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Fernandez-Falgueras A, Coll M, Iglesias A, Tiron C, Campuzano O, Brugada R. The importance of variant reinterpretation in inherited cardiovascular diseases: Establishing the optimal timeframe. PLoS One 2024; 19:e0297914. [PMID: 38691546 PMCID: PMC11062523 DOI: 10.1371/journal.pone.0297914] [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: 09/29/2023] [Accepted: 01/15/2024] [Indexed: 05/03/2024] Open
Abstract
Inherited cardiovascular diseases are rare diseases that are difficult to diagnose by non-expert professionals. Genetic analyses play a key role in the diagnosis of these diseases, in which the identification of a pathogenic genetic variant is often a diagnostic criterion. Therefore, genetic variant classification and routine reinterpretation as data become available represent one of the main challenges associated with genetic analyses. Using the genetic variants identified in an inherited cardiovascular diseases unit during a 10-year period, the objectives of this study were: 1) to evaluate the impact of genetic variant reinterpretation, 2) to compare the reclassification rates between different cohorts of cardiac channelopathies and cardiomyopathies, and 3) to establish the most appropriate periodicity for genetic variant reinterpretation. All the evaluated cohorts (full cohort of inherited cardiovascular diseases, cardiomyopathies, cardiac channelopathies, hypertrophic cardiomyopathy, dilated cardiomyopathy, arrhythmogenic cardiomyopathy, Brugada syndrome, long QT syndrome and catecholaminergic polymorphic ventricular tachycardia) showed reclassification rates above 25%, showing even higher reclassification rates when there is definitive evidence of the association between the gene and the disease in the cardiac channelopathies. Evaluation of genetic variant reclassification rates based on the year of the initial classification showed that the most appropriate frequency for the reinterpretation would be 2 years, with the possibility of a more frequent reinterpretation if deemed convenient. To keep genetic variant classifications up to date, genetic counsellors play a critical role in the reinterpretation process, providing clinical evidence that genetic diagnostic laboratories often do not have at their disposal and communicating changes in classification and the potential implications of these reclassifications to patients and relatives.
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Affiliation(s)
- Anna Fernandez-Falgueras
- Department of Cardiology, Hospital Trueta, Girona, Spain
- Molecular Diagnostics and Personalized Medicine Unit, Clinical Laboratory, Hospital Trueta, Girona, Spain
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Monica Coll
- Molecular Diagnostics and Personalized Medicine Unit, Clinical Laboratory, Hospital Trueta, Girona, Spain
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Anna Iglesias
- Molecular Diagnostics and Personalized Medicine Unit, Clinical Laboratory, Hospital Trueta, Girona, Spain
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Coloma Tiron
- Department of Cardiology, Hospital Trueta, Girona, Spain
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - Ramon Brugada
- Department of Cardiology, Hospital Trueta, Girona, Spain
- Molecular Diagnostics and Personalized Medicine Unit, Clinical Laboratory, Hospital Trueta, Girona, Spain
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain
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2
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Watts G, Newson AJ. Is there a duty to routinely reinterpret genomic variant classifications? JOURNAL OF MEDICAL ETHICS 2023; 49:808-814. [PMID: 37208157 DOI: 10.1136/jme-2022-108864] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/09/2023] [Indexed: 05/21/2023]
Abstract
Multiple studies show that periodic reanalysis of genomic test results held by clinical laboratories delivers significant increases in overall diagnostic yield. However, while there is a widespread consensus that implementing routine reanalysis procedures is highly desirable, there is an equally widespread understanding that routine reanalysis of individual patient results is not presently feasible to perform for all patients. Instead, researchers, geneticists and ethicists are beginning to turn their attention to one part of reanalysis-reinterpretation of previously classified variants-as a means of achieving similar ends to large-scale individual reanalysis but in a more sustainable manner. This has led some to ask whether the responsible implementation of genomics in healthcare requires that diagnostic laboratories routinely reinterpret their genomic variant classifications and reissue patient reports in the case of materially relevant changes. In this paper, we set out the nature and scope of any such obligation, and analyse some of the main ethical considerations pertaining to a putative duty to reinterpret. We discern and assess three potential outcomes of reinterpretation-upgrades, downgrades and regrades-in light of ongoing duties of care, systemic error risks and diagnostic equity. We argue against the existence of any general duty to reinterpret genomic variant classifications, yet we contend that a suitably restricted duty to reinterpret ought to be recognised, and that the responsible implementation of genomics into healthcare must take this into account.
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Affiliation(s)
- Gabriel Watts
- Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
| | - Ainsley J Newson
- Faculty of Medicine and Health, Sydney School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
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3
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Martorana D, Barili V, Uliana V, Ambrosini E, Riva M, De Sensi E, Luppi E, Messina C, Caleffi E, Pisani F, Percesepe A. Reassessment of the NF1 variants of unknown significance found during the 20-year activity of a genetics diagnostic laboratory. Eur J Med Genet 2023; 66:104847. [PMID: 37751797 DOI: 10.1016/j.ejmg.2023.104847] [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: 09/06/2022] [Revised: 07/05/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023]
Abstract
The finding of variants of uncertain significance (VUS) in the activity of a diagnostic genetic laboratory is a common issue, which is however provisional and needs to be periodically re-evaluated, due to the continuous advancements in our knowledge of the genetic diseases. Neurofibromatosis type 1, caused by the occurrence of heterozygous pathogenic NF1 variants, is a good model for studying the evolution of VUS, due to the widespread use of genetic testing for the disease, the constant enrichment of the international databases with NF1 variants and the full adult penetrance of the disease, which makes genotyping the parents a crucial step in the diagnostic workflow. The present study retrospectively reviewed and reinterpreted the genetic test results of NF1 in a diagnostic genetic laboratory in the period from January 1, 2000 to December 31, 2020. All the VUS were reinterpreted using the 2015 consensus standards and guidelines for the interpretation. Out of 589 NF1 genetic tests which were performed in the period, a total of 85 VUS were found and reinterpreted in 72 cases (84.7%): 21 (29.2%) were reclassified as benign/likely benign, whereas 51 (70.8%) were recoded as pathogenic/likely pathogenic with a significant trend distribution (Chi square test for trend p = 0.005). Synonymous VUS have mainly been reclassified as class 1 and 2 (7/8, 87.5%), whereas missense variants have been attributed to class 4 and 5 in 38 out of the 58 cases (65.5%). These findings underline an improvement in the classification of variants over time, suggesting that a reinterpretation of the genetic tests should be routinely performed to support the physicians in the clinical diagnosis of genetic diseases.
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Affiliation(s)
- Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy; CoreLAB Research Center, University Hospital of Parma, 43126, Italy
| | - Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Matteo Riva
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Elena Luppi
- Medical Genetics, University of Bologna, Italy
| | - Corinne Messina
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Edoardo Caleffi
- Plastic Surgery, University Hospital of Parma, 43126, Parma, Italy
| | - Francesco Pisani
- Children's Neuropsychological Services, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Percesepe
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy; Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy.
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Clayton EW, Tritell AM, Thorogood AM. Avoiding Liability and Other Legal Land Mines in the Evolving Genomics Landscape. Annu Rev Genomics Hum Genet 2023; 24:333-346. [PMID: 36630592 DOI: 10.1146/annurev-genom-100722-021725] [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] [Indexed: 01/13/2023]
Abstract
This article reviews evolving legal implications for clinicians and researchers as genomics is used more widely in both the clinic and in translational research, reflecting rapid changes in scientific knowledge as well as the surrounding cultural and political environment. Professionals will face new and changing duties to make or act upon a genetic diagnosis, address direct-to-consumer genetic testing in patient care, consider the health implications of results for patients' family members, and recontact patients when test results change over time. Professional duties in reproductive genetic testing will need to be recalibrated in response to disruptive changes to reproductive rights in the United States. We also review the debate over who controls the flow of genetic information and who is responsible for its protection, considering the globally influential European Union General Data Protection Regulation and the rapidly evolving data privacy law landscape of the United States.
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Affiliation(s)
- Ellen Wright Clayton
- Department of Pediatrics and Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- School of Law, Vanderbilt University, Nashville, Tennessee, USA;
| | - Alex M Tritell
- School of Law, Vanderbilt University, Nashville, Tennessee, USA;
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Outram SM, Rego S, Norstad M, Ackerman S. The Need to Standardize the Reanalysis of Genomic Sequencing Results: Findings from Interviews with Underserved Families in Genomic Research. JOURNAL OF BIOETHICAL INQUIRY 2023:10.1007/s11673-023-10267-2. [PMID: 37624546 DOI: 10.1007/s11673-023-10267-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/06/2023] [Indexed: 08/26/2023]
Abstract
The reanalysis of genomic sequencing results has the potential to provide results that are of considerable medical and personal importance to recipients. Employing interviews with forty-seven predominantly medically underserved families and ethnographic observations we argue that there is pressing need to standardize the approach taken to reanalysis. Our findings highlight that study participants were unclear as to the likelihood of reanalysis happening, the process of initiating reanalysis, and whether they would receive revised results. Their reflections mirror the lack a specific focus upon reanalysis within consent and results sessions as observed in clinical settings. Mechanisms need to be put into place that standardize the approach to reanalysis in research and in clinical contexts. This would enable clinicians and genetic counsellors to communicate clearly with research participants with respect to potential for reanalysis of results and the process of reanalysis. We argue that that the role of reanalysis is too important to be referred to in an ad-hoc manner. Furthermore, the ad-hoc nature of the current process may increase health inequities given the likelihood that only those families who have the means to press for reanalysis are likely to receive it.
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Affiliation(s)
- Simon M Outram
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA.
| | - Shannon Rego
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Matthew Norstad
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA
| | - Sara Ackerman
- Program in Bioethics, Institute for Health & Aging/Department of Social & Behavioral Sciences, University of California, 490 Illinois St., Floor 12, San Francisco, CA, 94143, USA
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6
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Papadopoulou E, Bouzarelou D, Tsaousis G, Papathanasiou A, Vogiatzi G, Vlachopoulos C, Miliou A, Papachristou P, Prappa E, Servos G, Ritsatos K, Seretis A, Frogoudaki A, Nasioulas G. Application of next generation sequencing in cardiology: current and future precision medicine implications. Front Cardiovasc Med 2023; 10:1202381. [PMID: 37424920 PMCID: PMC10327645 DOI: 10.3389/fcvm.2023.1202381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Inherited cardiovascular diseases are highly heterogeneous conditions with multiple genetic loci involved. The application of advanced molecular tools, such as Next Generation Sequencing, has facilitated the genetic analysis of these disorders. Accurate analysis and variant identification are required to maximize the quality of the sequencing data. Therefore, the application of NGS for clinical purposes should be limited to laboratories with a high level of technological expertise and resources. In addition, appropriate gene selection and variant interpretation can result in the highest possible diagnostic yield. Implementation of genetics in cardiology is imperative for the accurate diagnosis, prognosis and management of several inherited disorders and could eventually lead to the realization of precision medicine in this field. However, genetic testing should also be accompanied by an appropriate genetic counseling procedure that clarifies the significance of the genetic analysis results for the proband and his family. In this regard, a multidisciplinary collaboration among physicians, geneticists, and bioinformaticians is imperative. In the present review, we address the current state of knowledge regarding genetic analysis strategies employed in the field of cardiogenetics. Variant interpretation and reporting guidelines are explored. Additionally, gene selection procedures are accessed, with a particular emphasis on information concerning gene-disease associations collected from international alliances such as the Gene Curation Coalition (GenCC). In this context, a novel approach to gene categorization is proposed. Moreover, a sub-analysis is conducted on the 1,502,769 variation records with submitted interpretations in the Clinical Variation (ClinVar) database, focusing on cardiology-related genes. Finally, the most recent information on genetic analysis's clinical utility is reviewed.
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Affiliation(s)
| | | | | | | | - Georgia Vogiatzi
- Third Department of Cardiology, Sotiria Hospital, Athens, Greece
| | - Charalambos Vlachopoulos
- Unit of Inherited Cardiac Conditions and Sports Cardiology, First Department of Cardiology, National and Kapodistrian University of Athens, Athens, Greece
| | - Antigoni Miliou
- Unit of Inherited Cardiac Conditions and Sports Cardiology, First Department of Cardiology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Efstathia Prappa
- Second Department of Cardiology, Arrhythmia Unit, Evangelismos General Hospital of Athens, Athens, Greece
| | - Georgios Servos
- Pediatric Cardiology Unit, “P. & A. Kyriakou” Children’s Hospital, Athens, Greece
| | - Konstantinos Ritsatos
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Center, Athens, Greece
| | - Aristeidis Seretis
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Center, Athens, Greece
| | - Alexandra Frogoudaki
- Second Department of Cardiology, Attikon University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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7
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Mackley MP, Chad L. Equity implications of patient-initiated recontact and follow-up in clinical genetics. Eur J Hum Genet 2023; 31:495-496. [PMID: 36959498 PMCID: PMC10172361 DOI: 10.1038/s41431-023-01341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Affiliation(s)
- Michael P Mackley
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Lauren Chad
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
- Department Bioethics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
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8
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Berger SM, Appelbaum PS, Siegel K, Wynn J, Saami AM, Brokamp E, O'Connor BC, Hamid R, Martin DM, Chung WK. Challenges of variant reinterpretation: Opinions of stakeholders and need for guidelines. Genet Med 2022; 24:1878-1887. [PMID: 35767006 PMCID: PMC10407574 DOI: 10.1016/j.gim.2022.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
PURPOSE The knowledge used to classify genetic variants is continually evolving, and the classification can change on the basis of newly available data. Although up-to-date variant classification is essential for clinical management, reproductive planning, and identifying at-risk family members, there is no consistent practice across laboratories or clinicians on how or under what circumstances to perform variant reinterpretation. METHODS We conducted exploratory focus groups (N = 142) and surveys (N = 1753) with stakeholders involved in the process of variant reinterpretation (laboratory directors, clinical geneticists, genetic counselors, nongenetic providers, and patients/parents) to assess opinions on key issues, including initiation of reinterpretation, variants to report, termination of the responsibility to reinterpret, and concerns about consent, cost, and liability. RESULTS Stakeholders widely agreed that there should be no fixed termination point to the responsibility to reinterpret a previously reported genetic variant. There were significant concerns about liability and lack of agreement about many logistical aspects of variant reinterpretation. CONCLUSION Our findings suggest a need to (1) develop consensus and (2) create transparency and awareness about the roles and responsibilities of parties involved in variant reinterpretation. These data provide a foundation for developing guidelines on variant reinterpretation that can aid in the development of a low-cost, scalable, and accessible approach.
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Affiliation(s)
- Sara M Berger
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Karolynn Siegel
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Akilan M Saami
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Elly Brokamp
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | | | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Michigan Medicine, Ann Arbor, MI
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, Columbia University, New York, NY; Department of Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY.
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9
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Loong L, Garrett A, Allen S, Choi S, Durkie M, Callaway A, Drummond J, Burghel GJ, Robinson R, Torr B, Berry IR, Wallace AJ, Eccles DM, Ellard S, Baple E, Evans DG, Woodward ER, Kulkarni A, Lalloo F, Tischkowitz M, Lucassen A, Hanson H, Turnbull C. Reclassification of clinically-detected sequence variants: Framework for genetic clinicians and clinical scientists by CanVIG-UK (Cancer Variant Interpretation Group UK). Genet Med 2022; 24:1867-1877. [PMID: 35657381 DOI: 10.1016/j.gim.2022.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 02/05/2023] Open
Abstract
PURPOSE Variant classifications may change over time, driven by emergence of fresh or contradictory evidence or evolution in weighing or combination of evidence items. For variant classifications above the actionability threshold, which is classification of likely pathogenic or pathogenic, clinical actions may be irreversible, such as risk-reducing surgery or prenatal interventions. Variant reclassification up or down across the actionability threshold can therefore have significant clinical consequences. Laboratory approaches to variant reinterpretation and reclassification vary widely. METHODS Cancer Variant Interpretation Group UK is a multidisciplinary network of clinical scientists and genetic clinicians from across the 24 Molecular Diagnostic Laboratories and Clinical Genetics Services of the United Kingdom (NHS) and Republic of Ireland. We undertook surveys, polls, and national meetings of Cancer Variant Interpretation Group UK to evaluate opinions about clinical and laboratory management regarding variant reclassification. RESULTS We generated a consensus framework on variant reclassification applicable to cancer susceptibility genes and other clinical areas, which provides explicit recommendations for clinical and laboratory management of variant reclassification scenarios on the basis of the nature of the new evidence, the magnitude of evidence shift, and the final classification score. CONCLUSION In this framework, clinical and laboratory resources are targeted for maximal clinical effect and minimal patient harm, as appropriate to all resource-constrained health care settings.
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Affiliation(s)
- Lucy Loong
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Subin Choi
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NHS North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, United Kingdom
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Central and South Genomics Laboratory Hub, Salisbury NHS Foundation Trust, Salisbury District Hospital, Salisbury, Wiltshire, United Kingdom
| | - James Drummond
- Cambridge Genomic Laboratory, East Genomic Laboratory Hub, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - George J Burghel
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Rachel Robinson
- North East and Yorkshire Genomic Laboratory Hub, The Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - Beth Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom
| | - Ian R Berry
- Bristol Genetics Laboratory, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Diana M Eccles
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sian Ellard
- Exeter Genomics Laboratory, South West Genomic Laboratory Hub, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom; University of Exeter Medical School, Exeter, United Kingdom
| | - Emma Baple
- University of Exeter Medical School, Exeter, United Kingdom; Genomics England, London, United Kingdom
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Division of Evolution & Genomic Sciences, The University of Manchester, Manchester, United Kingdom
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom; Division of Evolution & Genomic Sciences, The University of Manchester, Manchester, United Kingdom
| | - Anjana Kulkarni
- Southeast Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine and North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Anneke Lucassen
- Wellcome Centre for Human Genetics/Centre for Personalised Medicine, University of Oxford, Oxford, United Kingdom; Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Helen Hanson
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Department of Clinical Genetics, St. George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, United Kingdom; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, United Kingdom.
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10
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Chowns J, Hoffman-Andrews L, Marzolf A, Reza N, Owens AT. Cardiovascular Genetics: The Role of Genetics in Predicting Risk. Med Clin North Am 2022; 106:313-324. [PMID: 35227433 PMCID: PMC8894793 DOI: 10.1016/j.mcna.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many cardiovascular disorders have underlying genetic causes. Clinical genetic testing for cardiovascular disease has become widely available and can be useful for diagnosis, management, and cascade screening in selected conditions and circumstances. This article gives an overview of the current state of genetic testing in inherited cardiovascular conditions, who can benefit from it, and the associated challenges.
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Affiliation(s)
- Jessica Chowns
- Division of Cardiovascular Medicine, Department of Medicine, Center for Inherited Cardiovascular Disease, Perelman School of Medicine at the University of Pennsylvania, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, 11th Floor South Pavilion, Philadelphia, PA 19104, USA.
| | - Lily Hoffman-Andrews
- Division of Cardiovascular Medicine, Department of Medicine, Center for Inherited Cardiovascular Disease, Perelman School of Medicine at the University of Pennsylvania, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, 11th Floor South Pavilion, Philadelphia, PA 19104, USA
| | - Amy Marzolf
- Division of Cardiovascular Medicine, Department of Medicine, Center for Inherited Cardiovascular Disease, Perelman School of Medicine at the University of Pennsylvania, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, 11th Floor South Pavilion, Philadelphia, PA 19104, USA
| | - Nosheen Reza
- Division of Cardiovascular Medicine, Department of Medicine, Center for Inherited Cardiovascular Disease, Perelman School of Medicine at the University of Pennsylvania, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, 11th Floor South Pavilion, Philadelphia, PA 19104, USA
| | - Anjali Tiku Owens
- Division of Cardiovascular Medicine, Department of Medicine, Center for Inherited Cardiovascular Disease, Perelman School of Medicine at the University of Pennsylvania, Perelman Center for Advanced Medicine, 3400 Civic Center Boulevard, 11th Floor South Pavilion, Philadelphia, PA 19104, USA.
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Takashima T, Brisset S, Furukawa A, Taniguchi H, Takeyasu R, Kawamura A, Tamura Y. Case Report: BMPR2-Targeted MinION Sequencing as a Tool for Genetic Analysis in Patients With Pulmonary Arterial Hypertension. Front Cardiovasc Med 2021; 8:711694. [PMID: 34589526 PMCID: PMC8473694 DOI: 10.3389/fcvm.2021.711694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Mutations in the bone morphogenetic protein receptor type 2 gene (BMPR2) represent a major genetic cause of pulmonary arterial hypertension (PAH). Identification of BMPR2 mutations is crucial for the genetic diagnosis of PAH. MinION nanopore sequencer is a portable third-generation technology that enables long-read sequencing at a low-cost. This nanopore technology-based device has not been used previously for PAH diagnosis. This study aimed to determine the feasibility of using MinION nanopore sequencing for the genetic analysis of PAH patients, focused on BMPR2. Methods: We developed a protocol for the custom bioinformatics pipeline analysis of long reads generated by long-PCR. To evaluate the potential of using MinION sequencing in PAH, we analyzed five samples, including those of two idiopathic PAH patients and a family of three members with one affected patient. Sanger sequencing analysis was performed to validate the variants. Results: The median read length was around 3.4 kb and a good mean quality score of approximately 19 was obtained. The total number of reads generated was uniform among the cases and ranged from 2,268,263 to 3,126,719. The coverage was consistent across flow cells in which the average number of reads per base ranged from 80,375 to 135,603. We identified two polymorphic variants and three mutations in four out of five patients. Certain indel variant calling-related errors were observed, mostly outside coding sequences. Conclusion: We have shown the ability of this portable nanopore sequencer to detect BMPR2 mutations in patients with PAH. The MinION nanopore sequencer is a promising tool for screening BMPR2 mutations, especially in small laboratories and research groups.
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Affiliation(s)
- Tomoya Takashima
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Sophie Brisset
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Faculty of Medicine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,Service d'Histologie, Embryologie et Cytogénétique, Assistance Publique Hôpitaux de Paris (AP-HP), Hôpital Antoine Béclère, Clamart, France
| | - Asuka Furukawa
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Hirohisa Taniguchi
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
| | - Rika Takeyasu
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan
| | - Akio Kawamura
- Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
| | - Yuichi Tamura
- Pulmonary Hypertension Center, International University of Health and Welfare, Mita Hospital, Tokyo, Japan.,Department of Cardiology, International University of Health and Welfare School of Medicine, Narita, Japan
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12
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Margolin A, Helm BM, Treat K, Prucka SK, Halverson CME. Assessing parental understanding of variant reclassification in pediatric neurology and developmental pediatrics clinics. J Community Genet 2021; 12:663-670. [PMID: 34558037 DOI: 10.1007/s12687-021-00552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/16/2021] [Indexed: 11/24/2022] Open
Abstract
Improvements in technology used for genetic testing have yielded an increased numbers of variants that are identified, each with a potential to return uninformative results. While some genetics providers may expect patients to be responsible for staying abreast of updates to their genetic testing results, it is unknown whether patients are even aware of the possibility of variant reclassification. Little research has assessed the comprehension and attitudes of parents of pediatric patients regarding reclassification of variants of uncertain significance (VUS). Semi-structured telephone interviews were conducted with parents (n = 15) whose children received a VUS from genetic testing in either the pediatric neurogenetics or developmental pediatrics clinics at Riley Hospital for Children in Indianapolis, Indiana. Most participants expressed understanding of the uncertainty surrounding their child's VUS test result. However, nearly half of participants shared that they had no prior knowledge of its potential reclassification. When asked whose responsibility it is to keep informed about changes to their child's VUS status, some participants stated that it belonged solely to healthcare providers - a distinctive finding of our study - whereas others felt that it was a joint responsibility between providers and the parents. We additionally found that some patients desire a support group for individuals with VUS. These results provide insight into the importance of pretest genetic counseling and the need for increased social and informational support for parents of children who receive inconclusive genetic testing results. We conclude that relying solely on the patient or guardian to manage uncertain results may be insufficient.
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Affiliation(s)
- Amy Margolin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Benjamin M Helm
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sandra K Prucka
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Colin M E Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Medicine, Indiana University School of Medicine, 410 W. 10th St., HITS 3131, Indianapolis, IN, 46202, USA.
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13
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Expanded Carrier Screening and the Complexity of Implementation. Obstet Gynecol 2021; 137:345-350. [PMID: 33416279 DOI: 10.1097/aog.0000000000004229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022]
Abstract
Advances in genetic technology have allowed for the development of multiplex panels that can test for hundreds of genetic disorders at the same time; these large panels are referred to as expanded carrier screening. This process can screen couples for far more conditions than the gene-by-gene approach used with traditional carrier screening; however, although expanded carrier screening has been promoted as an efficient means of detecting many more disorders, the complexities of genetic sequencing raise substantial challenges and concerns. In our practice, we have seen a number of complex cases in which only attention to detail on the part of thorough genetic counselors allowed identification of misclassified variants that could have resulted in significant patient harm. We raise issues that require urgent attention by professional societies, including: whether to endorse testing that uses sequencing compared with genotyping; required components of pretest and posttest counseling; reclassification of variants; whether obstetric health care professionals have a responsibility to assure that patients understand the iterative process of variant interpretation and how it relates to carrier screening results; and the question of rescreening in subsequent pregnancies. Implementation of expanded carrier screening needs to be considered thoughtfully in light of the complexity of genetic sequencing and limited knowledge of genetics of most front-line obstetric health care professionals.
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14
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iVar, an Interpretation-Oriented Tool to Manage the Update and Revision of Variant Annotation and Classification. Genes (Basel) 2021; 12:genes12030384. [PMID: 33800487 PMCID: PMC8001268 DOI: 10.3390/genes12030384] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 11/24/2022] Open
Abstract
The rapid evolution of Next Generation Sequencing in clinical settings, and the resulting challenge of variant reinterpretation given the constantly updated information, require robust data management systems and organized approaches. In this paper, we present iVar: a freely available and highly customizable tool with a user-friendly web interface. It represents a platform for the unified management of variants identified by different sequencing technologies. iVar accepts variant call format (VCF) files and text annotation files and elaborates them, optimizing data organization and avoiding redundancies. Updated annotations can be periodically re-uploaded and associated with variants as historically tracked attributes, i.e., modifications can be recorded whenever an updated value is imported, thus keeping track of all changes. Data can be visualized through variant-centered and sample-centered interfaces. A customizable search function can be exploited to periodically check if pathogenicity-related data of a variant has changed over time. Patient recontacting ensuing from variant reinterpretation is made easier by iVar through the effective identification of all patients present in the database carrying a specific variant. We tested iVar by uploading 4171 VCF files and 1463 annotation files, obtaining a database of 4166 samples and 22,569 unique variants. iVar has proven to be a useful tool with good performance in terms of collecting and managing data from a medium-throughput laboratory.
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15
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Clayton EW, Appelbaum PS, Chung WK, Marchant GE, Roberts JL, Evans BJ. Does the law require reinterpretation and return of revised genomic results? Genet Med 2021; 23:833-836. [PMID: 33420344 PMCID: PMC8107115 DOI: 10.1038/s41436-020-01065-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 02/02/2023] Open
Affiliation(s)
- Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA. .,School of Law, Vanderbilt University, Nashville, TN, USA.
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Gary E Marchant
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Sandra Day O'Connor School of Law, Arizona State University, Tempe, AZ, USA
| | - Jessica L Roberts
- University of Houston Law Center, Houston, TX, USA.,University of Houston College of Medicine, Houston, TX, USA
| | - Barbara J Evans
- University of Florida Levin College of Law, Gainesville, FL, USA.,University of Florida Wertheim College of Engineering, Gainesville, FL, USA
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16
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Salinas V, Vega P, Marsili L, Pérez‐Maturo J, Martínez N, Zavala L, González‐Morón D, Medina N, Rodriguez‐Quiroga SA, Amartino H, Maxit C, Sturchio A, Grimberg B, Duque K, Comas B, Silva W, Consalvo D, Sfaello I, Espay AJ, Kauffman MA. The odyssey of complex neurogenetic disorders: From undetermined to positive. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:876-884. [DOI: 10.1002/ajmg.c.31848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Valeria Salinas
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
| | - Patricia Vega
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Luca Marsili
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Josefina Pérez‐Maturo
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
| | - Nerina Martínez
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Lucia Zavala
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | | | - Nancy Medina
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | | | - Hernán Amartino
- Pediatric Neurology Unit Hospital Universitario Austral Buenos Aires Argentina
| | - Clarisa Maxit
- Pediatric Neurology Unit, Hospital Italiano de Buenos Aires Buenos Aires Argentina
| | - Andrea Sturchio
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Barbara Grimberg
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Kevin Duque
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Betiana Comas
- Neurology Unit, Hospital de la Baxada “Dra. Teresa Ratto” Paraná Entre Ríos Argentina
| | - Walter Silva
- Pediatric Neurology Unit, Hospital Italiano de Buenos Aires Buenos Aires Argentina
| | - Damián Consalvo
- Neurology Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Ignacio Sfaello
- CETES, Instituto de Neurología Infanto‐Juvenil Córdoba Argentina
| | - Alberto J. Espay
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Marcelo A. Kauffman
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
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17
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Peterlin B, Gualandi F, Maver A, Servidei S, van der Maarel SM, Lamy F, Mejat A, Evangelista T, Ferlini A. Genetic testing offer for inherited neuromuscular diseases within the EURO-NMD reference network: A European survey study. PLoS One 2020; 15:e0239329. [PMID: 32946487 PMCID: PMC7500674 DOI: 10.1371/journal.pone.0239329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/03/2020] [Indexed: 11/19/2022] Open
Abstract
The genetic diagnostics of inherited neuromuscular diseases (NMDs) is challenging due to their clinical and genetic heterogeneity. We launched an online survey within the EURO-NMD European Reference Network (ERN) to collect information about the availability/distribution of genetic testing across 61 ERN health care providers (HCPs). A 17 items questionnaire was designed to address methods used, the number of genetic tests available, the clinical pathway to access genetic testing, the use of next-generation sequencing (NGS) and participation to quality assessment schemes (QAs). A remarkable number of HCPs (49%) offers ≥ 500 genetic tests per year, 43,6% offers 100–500 genetic tests per year, and 7,2% ≤ 100 per year. NGS is used by 94% of centres, Sanger sequencing by 84%, MLPA by 66% and Southern blotting by 36%. The majority of centres (60%) offer NGS for all patients that fulfil criteria for NMD of genetic origin. Pipelines for NGS vary amongst centres, even within the same national system. Referral of patients to genetic laboratories by specialists was frequently reported (58%), and 65% of centres participates in genetic testing QAs. We specifically evaluated how many centres cover SMA, DMD, Pompe, LGMDs, and TTR genes/diseases genetic diagnosis, since these rare diseases benefit from personalised therapies. We used the Orphanet EUGT numbers, provided by 82% of HCPs. SMA, DMD, LGMD, TTR and GAA genes are covered by EUGTs although with different numbers and modalities. The number of genetic tests for NMDs offered across HCPs National Health systems is quite high, including routine techniques and NGS. The number and type of tests offered and the clinical practices differ among centres. We provided evidence that survey tools might be useful to learn about the state-of-the-art of ERN health-related activities and to foster harmonisation and standardisation of the complex care for the rare disease patients in the EU.
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Affiliation(s)
- Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Serenella Servidei
- Neurophysiopathology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | | | - Teresinha Evangelista
- Neuromuscular Morphology Unit, Myology Institute, GHU Pitié-Salpêtrière, Sorbonne Université, Paris, France
- * E-mail: (AF); (TE)
| | - Alessandra Ferlini
- Unit of Medical Genetics, University Hospital Ferrara, Ferrara, Italy
- * E-mail: (AF); (TE)
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18
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Halverson CME, Connors LM, Wessinger BC, Clayton EW, Wiesner GL. Patient perspectives on variant reclassification after cancer susceptibility testing. Mol Genet Genomic Med 2020; 8:e1275. [PMID: 32329193 PMCID: PMC7336756 DOI: 10.1002/mgg3.1275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Little is known about the impact of reclassification on patients' perception of medical uncertainty or trust in genetics-based clinical care. METHODS Semistructured telephone interviews were conducted with 20 patients who had received a reclassified genetic test result related to hereditary cancer. All participants had undergone genetic counseling and testing for cancer susceptibility at Vanderbilt-Ingram Cancer Center Hereditary Cancer Clinic within the last six years. RESULTS Most of the participants did not express distress related to the variant reclassification and only a minority expressed a decrease in trust in medical genetics. However, recall of the new interpretation was limited, even though all participants were recontacted by letter, phone, or clinic visit. CONCLUSION Reclassification of genetic tests is an important issue in modern healthcare because changes in interpretation have the potential to alter previously recommended management. Participants in this study did not express strong feelings of mistrust or doubt about their genetic evaluation. However, there was a low level of comprehension and information retention related to the updated report. Future research can build on this study to improve communication with patients about their reclassified results.
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Affiliation(s)
- Colin M E Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA.,Regenstrief Institute, Indianapolis, IN, USA
| | | | | | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,School of Law, Vanderbilt University, Nashville, TN, USA
| | - Georgia L Wiesner
- Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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19
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Appelbaum PS, Parens E, Berger SM, Chung WK, Burke W. Is there a duty to reinterpret genetic data? The ethical dimensions. Genet Med 2020; 22:633-639. [PMID: 31616070 PMCID: PMC7185819 DOI: 10.1038/s41436-019-0679-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The evolving evidence base for the interpretation of variants identified in genetic and genomic testing has presented the genetics community with the challenge of variant reinterpretation. In particular, it is unclear whether an ethical duty of periodic reinterpretation should exist, who should bear that duty, and what its dimensions should be. Based on an analysis of the ethical arguments for and against a duty to reinterpret, we conclude that a duty should be recognized. Most importantly, by virtue of ordering and conducting tests likely to produce data on variants that cannot be definitively interpreted today, the health-care system incurs a duty to reinterpret when more reliable data become available. We identify four elements of the proposed ethical duty: data storage, initiation of reinterpretation, conduct of reinterpretation, and patient recontact, and we identify the parties best situated to implement each component. We also consider the reasonable extent and duration of a duty, and the role of the patient's consent in the process, although we acknowledge that some details regarding procedures and funding still need to be addressed. The likelihood of substantial patient benefit from a systematic approach to reinterpretation suggests the importance for the genetics community to reach consensus on this issue.
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Affiliation(s)
- Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center and NY State Psychiatric Institute, New York, NY, USA.
| | | | - Sara M Berger
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
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20
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A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020; 87:338-344. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
Abstract
We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.
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21
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El Mecky J, Johansson L, Plantinga M, Fenwick A, Lucassen A, Dijkhuizen T, van der Hout A, Lyle K, van Langen I. Reinterpretation, reclassification, and its downstream effects: challenges for clinical laboratory geneticists. BMC Med Genomics 2019; 12:170. [PMID: 31779608 PMCID: PMC6883538 DOI: 10.1186/s12920-019-0612-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND In recent years, the amount of genomic data produced in clinical genetics services has increased significantly due to the advent of next-generation sequencing. This influx of genomic information leads to continuous changes in knowledge on how genetic variants relate to hereditary disease. These changes can have important consequences for patients who have had genetic testing in the past, as new information may affect their clinical management. When and how patients should be recontacted after new genetic information becomes available has been investigated extensively. However, the issue of how to handle the changing nature of genetic information remains underexplored in a laboratory setting, despite it being the first stage at which changes in genetic data are identified and managed. METHODS The authors organized a 7-day online focus group discussion. Fifteen clinical laboratory geneticists took part. All (nine) Dutch clinical molecular genetics diagnostic laboratories were represented. RESULTS Laboratories in our study reinterpret genetic variants reactively, e.g. at the request of a clinician or following identification of a previously classified variant in a new patient. Participants currently deemed active, periodic reinterpretation to be unfeasible and opinions differed on whether it is desirable, particularly regarding patient autonomy and the main responsibilities of the laboratory. The efficacy of reinterpretation was questioned in the presence of other strategies, such as reanalysis and resequencing of DNA. Despite absence of formal policy regarding when to issue a new report for clinicians due to reclassified genetic data, participants indicated similar practice across all laboratories. However, practice differed significantly between laboratory geneticists regarding the reporting of VUS reclassifications. CONCLUSION Based on the results, the authors formulated five challenges needing to be addressed in future laboratory guidelines: 1. Should active reinterpretation of variants be conducted by the laboratory as a routine practice? 2. How does reinterpretation initiated by the laboratory relate to patient expectations and consent? 3. When should reinterpreted data be considered clinically significant and communicated from laboratory to clinician? 4. Should reinterpretation, reanalysis or a new test be conducted? 5. How are reclassifications perceived and how might this affect laboratory practice?
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Affiliation(s)
- Julia El Mecky
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands. .,Clinical Ethics and Law Southampton, University of Southampton, Southampton, UK.
| | - Lennart Johansson
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Angela Fenwick
- Clinical Ethics and Law Southampton, University of Southampton, Southampton, UK
| | - Anneke Lucassen
- Clinical Ethics and Law Southampton, University of Southampton, Southampton, UK
| | - Trijnie Dijkhuizen
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Annemieke van der Hout
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Kate Lyle
- Clinical Ethics and Law Southampton, University of Southampton, Southampton, UK
| | - Irene van Langen
- Department of Clinical Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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22
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Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA, Relling MV, Rodriguez LL, Tamburro C, Green ED. Opportunities, resources, and techniques for implementing genomics in clinical care. Lancet 2019; 394:511-520. [PMID: 31395439 PMCID: PMC6699751 DOI: 10.1016/s0140-6736(19)31140-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Advances in technologies for assessing genomic variation and an increasing understanding of the effects of genomic variants on health and disease are driving the transition of genomics from the research laboratory into clinical care. Genomic medicine, or the use of an individual's genomic information as part of their clinical care, is increasingly gaining acceptance in routine practice, including in assessing disease risk in individuals and their families, diagnosing rare and undiagnosed diseases, and improving drug safety and efficacy. We describe the major types and measurement tools of genomic variation that are currently of clinical importance, review approaches to interpreting genomic sequence variants, identify publicly available tools and resources for genomic test interpretation, and discuss several key barriers in using genomic information in routine clinical practice.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomic and Precision Medicine, Duke University, Durham, NC, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary V Relling
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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23
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Ghani M, Nfonsam L, Pranckeviciene E, Daoud H, Potter R, Chisholm C, Harper PE, Schaffer A, Little L, Sinclair-Bourque E, McGowan-Jordan J, Smith A, Bronicki L, Jarinova O. Adopting High-Resolution Allele Frequencies Substantially Expedites Variant Interpretation in Genetic Diagnostic Laboratories. J Mol Diagn 2019; 21:602-611. [PMID: 31028938 DOI: 10.1016/j.jmoldx.2019.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 02/09/2019] [Accepted: 02/19/2019] [Indexed: 11/15/2022] Open
Abstract
A cohort of 1242 individuals tested in a clinical diagnostic laboratory was used to test whether the filtering allele frequencies (FAFs)-based framework, recently recommended for MHY7-associated cardiomyopathy, is extendable to 45 cardiomyopathy genes. Statistical analysis revealed a threshold of 0.00164% for the extreme outlier allele frequencies (AFs), based on the Genome Aggregation Database (exome fraction) total AFs of 138 unique pathogenic and likely pathogenic variants; 135 of them (97.8%) had AFs of <0.004%, the recommended threshold to apply moderate pathogenicity evidence for MYH7-associated cardiomyopathy. Of the 460 cases reported with only variant(s) of unknown clinical significance (VUCSs), 97 (21%) solely had VUCSs with FAFs >0.03%, frequencies above which were estimated herein as strong evidence against pathogenicity. Interestingly, 74.5% (172/231) of the unique VUCSs with FAFs >0.03% had Genome Aggregation Database maximum allele frequencies across all populations AFs >0.1%, deemed herein as stand-alone evidence against pathogenicity. Accordingly, using an FAF threshold of >0.1%, compared with AF >1%, led us to issue considerably more (25.9% versus 41.3%) negative patient reports. Also, 82.7% (N = 629) of the unique classified benign or likely benign variants with AFs <1% had FAFs >0.1%, reinforcing the use of this filtering strategy. Together, these data demonstrate that implementing FAF thresholds may considerably decrease the amount of variant interpretations and significantly reduce the cost of genetic testing for clinical genetic laboratories, without compromising the accuracy of genetic diagnostic services.
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Affiliation(s)
- Mahdi Ghani
- Department of Genetics, CHEO, Ottawa, Ontario, Canada.
| | | | - Erinija Pranckeviciene
- Department of Genetics, CHEO, Ottawa, Ontario, Canada; Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Hussein Daoud
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | - Ryan Potter
- Department of Genetics, CHEO, Ottawa, Ontario, Canada
| | | | | | | | | | | | - Jean McGowan-Jordan
- Department of Genetics, CHEO, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Amanda Smith
- Department of Genetics, CHEO, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Lucas Bronicki
- Department of Genetics, CHEO, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Genetics, CHEO, Ottawa, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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24
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Feliubadaló L, López-Fernández A, Pineda M, Díez O, Del Valle J, Gutiérrez-Enríquez S, Teulé A, González S, Stjepanovic N, Salinas M, Capellá G, Brunet J, Lázaro C, Balmaña J. Opportunistic testing of BRCA1, BRCA2 and mismatch repair genes improves the yield of phenotype driven hereditary cancer gene panels. Int J Cancer 2019; 145:2682-2691. [PMID: 30927264 DOI: 10.1002/ijc.32304] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 02/07/2019] [Accepted: 03/14/2019] [Indexed: 12/29/2022]
Abstract
Multigene panels provide a powerful tool for analyzing several genes simultaneously. We evaluated the frequency of pathogenic variants (PV) in customized predefined panels according to clinical suspicion by phenotype and compared it to the yield obtained in the analysis of our clinical research gene panel. We also investigated mutational yield of opportunistic testing of BRCA1/2 and mismatch repair (MMR) genes in all patients. A total of 1,205 unrelated probands with clinical suspicion of hereditary cancer were screened for germline mutations using panel testing. Overall, 1,048 females and 157 males were analyzed, mean age at cancer diagnosis was 48; 883 had hereditary breast/ovarian cancer-suspicion, 205 hereditary nonpolyposis colorectal cancer (HNPCC)-suspicion, 73 adenomatous-polyposis-suspicion and 44 with other/multiple clinical criteria. At least one PV was found in 150 probands (12%) analyzed by our customized phenotype-driven panel. Tumoral MMR deficiency predicted for the presence of germline MMR gene mutations in patients with HNPCC-suspicion (46/136 vs. 0/56 in patients with and without MMR deficiency, respectively). Opportunistic testing additionally identified five MSH6, one BRCA1 and one BRCA2 carriers (0.6%). The analysis of the extended 24-gene panel provided 25 additional PVs (2%), including in 4 out of 51 individuals harboring MMR-proficient colorectal tumors (2 CHEK2 and 2 ATM). Phenotype-based panels provide a notable rate of PVs with clinical actionability. Opportunistic testing of MMR and BRCA genes leads to a significant straightforward identification of MSH6, BRCA1 and BRCA2 mutation carriers, and endorses the model of opportunistic testing of genes with clinical utility within a standard genetic counseling framework.
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Affiliation(s)
- Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | | | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology Barcelona, Barcelona, Spain.,Molecular and Clinical Genetics Area. Hospital Vall d'Hebron, Universitat Autonòma de Barcelona, Barcelona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | | | - Alex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Sara González
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Neda Stjepanovic
- High Risk and Familial Cancer, Vall d'Hebron Institute of Oncology, Barcelona.,Medical Oncology Department. Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mónica Salinas
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, Girona, Spain.,Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Judith Balmaña
- High Risk and Familial Cancer, Vall d'Hebron Institute of Oncology, Barcelona.,Medical Oncology Department. Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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25
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Variant classification changes over time in BRCA1 and BRCA2. Genet Med 2019; 21:2248-2254. [PMID: 30971832 DOI: 10.1038/s41436-019-0493-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 03/12/2019] [Indexed: 12/17/2022] Open
Abstract
PURPOSE To report BRCA1 and BRCA2 (BRCA1/2) variant reassessments and reclassifications between 2012 and 2017 at the Advanced Molecular Diagnostics Laboratory (AMDL) in Toronto, Canada, which provides BRCA1/2 testing for patients in Ontario, and to compare AMDL variant classifications with submissions in ClinVar. METHODS Variants were assessed using a standardized variant assessment tool based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology's guidelines and tracked in an in-house database. Variants were shared through the Canadian Open Genetics Repository and submitted to ClinVar for comparison against other laboratories. RESULTS AMDL identified 1209 BRCA1/2 variants between 2012 and 2017. During this period, 32.9% (398/1209) of variants were reassessed and 12.4% (150/1209) were reclassified. The majority of reclassified variants were downgraded (112/150, 74.7%). Of the reclassified variants, 63.3% (95/150) were reclassified to benign, 20.7% (31/150) to likely benign, 10.0% (15/150) to variant of uncertain significance, 2.0% (3/150) to likely pathogenic, and 4.0% (6/150) to pathogenic. Discordant ClinVar submissions were found for 40.4% (488/1209) of variants. CONCLUSION BRCA1/2 variants may be reclassified over time. Reclassification presents ethical and practical challenges related to recontacting patients. Data sharing is essential to improve variant interpretation, to help patients receive appropriate care based on their genetic results.
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26
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Bombard Y, Brothers KB, Fitzgerald-Butt S, Garrison NA, Jamal L, James CA, Jarvik GP, McCormick JB, Nelson TN, Ormond KE, Rehm HL, Richer J, Souzeau E, Vassy JL, Wagner JK, Levy HP. The Responsibility to Recontact Research Participants after Reinterpretation of Genetic and Genomic Research Results. Am J Hum Genet 2019; 104:578-595. [PMID: 30951675 PMCID: PMC6451731 DOI: 10.1016/j.ajhg.2019.02.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 11/16/2022] Open
Abstract
The evidence base supporting genetic and genomic sequence-variant interpretations is continuously evolving. An inherent consequence is that a variant's clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis. There has been discussion concerning the extent of this obligation in the context of both research and clinical care. Although clinical recommendations have begun to emerge, guidance is lacking on the responsibilities of researchers to inform participants of reinterpreted results. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in November 2018. The workgroup included representatives from the National Society of Genetic Counselors, the Canadian College of Medical Genetics, and the Canadian Association of Genetic Counsellors. The final statement includes twelve position statements that were endorsed or supported by the following organizations: Genetic Alliance, European Society of Human Genetics, Canadian Association of Genetic Counsellors, American Association of Anthropological Genetics, Executive Committee of the American Association of Physical Anthropologists, Canadian College of Medical Genetics, Human Genetics Society of Australasia, and National Society of Genetic Counselors.
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Affiliation(s)
- Yvonne Bombard
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Institute of Health Policy, Management, and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada.
| | - Kyle B Brothers
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Sara Fitzgerald-Butt
- National Society of Genetic Counselors, Chicago, IL 60611, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Nanibaa' A Garrison
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Leila Jamal
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; National Society of Genetic Counselors, Chicago, IL 60611, USA; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cynthia A James
- National Society of Genetic Counselors, Chicago, IL 60611, USA; Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Gail P Jarvik
- Executive Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jennifer B McCormick
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Humanities, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Tanya N Nelson
- Canadian College of Medical Geneticists, Kingston, ON K7K 1Z7, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Department of Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, BC V6H 3N1, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Kelly E Ormond
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Heidi L Rehm
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Medical and Populations Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Julie Richer
- Canadian College of Medical Geneticists, Kingston, ON K7K 1Z7, Canada; Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), Ottawa, ON K1H 8L1, Canada; University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emmanuelle Souzeau
- Canadian Association of Genetic Counsellors, Oakville, ON L6J 7N5, Canada; Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, SA 5042, Australia
| | - Jason L Vassy
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; VA Boston Healthcare System, Boston, MA 02130, USA
| | - Jennifer K Wagner
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA 17822, USA
| | - Howard P Levy
- Social Issues Committee, American Society of Human Genetics, Rockville, MD 20852, USA; Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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27
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Yauy K, Baux D, Pegeot H, Van Goethem C, Mathieu C, Guignard T, Juntas Morales R, Lacourt D, Krahn M, Lehtokari VL, Bonne G, Tuffery-Giraud S, Koenig M, Cossée M. MoBiDiC Prioritization Algorithm, a Free, Accessible, and Efficient Pipeline for Single-Nucleotide Variant Annotation and Prioritization for Next-Generation Sequencing Routine Molecular Diagnosis. J Mol Diagn 2018; 20:465-473. [PMID: 29689380 DOI: 10.1016/j.jmoldx.2018.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/16/2018] [Accepted: 03/09/2018] [Indexed: 12/22/2022] Open
Abstract
Interpretation of next-generation sequencing constitutes the main limitation of molecular diagnostics. In diagnosing myopathies and muscular dystrophies, another issue is efficiency in predicting the pathogenicity of variants identified in large genes, especially TTN; current in silico prediction tools show limitations in predicting and ranking the numerous variants of such genes. We propose a variant-prioritization tool, the MoBiDiCprioritization algorithm (MPA). MPA is based on curated interpretation of data on previously reported variants, biological assumptions, and splice and missense predictors, and is used to prioritize all types of single-nucleotide variants. MPA was validated by comparing its sensitivity and specificity to those of dbNSFP database prediction tools, using a data set composed of DYSF, DMD, LMNA, NEB, and TTN variants extracted from expert-reviewed and ExAC databases. MPA obtained the best annotation rates for missense and splice variants. As MPA aggregates the results from several predictors, individual predictor errors are counterweighted, improving the sensitivity and specificity of missense and splice variant predictions. We propose a sequential use of MPA, beginning with the selection of variants with higher scores and followed by, in the absence of candidate pathologic variants, consideration of variants with lower scores. We provide scripts and documentation for free academic use and a validated annotation pipeline scaled for panel and exome sequencing to prioritize single-nucleotide variants from a VCF file.
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Affiliation(s)
- Kevin Yauy
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France.
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Henri Pegeot
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Charles Van Goethem
- Laboratoire de Biopathologie Cellulaire et Tissulaire des Tumeurs, Hôpital Arnaud de Villeneuve, CHU Montpellier, Montpellier, France
| | - Charly Mathieu
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Thomas Guignard
- Plateforme Recherche de Microremaniements Chromosomiques-Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France; Faculté de Médecine Montpellier-Nîmes, Université de Montpellier, Montpellier, France
| | | | - Delphine Lacourt
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - Martin Krahn
- Unité de Génétique Médicale et Génomique Fonctionnelle INSERM UMRS910, Université d'Aix Marseille, Marseille, France; Département de Génétique Médicale, Hôpital Timone Enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Vilma-Lotta Lehtokari
- The Folkhalsan Institute of Genetics and the Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Gisele Bonne
- Unité INSERM U974-Thérapie des Maladies du Muscle Striée, Center of Research in Myology, Institut de Myologie, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Sylvie Tuffery-Giraud
- Laboratoire de Génétique des Maladies Rares EA7402, Université de Montpellier, Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France; Laboratoire de Génétique des Maladies Rares EA7402, Université de Montpellier, Montpellier, France
| | - Mireille Cossée
- Laboratoire de Génétique Moléculaire, CHU Montpellier, Montpellier, France; Laboratoire de Génétique des Maladies Rares EA7402, Université de Montpellier, Montpellier, France
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