognostic and predictive insights for clinicians. In addition to healthcare development, they could also become a tool to promote knowledge and research spreading. A growing body of evidence on the application of molecular tumor boards to clinical practice is forming and positive signals are emerging, although a certain degree of heterogeneity exists. This work analyzes molecular tumor boards' potential workflows, figures involved, data sources, sample matrices and eligible patients, as well as available evidence and learning examples. The emerging concept of multi-institutional, disease-specific molecular tumor boards is also considered by presenting two ongoing nationwide experiences.
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Affiliation(s)
- Brenno Pastò
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Giulia Buzzatti
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy
| | - Clorinda Schettino
- Clinical Trials Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, Napoli 80131, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Napoli 80131, Italy
| | - Alice Bergamini
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milano 20132, Italy; Unit of Obstetrics and Gynaecology, IRCCS San Raffaele Scientific Institute, Milano 20132, Italy
| | - Carmine De Angelis
- Oncology Unit - Department of Clinical Medicine and Surgery, University of Naples Federico II, Napoli 80131, Italy
| | - Lucia Musacchio
- Department of Women and Child Health, Division of Gynaecologic Oncology, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma 00168, Italy
| | - Maria Vittoria Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova 35122, Italy; Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova 35128, Italy
| | - Elisabetta Kuhn
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milano 20122, Italy; Pathology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano 20122, Italy
| | - Matteo Lambertini
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova 16132, Italy; Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova 16132, Italy
| | - Anna Passarelli
- Department of Urology and Gynaecology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli 80131, Italy
| | - Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena 41124, Italy; Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena 41124, Italy
| | - Alberto Farolfi
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola 47014, Italy
| | - Rossana Roncato
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano 33081, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Napoli 80131, Italy; Clinical Pathology Unit, Azienda Ospedaliera San Giovanni Addolorata, Roma 00184, Italy
| | - Riccardo Vida
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Sandro Pignata
- Department of Urology and Gynaecology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Napoli 80131, Italy
| | | | - Gustavo Baldassarre
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Aviano 33081, Italy
| | - Michele Bartoletti
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy.
| | - Fabio Puglisi
- Department of Medicine (DMED), University of Udine, Udine 33100, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano 33081, Italy
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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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Offit K, Sharkey CM, Green D, Wu X, Trottier M, Hamilton JG, Walsh MF, Dandiker S, Belhadj S, Lipkin SM, Sugrañes TA, Caggana M, Stadler ZK. Regulation of Laboratory-Developed Tests in Preventive Oncology: Emerging Needs and Opportunities. J Clin Oncol 2023; 41:11-21. [PMID: 35944238 PMCID: PMC10409443 DOI: 10.1200/jco.22.00995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/19/2022] [Accepted: 06/27/2022] [Indexed: 12/27/2022] Open
Abstract
Cancer predictive or diagnostic assays, offered as Laboratory-Developed Tests (LDTs), have been subject to regulatory authority and enforcement discretion by the US Food and Drug Administration. Many LDTs enter the market without US Food and Drug Administration or any regulatory review. The Centers for Medicare & Medicaid Services under the Clinical Laboratory Improvement Amendments focuses on analytic performance, but has limited oversight of the quality or utility of LDTs, including whether patients have been harmed as a result of their use. Increasingly, LDTs for cancer risk or early detection have been marketed directly to consumers, with many LDT developers depicting these tests, requested by patients but ordered by personal or company-associated physicians, as procedures falling under the practice of medicine. This patchwork of regulation and enforcement uncertainty regarding LDTs and public concerns about accuracy of tests given emergency authorization during the COVID-19 pandemic led to the Verifying Accurate Leading-edge IVCT (in vitro clinical test) Development Act of 2021. This pending federal legislation represents an opportunity to harmonize regulatory policies and address growing concerns over quality, utility, and safety of LDTs for cancer genomics, including tests marketed directly to consumers. We review here questions regarding the potential benefits and harms of some cancer-related LDTs for cancer risk and presymptomatic molecular diagnosis, increasingly marketed to oncologists or directly to the worried well. We offer specific proposals to strengthen oversight of the accuracy and clinical utility of cancer genetic testing to ensure public safety.
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Affiliation(s)
- Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | - Dina Green
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaohan Wu
- The University of California, Berkeley School of Law, Berkeley, CA
| | - Magan Trottier
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jada G. Hamilton
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Michael F. Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Sita Dandiker
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sami Belhadj
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
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Hunter CL, Helft PR. Yes, We Can, But Should We? Ethical Considerations in Reporting Germline Findings From Paired Tumor-Normal Genomic Testing in Patients With Advanced Cancer. J Clin Oncol 2022; 41:1982-1985. [PMID: 36469841 DOI: 10.1200/jco.22.00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Cynthia L. Hunter
- Indiana University Health Department of Medical and Molecular Genetics, Indianapolis, IN
- Indiana University Health Precision Genomics, Indianapolis, IN
| | - Paul R. Helft
- Division of Hematology/Oncology, Department of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Charles Warren Fairbanks Center for Medical Ethics, Indiana University Health, Indianapolis, IN
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Toward More Comprehensive Homologous Recombination Deficiency Assays in Ovarian Cancer, Part 1: Technical Considerations. Cancers (Basel) 2022; 14:cancers14051132. [PMID: 35267439 PMCID: PMC8909526 DOI: 10.3390/cancers14051132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) is the most frequent and lethal form of ovarian cancer and is associated with homologous recombination deficiency (HRD) in 50% of cases. This specific alteration is associated with sensitivity to PARP inhibitors (PARPis). Despite vast prognostic improvements due to PARPis, current molecular assays assessing HRD status suffer from several limitations, and there is an urgent need for a more accurate evaluation. In these companion reviews (Part 1: Technical considerations; Part 2: Medical perspectives), we develop an integrative review to provide physicians and researchers involved in HGSOC management with a holistic perspective, from translational research to clinical applications. Abstract High-grade serous ovarian cancer (HGSOC), the most frequent and lethal form of ovarian cancer, exhibits homologous recombination deficiency (HRD) in 50% of cases. In addition to mutations in BRCA1 and BRCA2, which are the best known thus far, defects can also be caused by diverse alterations to homologous recombination-related genes or epigenetic patterns. HRD leads to genomic instability (genomic scars) and is associated with PARP inhibitor (PARPi) sensitivity. HRD is currently assessed through BRCA1/2 analysis, which produces a genomic instability score (GIS). However, despite substantial clinical achievements, FDA-approved companion diagnostics (CDx) based on GISs have important limitations. Indeed, despite the use of GIS in clinical practice, the relevance of such assays remains controversial. Although international guidelines include companion diagnostics as part of HGSOC frontline management, they also underscore the need for more powerful and alternative approaches for assessing patient eligibility to PARP inhibitors. In these companion reviews, we review and present evidence to date regarding HRD definitions, achievements and limitations in HGSOC. Part 1 is dedicated to technical considerations and proposed perspectives that could lead to a more comprehensive and dynamic assessment of HR, while Part 2 provides a more integrated approach for clinicians.
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Chiang J, Chia TH, Yuen J, Shaw T, Li ST, Binte Ishak ND, Chew EL, Chong ST, Chan SH, Ngeow J. Impact of Variant Reclassification in Cancer Predisposition Genes on Clinical Care. JCO Precis Oncol 2022; 5:577-584. [PMID: 34994607 DOI: 10.1200/po.20.00399] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Genetic testing has clinical utility in the management of patients with hereditary cancer syndromes. However, the increased likelihood of encountering a variant of uncertain significance in individuals of non-European descent such as Asians may be challenging to both clinicians and patients. This study aims to evaluate the impact of variant reclassification in an Asian country with variants of uncertain significance reported in cancer predisposition genes. METHODS A retrospective analysis of patients seen at the Cancer Genetics Service at the National Cancer Centre Singapore between February 2014 and March 2020 was conducted. The frequency, direction, and time to variant reclassification were evaluated by comparing the reclassified report against the original report. RESULTS A total of 1,412 variants of uncertain significance were reported in 49.9% (845 of 1,695) of patients. Over 6 years, 6.7% (94 of 1,412) of variants were reclassified. Most variants of uncertain significance (94.1%, 80 of 85) were downgraded to benign or likely benign variant, with a smaller proportion of variants of uncertain significance (5.9%, 5 of 85) upgraded to pathogenic or likely pathogenic variant. Actionable variants of uncertain significance upgrades and pathogenic or likely pathogenic variant downgrades, which resulted in management changes, happened in 31.0% (39 of 126) of patients. The median and mean time taken for reclassification were 1 and 1.62 year(s), respectively. CONCLUSION We propose a clinical guideline to standardize management of patients reported to have variants of uncertain significance. Management should be based on the patient's personal history, family history, and variant interpretation. For clinically relevant or suspicious variants of uncertain significance, follow-up is recommended every 2 years, as actionable reclassifications may happen during this period.
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Affiliation(s)
- Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tze Hao Chia
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jeanette Yuen
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tarryn Shaw
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Shao-Tzu Li
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Nur Diana Binte Ishak
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Ee Ling Chew
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Siao Ting Chong
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore.,Institute of Molecular and Cellular Biology, Agency for Science, Technology and Research, Singapore, Singapore
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Scott RJ, Mehta A, Macedo GS, Borisov PS, Kanesvaran R, El Metnawy W. Genetic testing for homologous recombination repair (HRR) in metastatic castration-resistant prostate cancer (mCRPC): challenges and solutions. Oncotarget 2021; 12:1600-1614. [PMID: 34381565 PMCID: PMC8351605 DOI: 10.18632/oncotarget.28015] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Patients with metastatic castration-resistant prostate cancer (mCRPC) have an average survival of only 13 months. Identification of novel predictive and actionable biomarkers in the homologous recombination repair (HRR) pathway in up to a quarter of patients with mCRPC has led to the approval of targeted therapies like poly-ADP ribose polymerase inhibitors (PARPi), with the potential to improve survival outcomes. The approval of PARPi has led to guideline bodies such as the National Comprehensive Cancer Network (NCCN) to actively recommend germline and or somatic HRR gene panel testing to identify patients who will benefit from PARPi. However, there are several challenges as genetic testing is still at an early stage especially in low- and middle-income countries, with cost and availability being major impediments. In addition, there are issues such as choice of optimal tissue for genetic testing, archival, storage, retrieval of tissue blocks, interpretation and classification of variants in the HRR pathway, and the need for pretest and post-test genetic counseling. This review provides insights into the HRR gene mutations prevalent in mCRPC and the challenges for a more widespread gene testing to identify actionable germline pathogenic variants and somatic mutations in the HRR pathway, and proposes a clinical algorithm to enhance the efficiency of the gene testing process.
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Affiliation(s)
- Rodney J. Scott
- Laureate Professor, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Anurag Mehta
- Director, Department of Laboratory & Transfusion Services and Director Research, Rajiv Gandhi Cancer Institute, Delhi, India
| | - Gabriel S. Macedo
- Programa de Medicina Personalizada – Coordenador, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Pavel S. Borisov
- Oncologist Urologist, FSBI “N.N. Petrov NMRC of Oncology” of the Ministry Healthcare of the Russian Federation, St Petersburg, Russia
| | - Ravindran Kanesvaran
- Deputy Head and Senior Consultant, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Wafaa El Metnawy
- Professor of Molecular Pathology, Oncology Center School of Medicine, Cairo University, Giza, Egypt
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Local Laboratory Testing of Germline BRCA Mutations vs. Myriad: A Single-Institution Experience in Korea. Diagnostics (Basel) 2021; 11:diagnostics11020370. [PMID: 33671539 PMCID: PMC7926822 DOI: 10.3390/diagnostics11020370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 01/26/2023] Open
Abstract
Genetic diagnosis for human epidermal growth factor receptor 2-negative metastatic breast cancer patients with the germline BRCA (gBRCA) mutation has been emphasized since the development of polyadenosine diphosphate-ribose polymerase inhibitors. Myriad Genetics, Inc.’s (Salt Lake City, UT, USA) companion diagnostics service is almost exclusively used for genetic testing. The aim of this study was to compare the results of germline BRCA mutation tests returned by a local laboratory and those performed by Myriad. Between April 2014 and February 2018, 31 patients with gBRCA 1/2 mutation test results from both Samsung Medical Center (Seoul, Korea) and Myriad were enrolled. “Discordant: Opposite classification” was observed for only one among 27 (3.7%). This discrepancy was due to the detection of a deleterious large genomic rearrangement of BRCA 1 by Myriad. Samsung Medical Center performed multiple ligation-dependent probe amplifications (MLPA) to detect large genomic rearrangements only in high-risk patients. This one case was not suspected as high risk and MLPA was not performed. The concordant rate was 74.1% for all 27 patients. “Discordant: Laboratory’s uncertain classification” was found in 22.2% of the sample (six patients). All discrepancies were generated during interpretation of BRCA 2 gene sequencing. Further studies and standardization of genetic testing for BRCA 1/2 genes are required.
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Banck H, Dugas M, MÜller-Tidow C, Sandmann S. Comparison of Open-access Databases for Clinical Variant Interpretation in Cancer: A Case Study of MDS/AML. Cancer Genomics Proteomics 2021; 18:157-166. [PMID: 33608312 DOI: 10.21873/cgp.20250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/23/2021] [Accepted: 01/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recently, guidelines for variant interpretation in cancer have been established. However, these guidelines do not mention which databases are most suited to performing this task. MATERIALS AND METHODS We give an overview of existing databases and evaluate their benefit in practical application. We compared three meta-databases and 12 databases for a dataset of patients with myelodysplastic syndrome or acute myeloid leukemia. RESULTS Clinical implications were found for 13% of all variants. One-third of variants with therapeutic implications were uniquely contained in one database. The VICC meta-database was the most extensive source of information, featuring 92% of variants with a drug association. However, a comparison of meta-databases and original sources indicated that some variants are missing in those meta-databases. CONCLUSION Public databases provide decision support for interpreting variants but there is still need for manual curation. Meta-databases facilitate the use of multiple resources but should be interpreted with caution.
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Affiliation(s)
- Henrik Banck
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Carsten MÜller-Tidow
- Medizinische Klinik, Abteilung Innere Medizin V, University Hospital Heidelberg, Heidelberg, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster, Germany;
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Chunn LM, Nefcy DC, Scouten RW, Tarpey RP, Chauhan G, Lim MS, Elenitoba-Johnson KSJ, Schwartz SA, Kiel MJ. Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation. Front Genet 2020; 11:577152. [PMID: 33281875 PMCID: PMC7691534 DOI: 10.3389/fgene.2020.577152] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 10/19/2020] [Indexed: 12/21/2022] Open
Abstract
Design and interpretation of genome sequencing assays in clinical diagnostics and research labs is complicated by an inability to identify information from the medical literature and related databases quickly, comprehensively and reproducibly. This challenge is compounded by the complexity and heterogeneity of nomenclatures used to describe diseases, genes and genetic variants. Mastermind is a widely-used bioinformatic platform of genomic associations that has indexed more than 7.5 M full-text articles and 2.5 M supplemental datasets. It has automatically identified, disambiguated and annotated >6.1 M genetic variants and identified >50 K disease-gene associations. Here, we describe how Mastermind improves the sensitivity and reproducibility of clinical variant interpretation and produces comprehensive genomic landscapes of genetic variants driving pharmaceutical research. We demonstrate an alarmingly high degree of heterogeneity across commercially available panels for hereditary cancer that is resolved by evidence from Mastermind. We further examined the sensitivity of Mastermind for variant interpretation by examining 108 clinically-encountered variants and comparing the results to alternate methods. Mastermind demonstrated a sensitivity of 98.4% compared to 4.4, 45.6, and 37.4% for alternatives PubMed, Google Scholar, and ClinVar, respectively, and a specificity of 98.5% compared to 45.1, 57.6, and 68.8% as well as an increase in content yield of 22.6-, 2.2-, and 2.6-fold. When curated for clinical significance, Mastermind identified more than 4.9-fold more pathogenic variants than ClinVar for representative genes. For structural variants, we compared Mastermind's ability to sensitively identify evidence for 10 representative disease-causing CNVs versus results identified in PubMed, as well as its ability to identify evidence for fusion events compared to COSMIC. Mastermind demonstrated a 4.0- to 43.9-fold increase in references for specific CNVs compared to PubMed, as well as 5.4-fold more fusion genes when compared with COSMIC's curated database. Additionally, Mastermind produced an 8.0-fold increase in reference citations for fusion events common to Mastermind and outside databases. Taken together, these results demonstrate the utility and superiority of Mastermind in terms of both sensitivity and specificity of automated results for clinical diagnostic variant interpretation for multiple genetic variant types and highlight the potential benefit in informing pharmaceutical research.
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Affiliation(s)
| | | | | | - Ryan P. Tarpey
- The Johns Hopkins Hospital, Department of Pharmacy, Baltimore, MD, United States
| | | | - Megan S. Lim
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kojo S. J. Elenitoba-Johnson
- Division of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Nix P, Mundt E, Manley S, Coffee B, Roa B. Functional RNA Studies Are a Useful Tool in Variant Classification but Must Be Used With Caution: A Case Study of One BRCA2 Variant. JCO Precis Oncol 2020; 4:730-735. [PMID: 35050751 DOI: 10.1200/po.20.00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Paola Nix
- Myriad Genetic Laboratories, Salt Lake City, UT
| | - Erin Mundt
- Myriad Genetic Laboratories, Salt Lake City, UT
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12
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Schneider BP, Stout LA, Philips S, Schroeder C, Scott SF, Hunter C, Kassem N, Kiel PJ, Radovich M. Implications of Incidental Germline Findings Identified In the Context of Clinical Whole Exome Sequencing for Guiding Cancer Therapy. JCO Precis Oncol 2020; 4:1109-1121. [PMID: 35050776 DOI: 10.1200/po.19.00354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Identification of incidental germline mutations in the context of next-generation sequencing is an unintended consequence of advancing technologies. These data are critical for family members to understand disease risks and take action. PATIENTS AND METHODS A retrospective cohort analysis was conducted of 1,028 adult patients with metastatic cancer who were sequenced with tumor and germline whole exome sequencing (WES). Germline variant call files were mined for pathogenic/likely pathogenic (P/LP) variants using the ClinVar database and narrowed to high-quality submitters. RESULTS Median age was 59 years, with 16% of patients ≤ 45 years old. The most common tumor types were breast cancer (12.5%), colorectal cancer (11.5%), sarcoma (9.3%), prostate cancer (8.4%), and lung cancer (6.6%). We identified 3,427 P/LP variants in 471 genes, and 84% of patients harbored one or more variant. One hundred thirty-two patients (12.8%) carried a P/LP variant in a cancer predisposition gene, with BRCA2 being the most common (1.6%). Patients with breast cancer were most likely to carry a P/LP variant (19.2%). One hundred ten patients (10.7%) carried a P/LP variant in a gene that would be recommended by the American College of Medical Genetics and Genomics to be reported as a result of clinical actionability, with the most common being ATP7B (2.7%), BRCA2 (1.6%), MUTYH (1.4%), and BRCA1 (1%). Of patients who carried a P/LP variant in a cancer predisposition gene, only 53% would have been offered correct testing based on current clinical practice guidelines. Of 471 mutated genes, 231 genes had a P/LP variant identified in one patient, demonstrating significant genetic heterogeneity. CONCLUSION The majority of patients undergoing clinical cancer WES harbor a pathogenic germline variation. Identification of clinically actionable germline findings will create additional burden on oncology clinics as broader WES becomes common.
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Affiliation(s)
- Bryan P Schneider
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | | | - Courtney Schroeder
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Susanna F Scott
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Cynthia Hunter
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Patrick J Kiel
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
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13
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Park KJ, Lee W, Chun S, Min WK. The Frequency of Discordant Variant Classification in the Human Gene Mutation Database: A Comparison of the American College of Medical Genetics and Genomics Guidelines and ClinVar. Lab Med 2020; 52:250-259. [PMID: 32926152 DOI: 10.1093/labmed/lmaa072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Discordant variant classifications among public databases is one of the well-documented limitations when interpreting the pathogenicity of variants. The aim of this study is to investigate the level of germline variant misannotation from the Human Gene Mutation Database (HGMD) and the annotation concordance between databases. METHODS We used a total of 188,106 classified variants (disease-causing mutations [n = 179,454] and polymorphisms [n = 8652]) in 6466 genes from the HGMD. All variants were reanalyzed based on the American College of Medical Genetics and Genomics (ACMG) guidelines and compared to ClinVar database variants. RESULTS When variants were classified based on the ACMG guidelines, misclassification was observed in 3.47% (2289/65,896) of variants. The overall concordance between HGMD and ClinVar was 97.62% (52,499/53,780) of variants studied. CONCLUSION Variants in databases must be used with caution when variant pathogenicity is interpreted. This study reveals the frequency of misannotation of the HGMD variants and annotation concordance between databases in depth.
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Affiliation(s)
- Kyoung-Jin Park
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang-Si, Gyeonggi-Do, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sail Chun
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Won-Ki Min
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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14
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Esterling L, Wijayatunge R, Brown K, Morris B, Hughes E, Pruss D, Manley S, Bowles KR, Ross TS. Impact of a Cancer Gene Variant Reclassification Program Over a 20-Year Period. JCO Precis Oncol 2020; 4:PO.20.00020. [PMID: 32923914 PMCID: PMC7469614 DOI: 10.1200/po.20.00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Hereditary cancer genetic testing can inform personalized medical management for individuals at increased cancer risk. However, many variants in cancer predisposition genes are individually rare, and traditional tools may be insufficient to evaluate pathogenicity. This analysis presents data on variant classification and reclassification over a 20-year period. PATIENTS AND METHODS This is a retrospective analysis of > 1.9 million individuals who received hereditary cancer genetic testing from a single clinical laboratory (March 1997 to December 2017). Variant classification included review of evidence from traditional tools (eg, population frequency databases, literature) and laboratory-developed tools (eg, novel statistical methods, in-house RNA analysis) by a multidisciplinary expert committee. Variants may have been reclassified more than once and with more than one line of evidence. RESULTS In this time period, 62,842 unique variants were observed across 25 cancer predisposition genes, and 2,976 variants were reclassified. Overall, 82.1% of reclassification events were downgrades (eg, variant of uncertain significance [VUS] to benign), and 17.9% were upgrades (eg, VUS to pathogenic). Among reclassified variants, 82.8% were initially classified as VUS, and 47.5% were identified in ≤ 20 individuals (allele frequency ≤ 0.001%). Laboratory-developed tools were used in 72.3% of variant reclassification events, which affected > 600,000 individuals. More than 1.3 million patients were identified as carrying a variant that was reclassified within this 20-year time period. CONCLUSION The variant classification program used by the laboratory evaluated here enabled the reclassification of variants that were individually rare. Laboratory-developed tools were a key component of this program and were used in the majority of reclassifications. This demonstrates the importance of using robust and novel tools to reclassify rare variants to appropriately inform personalized medical management.
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15
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Huang WC, Huang HT, Chen PY, Wang WC, Ko TM, Shrestha S, Yang CD, Tai CS, Chiew MY, Chou YP, Hu YF, Huang HD. SVAD: A genetic database curates non-ischemic sudden cardiac death-associated variants. PLoS One 2020; 15:e0237731. [PMID: 32813752 PMCID: PMC7437891 DOI: 10.1371/journal.pone.0237731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/31/2020] [Indexed: 11/19/2022] Open
Abstract
Sudden cardiac death (SCD) is an important cause of mortality worldwide. It accounts for approximately half of all deaths from cardiovascular disease. While coronary artery disease and acute myocardial infarction account for the majority of SCD in the elderly population, inherited cardiac diseases (inherited CDs) comprise a substantial proportion of younger SCD victims with a significant genetic component. Currently, the use of next-generation sequencing enables the rapid analysis to investigate relationships between genetic variants and inherited CDs causing SCD. Genetic contribution to risk has been considered an alternate predictor of SCD. In the past years, large numbers of SCD susceptibility variants were reported, but these results are scattered in numerous publications. Here, we present the SCD-associated Variants Annotation Database (SVAD) to facilitate the interpretation of variants and to meet the needs of data integration. SVAD contains data from a broad screening of scientific literature. It was constructed to provide a comprehensive collection of genetic variants along with integrated information regarding their effects. At present, SVAD has accumulated 2,292 entries within 1,239 variants by manually surveying pertinent literature, and approximately one-third of the collected variants are pathogenic/likely-pathogenic following the ACMG guidelines. To the best of our knowledge, SVAD is the most comprehensive database that can provide integrated information on the associated variants in various types of inherited CDs. SVAD represents a valuable source of variant information based on scientific literature and benefits clinicians and researchers, and it is now available on http://svad.mbc.nctu.edu.tw/.
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Affiliation(s)
- Wei-Chih Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Hsin-Tzu Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Industrial Development Graduate Program of College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Po-Yuan Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Wei-Chi Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, R.O.C
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan, R.O.C
| | - Sirjana Shrestha
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Chi-Dung Yang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Chun-San Tai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Men-Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Yu-Pao Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, R.O.C
| | - Yu-Feng Hu
- Division of Cardiology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
- Institute of Clinical Medicine, and Cardiovascular Research Center, National Yang-Ming University, Taipei, Taiwan, R.O.C
- * E-mail: (HDH); (YFH)
| | - Hsien-Da Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China
- * E-mail: (HDH); (YFH)
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16
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Carraway HE, LaFramboise T. Myeloid neoplasms with germline predisposition: Practical considerations and complications in the search for new susceptibility loci. Best Pract Res Clin Haematol 2020; 33:101191. [PMID: 33038980 DOI: 10.1016/j.beha.2020.101191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Abstract
Genomic research in hematological malignancies has focused far more prominently on somatic mutations than on germline variants. Although increasing numbers of germline variants are being identified, a substantial proportion of familial myeloid malignancies have no causal allele pinpointed. Here we review the biological, technological, and clinical challenges that stand in the way of the goal of establishing, implementing, and interpreting a comprehensive panel of germline variants for testing. Achieving this goal would inform care for large numbers of myeloid malignancy patients. Furthermore, knowledge of germline susceptibility variants and their corresponding genes will shed light on disease processes, potentially suggesting therapeutic strategies tailored to specific variants.
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Affiliation(s)
- Hetty E Carraway
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900, Euclid Avenue, Cleveland, OH, 44106, USA.
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17
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Affiliation(s)
- Amy E Cyr
- Washington University School of Medicine, Box 8109, 660 South Euclid Avenue, Saint Louis, MO, 63110, USA.
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18
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Yin K, Liu Y, Lamichhane B, Sandbach JF, Patel G, Compagnoni G, Kanak RH, Rosen B, Ondrula DP, Smith L, Brown E, Gold L, Whitworth P, App C, Euhus D, Semine A, Dwight Lyons S, Lazarte MAC, Parmigiani G, Braun D, Hughes KS. Legacy Genetic Testing Results for Cancer Susceptibility: How Common are Conflicting Classifications in a Large Variant Dataset from Multiple Practices? Ann Surg Oncol 2020; 27:2212-2220. [PMID: 32342295 DOI: 10.1245/s10434-020-08492-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE The classification of germline variants may differ between labs and change over time. We apply a variant harmonization tool, Ask2Me VarHarmonizer, to map variants to ClinVar and identify discordant variant classifications in a large multipractice variant dataset. METHODS A total of 7496 variants sequenced between 1996 and 2019 were collected from 11 clinical practices. Variants were mapped to ClinVar, and lab-reported and ClinVar variant classifications were analyzed and compared. RESULTS Of the 4798 unique variants identified, 3699 (77%) were mappable to ClinVar. Among mappable variants, variants of unknown significance (VUS) accounted for 74% of lab-reported classifications and 60% of ClinVar classifications. Lab-reported and ClinVar discordances were present in 783 unique variants (21.2% of all mappable variants); 121 variants (2.5% of all unique variants) had within-practice lab-reported discordances; and 56 variants (1.2% of all unique variants) had lab-reported discordances across practices. The unmappable variants were associated with a higher proportion of lab-reported pathogenic classifications (50% vs. 21%, p < 0.0001) and a lower proportion of lab-reported VUS classifications (46% vs. 74%, p < 0.0001). CONCLUSIONS Our study shows that discordant variant classification occurs frequently, which may lead to inappropriate recommendations for prophylactic treatments or clinical management.
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Affiliation(s)
- Kanhua Yin
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yuxi Liu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | | | - Gia Compagnoni
- Advanced Surgical Care of Northern Illinois, Advocate Health Care, Barrington, IL, USA
| | - Richard H Kanak
- Advanced Surgical Care of Northern Illinois, Advocate Health Care, Barrington, IL, USA
| | - Barry Rosen
- Advanced Surgical Care of Northern Illinois, Advocate Health Care, Barrington, IL, USA
| | - David P Ondrula
- Advanced Surgical Care of Northern Illinois, Advocate Health Care, Barrington, IL, USA
| | - Linda Smith
- New Mexico Comprehensive Breast Care, Albuquerque, NM, USA
| | - Eric Brown
- Comprehensive Breast Care, A Division of Michigan Healthcare Professionals, Troy, MI, USA
| | - Linsey Gold
- Comprehensive Breast Care, A Division of Michigan Healthcare Professionals, Troy, MI, USA
| | | | - Colleen App
- The Breast Health and Wellness Center, Grand Rapids, MI, USA
| | - David Euhus
- Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | | | - Giovanni Parmigiani
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Danielle Braun
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Kevin S Hughes
- Division of Surgical Oncology, Massachusetts General Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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19
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Watkins M, Rynearson S, Henrie A, Eilbeck K. Implementing the VMC Specification to Reduce Ambiguity in Genomic Variant Representation. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:1226-1235. [PMID: 32308920 PMCID: PMC7153148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Current methods used for representing biological sequence variants allow flexibility, which has created redundancy within variant archives and discordance among variant representation tools. While research methodologies have been able to adapt to this ambiguity, strict clinical standards make it difficult to use this data in what would otherwise be useful clinical interventions. We implemented a specification developed by the GA4GH Variant Modeling Collaboration (VMC), which details a new approach to unambiguous representation of variants at the allelic level, as a haplotype, or as a genotype. Our implementation, called the VMC Test Suite (http://vcfclin.org), offers web tools to generate and insert VMC identifiers into a VCF file and to generate a VMC bundle JSON representation of a VCF file or HGVS expression. A command line tool with similar functionality is also introduced. These tools facilitate use of this standard-an important step toward reliable querying of variants and their associated annotations.
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Affiliation(s)
- Michael Watkins
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Shawn Rynearson
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Alex Henrie
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
| | - Karen Eilbeck
- Biomedical Informatics, 421 Wakara Way, University of Utah, Salt Lake City, Utah 84108
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20
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Zeng Z, Bromberg Y. Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives. Front Genet 2019; 10:914. [PMID: 31649718 PMCID: PMC6791167 DOI: 10.3389/fgene.2019.00914] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in high-throughput experimentation have put the exploration of genome sequences at the forefront of precision medicine. In an effort to interpret the sequencing data, numerous computational methods have been developed for evaluating the effects of genome variants. Interestingly, despite the fact that every person has as many synonymous (sSNV) as non-synonymous single nucleotide variants, our ability to predict their effects is limited. The paucity of experimentally tested sSNV effects appears to be the limiting factor in development of such methods. Here, we summarize the details and evaluate the performance of nine existing computational methods capable of predicting sSNV effects. We used a set of observed and artificially generated variants to approximate large scale performance expectations of these tools. We note that the distribution of these variants across amino acid and codon types suggests purifying evolutionary selection retaining generated variants out of the observed set; i.e., we expect the generated set to be enriched for deleterious variants. Closer inspection of the relationship between the observed variant frequencies and the associated prediction scores identifies predictor-specific scoring thresholds of reliable effect predictions. Notably, across all predictors, the variants scoring above these thresholds were significantly more often generated than observed. which confirms our assumption that the generated set is enriched for deleterious variants. Finally, we find that while the methods differ in their ability to identify severe sSNV effects, no predictor appears capable of definitively recognizing subtle effects of such variants on a large scale.
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Affiliation(s)
- Zishuo Zeng
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, United States
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Genetics, Rutgers University, Human Genetics Institute, Piscataway, NJ, United States
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21
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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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22
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Management of Gynecologic Cancers In Relation to Genetic Predisposition. Semin Oncol Nurs 2019; 35:182-191. [PMID: 30871842 DOI: 10.1016/j.soncn.2019.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To review hereditary gynecologic cancer syndromes and outline current clinical management considerations. DATA SOURCES Retrieved articles and guidelines dated 2013-2018 from PubMed, National Comprehensive Cancer Network, American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, American Cancer Society, National Cancer Institute, Centers for Disease Control and Prevention, and National Institutes of Health databases. CONCLUSION Advances in genetic testing technology have allowed for the identification of a growing number of patients with genetic mutations associated with hereditary cancer. Individuals with a hereditary predisposition to cancer may qualify for targeted drug therapies, risk-reducing surgeries, and/or high-risk cancer surveillance depending on the specific gene mutation(s) they harbor. Furthermore, there are clinical implications for relatives. IMPLICATIONS FOR NURSING PRACTICE This article is an educational guide for oncology nurses who often play a key role in identifying patients at risk for hereditary cancer, prompting referrals for genetic evaluation, and providing follow-up care for these patients.
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23
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Wright CF, Ware JS, Lucassen AM, Hall A, Middleton A, Rahman N, Ellard S, Firth HV. Genomic variant sharing: a position statement. Wellcome Open Res 2019; 4:22. [PMID: 31886409 PMCID: PMC6913213 DOI: 10.12688/wellcomeopenres.15090.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
Sharing de-identified genetic variant data is essential for the practice of genomic medicine and is demonstrably beneficial to patients. Robust genetic diagnoses that inform medical management cannot be made accurately without reference to genetic test results from other patients, as well as population controls. Errors in this process can result in delayed, missed or erroneous diagnoses, leading to inappropriate or missed medical interventions for the patient and their family. The benefits of sharing individual genetic variants, and the harms of not sharing them, are numerous and well-established. Databases and mechanisms already exist to facilitate deposition and sharing of pseudonomised genetic variants, but clarity and transparency around best practice is needed to encourage widespread use, prevent inconsistencies between different communities, maximise individual privacy and ensure public trust. We therefore recommend that widespread sharing of a small number of individual genetic variants associated with limited clinical information should become standard practice in genomic medicine. Information robustly linking genetic variants with specific conditions is fundamental biological knowledge, not personal information, and therefore should not require consent to share. For additional case-level detail about individual patients or more extensive genomic information, which is often essential for clinical interpretation, it may be more appropriate to use a controlled-access model for data sharing, with the ultimate aim of making as much information as open and de-identified as possible with appropriate consent.
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Affiliation(s)
- Caroline F. Wright
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - James S. Ware
- National Heart and Lung Institute, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Anneke M. Lucassen
- Department of Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Anna Middleton
- Faculty of Education, University of Cambridge, Cambridge, UK
- Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, UK, London, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, UK
| | - Helen V. Firth
- Department of Clinical Genetics, University of Cambridge Addenbrooke's Hospital Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
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24
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Kim J, Luo W, Wang M, Wegman-Ostrosky T, Frone MN, Johnston JJ, Nickerson ML, Rotunno M, Li SA, Achatz MI, Brodie SA, Dean M, de Andrade KC, Fortes FP, Gianferante M, Khincha P, McMaster ML, McReynolds LJ, Pemov A, Pinheiro M, Santiago KM, Alter BP, Caporaso NE, Gadalla SM, Goldin LR, Greene MH, Loud J, Yang XR, Freedman ND, Gapstur SM, Gaudet MM, Calista D, Ghiorzo P, Fargnoli MC, Nagore E, Peris K, Puig S, Landi MT, Hicks B, Zhu B, Liu J, Sampson JN, Chanock SJ, Mirabello LJ, Morton LM, Biesecker LG, Tucker MA, Savage SA, Goldstein AM, Stewart DR. Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls. Genome Med 2018; 10:99. [PMID: 30583724 PMCID: PMC6305568 DOI: 10.1186/s13073-018-0607-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
Background Prior research has established that the prevalence of pathogenic/likely pathogenic (P/LP) variants across all of the American College of Medical Genetics (ACMG) Secondary Findings (SF) genes is approximately 0.8–5%. We investigated the prevalence of P/LP variants in the 24 ACMG SF v2.0 cancer genes in a family-based cancer research cohort (n = 1173) and in cancer-free ethnicity-matched controls (n = 982). Methods We used InterVar to classify variants and subsequently conducted a manual review to further examine variants of unknown significance (VUS). Results In the 24 genes on the ACMG SF v2.0 list associated with a cancer phenotype, we observed 8 P/LP unique variants (8 individuals; 0.8%) in controls and 11 P/LP unique variants (14 individuals; 1.2%) in cases, a non-significant difference. We reviewed 115 VUS. The median estimated per-variant review time required was 30 min; the first variant within a gene took significantly (p = 0.0009) longer to review (median = 60 min) compared with subsequent variants (median = 30 min). The concordance rate was 83.3% for the variants examined by two reviewers. Conclusion The 115 VUS required database and literature review, a time- and labor-intensive process hampered by the difficulty in interpreting conflicting P/LP determinations. By rigorously investigating the 24 ACMG SF v2.0 cancer genes, our work establishes a benchmark P/LP variant prevalence rate in a familial cancer cohort and controls. Electronic supplementary material The online version of this article (10.1186/s13073-018-0607-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,División de Investigación, Instituto Nacional de Cancerología, 14080, Mexico City, Mexico
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Melissa Rotunno
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shengchao A Li
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Maria I Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,Centro de Oncologia, Hospital Sirio-Libanes, Sao Paulo, SP, 013050-050, Brazil
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, 20877, USA
| | - Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Fernanda P Fortes
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Matthew Gianferante
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Payal Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mary L McMaster
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Maisa Pinheiro
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Karina M Santiago
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.,International Research Center, A.C. Camargo Cancer Center, São Paulo, 01508-010, Brazil
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neil E Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lynn R Goldin
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Jennifer Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Xiaohong R Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, IRCCS Ospedale Policinico San Martino, Genoa, Italy
| | | | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Ketty Peris
- Institute of Dermatology, Catholic University - Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clinic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain & Centro de Investigacion Biomedica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Maria Teresa Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Stephen J Chanock
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lisa J Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Lindsay M Morton
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, Human Genetics Program National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Alisa M Goldstein
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, 20850, USA.
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25
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Landrum MJ, Kattman BL. ClinVar at five years: Delivering on the promise. Hum Mutat 2018; 39:1623-1630. [DOI: 10.1002/humu.23641] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/10/2018] [Accepted: 08/30/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Melissa J. Landrum
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of Health Bethesda Maryland
| | - Brandi L. Kattman
- National Center for Biotechnology InformationNational Library of MedicineNational Institutes of Health Bethesda Maryland
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26
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Papoutsidakis N, Heitner SB, Mannello MC, Rodonski A, Campbell W, McElheran K, Jacoby DL. Machine-Assisted Genotype Update System (MAGUS) for Inherited Cardiomyopathies. Circ Cardiovasc Qual Outcomes 2018; 11:e004835. [DOI: 10.1161/circoutcomes.118.004835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nikolaos Papoutsidakis
- Section of Cardiovascular Medicine, Department of Internal Medicine Yale School of Medicine, New Haven, CT (N.P., D.L.J.)
| | - Stephen B. Heitner
- Oregon Health and Science University, Knight Cardiovascular Institute Hypertrophic Cardiomyopathy and Cardiogenetics Centers, Portland (S.B.H., M.C.M., K.E.)
| | - Meghan C. Mannello
- Oregon Health and Science University, Knight Cardiovascular Institute Hypertrophic Cardiomyopathy and Cardiogenetics Centers, Portland (S.B.H., M.C.M., K.E.)
| | - Anna Rodonski
- Yale New Haven Hospital Heart and Vascular Center, New Haven, CT (A.R.)
| | - William Campbell
- Yale New Haven Hospital Heart and Vascular Center, New Haven, CT (A.R.)
| | - Kylie McElheran
- Oregon Health and Science University, Knight Cardiovascular Institute Hypertrophic Cardiomyopathy and Cardiogenetics Centers, Portland (S.B.H., M.C.M., K.E.)
| | - Daniel L. Jacoby
- Section of Cardiovascular Medicine, Department of Internal Medicine Yale School of Medicine, New Haven, CT (N.P., D.L.J.)
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27
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Henrie A, Hemphill SE, Ruiz-Schultz N, Cushman B, DiStefano MT, Azzariti D, Harrison SM, Rehm HL, Eilbeck K. ClinVar Miner: Demonstrating utility of a Web-based tool for viewing and filtering ClinVar data. Hum Mutat 2018; 39:1051-1060. [PMID: 29790234 DOI: 10.1002/humu.23555] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/20/2018] [Accepted: 05/19/2018] [Indexed: 11/12/2022]
Abstract
ClinVar Miner is a Web-based suite that utilizes the data held in the National Center for Biotechnology Information's ClinVar archive. The goal is to render the data more accessible to processes pertaining to conflict resolution of variant interpretation as well as tracking details of data submission and data management for detailed variant curation. Here, we establish the use of these tools to address three separate use cases and to perform analyses across submissions. We demonstrate that the ClinVar Miner tools are an effective means to browse and consolidate data for variant submitters, curation groups, and general oversight. These tools are also relevant to the variant interpretation community in general.
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Affiliation(s)
- Alex Henrie
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Nicole Ruiz-Schultz
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Brandon Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Danielle Azzariti
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Steven M Harrison
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
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28
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Abstract
Next-generation sequencing (NGS) technology has led to the ability to test for multiple cancer susceptibility genes simultaneously without significantly increasing cost or turnaround time. With growing usage of multigene testing for inherited cancer, ongoing education for nurses and other health-care providers about hereditary cancer screening is imperative to ensure appropriate testing candidate identification, test selection, and posttest management. The purpose of this review article is to (1) provide an overview of how NGS works to detect germline mutations, (2) summarize the benefits and limitations of multigene panel testing, (3) describe risk categories of cancer susceptibility genes, and (4) highlight the counseling considerations for patients pursuing multigene testing.
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29
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Macklin S, Durand N, Atwal P, Hines S. Observed frequency and challenges of variant reclassification in a hereditary cancer clinic. Genet Med 2017; 20:346-350. [PMID: 29215655 DOI: 10.1038/gim.2017.207] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/18/2017] [Indexed: 12/22/2022] Open
Abstract
PurposeEfforts have been made by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology to make variant classification more uniform, but many limitations remain. Reclassification of a variant of uncertain significance (VUS) is expected, but other more certain calls, like pathogenic or benign, can also be reclassified once additional information is gathered. Variant reclassification can create difficult circumstances for both patients and clinicians.MethodsRetrospective review of all variant reclassifications in genes associated with hereditary cancer syndromes at one clinic between September 2013 and February 2017 was completed. All variant reclassifications were completed and reported by the original testing laboratory.ResultsA total of 1,103 hereditary cancer tests were ordered. Fewer than 5% (40/1,103) of the initial reports were updated during that time period. Most reclassifications (29/40) were downgrades of VUS to likely benign. Only three reclassifications could potentially alter medical management.ConclusionThe majority of variant reclassifications do not impact medical management. Upgrading a variant call to pathogenic could be important for a patient's care and shows the importance of open communication between laboratories and clinicians. A variant downgrade from pathogenic can be a significant reclassification as well, especially if prophylactic surgery has been completed.
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Affiliation(s)
- Sarah Macklin
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida, USA
| | - Nisha Durand
- Laboratory Medicine and Pathology, Mayo Clinic, Jacksonville, Florida, USA
| | - Paldeep Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Stephanie Hines
- Department of Medicine, Division of Diagnostic & Consultative Medicine, Mayo Clinic, Jacksonville, Florida, USA
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30
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Lim MC, Randall LM. Role and clinical application of next-generation sequencing (NGS) for ovarian cancer. J Gynecol Oncol 2017; 28:e51. [PMID: 28541638 PMCID: PMC5447149 DOI: 10.3802/jgo.2017.28.e51] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 12/22/2022] Open
Affiliation(s)
- Myong Cheol Lim
- Cancer Healthcare Research Branch, Center for Uterine Cancer and Center for Clinical Trials, Research Institute and Hospital, Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Irvine Medical Center, University of California, Orange, CA, USA
| | - Leslie M Randall
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Irvine Medical Center, University of California, Orange, CA, USA.
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31
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Mundt E, Nix P, Brown K, Bowles KR, Manley S. Complexities of Variant Classification in Clinical Hereditary Cancer Genetic Testing. J Clin Oncol 2017; 35:3796-3799. [PMID: 28981386 DOI: 10.1200/jco.2017.74.5182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Erin Mundt
- Erin Mundt, Paola Nix, Krystal Brown, Karla R. Bowles, and Susan Manley, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Paola Nix
- Erin Mundt, Paola Nix, Krystal Brown, Karla R. Bowles, and Susan Manley, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Krystal Brown
- Erin Mundt, Paola Nix, Krystal Brown, Karla R. Bowles, and Susan Manley, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Karla R Bowles
- Erin Mundt, Paola Nix, Krystal Brown, Karla R. Bowles, and Susan Manley, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Susan Manley
- Erin Mundt, Paola Nix, Krystal Brown, Karla R. Bowles, and Susan Manley, Myriad Genetic Laboratories, Salt Lake City, UT
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32
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Abstract
Introduction Effective data sharing does not occur in the UK despite being essential for the delivery of high-quality genomic services to patients across clinical specialities and to optimize advances in genomic medicine. Sources of data Original papers, reviews, guidelines, policy papers and web-resources. Areas of agreement Data sharing for genomic medicine requires appropriate infrastructure and policies, together with acceptance by health professionals and the public of the necessity of data sharing for clinical care. Areas of controversy There is ongoing debate around the different technical approaches and safeguards that could be used to facilitate data sharing while minimizing the risks to individuals of identification. Lack of consensus undermines trust and confidence. Growing points Ongoing policy developments around genomics and health data create opportunities to ensure systems and policies are in place to support proportionate, effective and safeguarded data sharing. Areas timely for developing research Mechanisms to improve public trust.
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Affiliation(s)
- Sobia Raza
- PHG Foundation, 2 Worts Causeway, Cambridge, CB1 8RN, UK
| | - Alison Hall
- PHG Foundation, 2 Worts Causeway, Cambridge, CB1 8RN, UK
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33
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Abstract
In this Letter to the Editor, potentially flawed conclusions of a recent study are discussed.
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Affiliation(s)
- Heidi L Rehm
- Partners Healthcare and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven M Harrison
- Partners Healthcare and Harvard Medical School, Boston, Massachusetts, USA
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34
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Rehm HL. A new era in the interpretation of human genomic variation. Genet Med 2017; 19:1092-1095. [PMID: 28703787 DOI: 10.1038/gim.2017.90] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 01/19/2023] Open
Affiliation(s)
- Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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