51
|
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?
Collapse
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
| |
Collapse
|
52
|
Jonsson JJ, Stefansdottir V. Ethical issues in precision medicine. Ann Clin Biochem 2019; 56:628-629. [DOI: 10.1177/0004563219870824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jon J Jonsson
- Department of Genetics and Molecular Medicine, Landspitali – National University Hospital, Reykjavik, Iceland
- Department of Biochemistry and Molecular Biology, University of Iceland, Reykjavik, Iceland
| | - Vigdis Stefansdottir
- Department of Genetics and Molecular Medicine, Landspitali – National University Hospital, Reykjavik, Iceland
| |
Collapse
|
53
|
GfH-Stellungnahme zum Rekontaktieren von Patienten. MED GENET-BERLIN 2019. [DOI: 10.1007/s11825-019-00256-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
54
|
ESHG PPPC Comments on postmortem use of genetic data for research purposes. Eur J Hum Genet 2019; 28:144-146. [PMID: 31595045 PMCID: PMC6974591 DOI: 10.1038/s41431-019-0525-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 01/25/2023] Open
|
55
|
Haidar CE, Relling MV, Hoffman JM. Preemptively Precise: Returning and Updating Pharmacogenetic Test Results to Realize the Benefits of Preemptive Testing. Clin Pharmacol Ther 2019; 106:942-944. [PMID: 31520409 DOI: 10.1002/cpt.1613] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/17/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Cyrine E Haidar
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - James M Hoffman
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Office of Quality and Patient Care, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
56
|
|
57
|
Wong EK, Bartels K, Hathaway J, Burns C, Yeates L, Semsarian C, Krahn AD, Virani A, Ingles J. Perceptions of genetic variant reclassification in patients with inherited cardiac disease. Eur J Hum Genet 2019; 27:1134-1142. [PMID: 30903112 PMCID: PMC6777462 DOI: 10.1038/s41431-019-0377-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/16/2019] [Accepted: 03/01/2019] [Indexed: 01/08/2023] Open
Abstract
Interpretation of sequence variants is an ongoing challenge and new approaches aim to increase stringency. The reclassification of variants has the potential to alter medical management and elicit psychosocial consequences for patients. The perspective of patients with an inherited cardiac disease and a clinically significant variant reclassification was explored through semi-structured phone interviews. Participants were recruited from two specialized multidisciplinary centers in Canada and Australia. Qualitative analysis was performed through a thematic analysis approach. Fifteen participants were interviewed, including 9 (60%) with an inherited cardiomyopathy and 6 (40%) with an inherited arrhythmia syndrome. Six (40%) patients had a classification upgrade, while 9 (60%) had a downgrade. Four major themes emerged: (1) reactions towards the reclassified variant; (2) impact on decision-making; (3) perception of the reclassification process; and (4) improvement of the reclassification process. Many patients adjusted to the reclassification, however some misunderstood the implications, impacting their responses and decision-making. In conclusion, careful discussion with patients about uncertainty and the potential for reclassification are crucial to ensure a deeper understanding of the outcome of genetic testing and impact on families.
Collapse
Affiliation(s)
- Eugene K Wong
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Charlotte Burns
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Laura Yeates
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | | | - Alice Virani
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jodie Ingles
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, The University of Sydney, Sydney, NSW, Australia.
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
| |
Collapse
|
58
|
Briggs S, Slade I. Evaluating the Integration of Genomics into Cancer Screening Programmes: Challenges and Opportunities. CURRENT GENETIC MEDICINE REPORTS 2019; 7:63-74. [PMID: 32117599 PMCID: PMC7019642 DOI: 10.1007/s40142-019-00162-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW As the costs of genomic testing have fallen, and our understanding of genetic susceptibility to cancers has grown, there has been increasing interest in incorporating testing for cancer susceptibility genes, and polygenic risk estimates, into population cancer screening. A growing body of evidence suggests that this would be both clinically and cost-effective. In this article, we aim to explore the frameworks used to evaluate screening programmes, evaluate whether population screening for cancer susceptibility can be assessed using these standards, and consider additional issues and outcomes of importance in this context. RECENT FINDINGS There are tensions between traditional approaches of genetic testing (utilising tests with high sensitivity and specificity) and the principles of population screening (in which the screening test typically has low specificity), as well as the frameworks used to evaluate the two. Despite the existence of many screening guidelines, including consensus papers, these often do not align fully with broader considerations of genetic test evaluation. Population screening for genetic risk in cancer shifts the focus from diagnostics to prognostication and has wider implications for personal and familial health than existing screening programmes. In addition, understanding of the prevalence and penetrance of cancer susceptibility genes, required by many screening guidelines, may only be obtainable through population-level testing; prospective multi-disciplinary research alongside implementation will be essential. SUMMARY Appropriate evaluation of genetic screening for cancer risk will require modification of existing screening frameworks to incorporate additional complexity of outcomes and population values. As evidence supporting population screening for cancer susceptibility mounts, development of an appropriate evaluative framework, and expansion of public dialogue will be key to informing policy.
Collapse
Affiliation(s)
- Sarah Briggs
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Ingrid Slade
- Wellcome Centre for Ethics and Humanities and Ethox Centre, Nuffield Department of Population Health, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, OX3 7LF UK
| |
Collapse
|
59
|
Knoppers BM, Thorogood A, Zawati MH. Letter: Relearning the 3 R's? Reinterpretation, recontact, and return of genetic variants. Genet Med 2019; 21:2401-2402. [PMID: 30971835 DOI: 10.1038/s41436-019-0494-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Adrian Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Ma'n H Zawati
- Centre of Genomics and Policy, McGill University, Montreal, QC, Canada
| |
Collapse
|
60
|
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: 34] [Impact Index Per Article: 6.8] [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.
Collapse
|
61
|
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.
Collapse
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
| |
Collapse
|
62
|
Analysis of VUS reporting, variant reinterpretation and recontact policies in clinical genomic sequencing consent forms. Eur J Hum Genet 2018; 26:1743-1751. [PMID: 30143804 DOI: 10.1038/s41431-018-0239-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
There are several key unsolved issues relating to the clinical use of next generation sequencing, such as: should laboratories report variants of uncertain significance (VUS) to clinicians and/or patients? Should they reinterpret VUS in response to growing knowledge in the field? And should patients be recontacted regarding such results? We systematically analyzed 58 consent forms in English used in the diagnostic context to investigate their policies for (a) reporting VUS, (b) reinterpreting variants, including who should initiate this, and (c) recontacting patients and the mechanisms for undertaking any recontact. One-third (20/58) of the forms did not mention VUS in any way. Of the 38 forms that mentioned VUS, only half provided some description of what a VUS is. Approximately one-third of forms explicitly stated that reinterpretation of variants for clinical purposes may occur. Less than half mentioned recontact for clinical purposes, with variation as to whether laboratories, patients, or clinicians should initiate this. We suggest that the variability in variant reporting, reinterpretation, and recontact policies and practices revealed by our analysis may lead to diffused responsibility, which could result in missed opportunities for patients or family members to receive a diagnosis in response to updated variant classifications. Finally, we provide some suggestions for ethically appropriate inclusion of policies for reporting VUS, reinterpretation, and recontact on consent forms.
Collapse
|