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Martin BE, Sands T, Bier L, Bergner A, Boehme AK, Lippa N. Comparing the frequency of variants of uncertain significance (VUS) between ancestry groups in a paediatric epilepsy cohort. J Med Genet 2024; 61:645-651. [PMID: 38453479 DOI: 10.1136/jmg-2023-109450] [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: 06/30/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Studies indicate that variants of uncertain significance are more common in non-European populations due to lack of a diversity in population databases. This difference has not been explored in epilepsy, which is increasingly found to be genetic in paediatric populations, and has precision medicine applications. This study examines the differences in the frequency of uncertain next-generation sequencing (NGS) results among a paediatric epilepsy cohort between ancestral groups historically under-represented in biomedical research (UBR) and represented in biomedical research (RBR). METHODS A retrospective chart review of patients with epilepsy seen at Columbia University Irving Medical Center (CUIMC). One hundred seventy-eight cases met the following criteria: (1) visited any provider within the Pediatric Neurology Clinic at CUIMC, (2) had an ICD code indicating a diagnosis of epilepsy, (3) underwent NGS testing after March 2015 and (4) had self-reported ancestry that fit into a single dichotomous category of either historically represented or under-represented in biomedical research. RESULTS UBR cases had significantly higher rates of uncertain results when compared with RBR cases (79.2% UBR, 20.8% RBR; p value=0.002). This finding remained true after controlling for potential confounding factors, including sex, intellectual disability or developmental delay, epilepsy type, age of onset, number of genes tested and year of testing. CONCLUSION Our results add to the literature that individuals who are of ancestries historically under-represented in genetics research are more likely to receive uncertain genetic results than those of represented majority ancestral groups and establishes this finding in an epilepsy cohort.
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Affiliation(s)
- Bree E Martin
- Department of General Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tristan Sands
- Department of Neurology, Columbia University, New York, New York, USA
- Columbia University Irving Medical Center, New York, New York, USA
| | - Louise Bier
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amanda Bergner
- Genetic Counseling Graduate Program, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
- Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Amelia K Boehme
- Department of Neurology, Columbia University, New York, New York, USA
| | - Natalie Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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2
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Lu D, Yang J, Shen W, Chen M. Attitudes toward uncertain results from prenatal exome sequencing: a national survey among healthcare professionals working in the prenatal setting. Front Med (Lausanne) 2024; 11:1335649. [PMID: 38813373 PMCID: PMC11133618 DOI: 10.3389/fmed.2024.1335649] [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: 11/09/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Objective The objective of this study was to investigate the attitudes of healthcare professionals (HPs) working in the prenatal setting toward uncertain results (UR) from prenatal exome sequencing (pES) in China. Methods We conducted a national survey among HPs working in the prenatal setting. UR in our study include variants of uncertain significance (VUS), variants with variable penetrance/expressivity (VVPE), and secondary findings unrelated to the indication for testing (SFs). A total of 285 questionnaires that met the inclusion criteria were collected. Data were analyzed using IBM SPSS Statistics 26. Results When performing the pre-test counseling, only 7.4% of HPs mentioned the possibility of VUS, 6.3% discussed the possibility of VVPE, and 7.4% introduced the SFs with parents with the option to not report these variants. In post-test counseling, 73.0-82.8% HPs discussed with the parents but did not make any recommendations for managing the pregnancy after reporting UR (73.0% for VUS, 82.8% for VVPE, 74.7% for SFs, respectively). Conclusion Most parents did not have the option of opting out of reporting UR from pES in pre-test counseling. UR did not influence the pregnancy recommendation made by most HPs. Establishing national guidelines for reporting UR from pES and developing strategies to improve counseling skills may help HPs manage UR.
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Affiliation(s)
- Dongfang Lu
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Jing Yang
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Wei Shen
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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van der Geest MA, Maeckelberghe ELM, van Gijn ME, Lucassen AM, Swertz MA, van Langen IM, Plantinga M. Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications. Eur J Hum Genet 2024; 32:489-497. [PMID: 38480795 PMCID: PMC11061183 DOI: 10.1038/s41431-023-01529-z] [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: 07/26/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 05/02/2024] Open
Abstract
With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.
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Affiliation(s)
- Marije A van der Geest
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Els L M Maeckelberghe
- Institute for Medical Education, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Faculty of Medicine, Clinical Ethics and Law, University of Southampton, Southampton, UK
- Centre for Personalised Medicine, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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4
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Schott C, Colaiacovo S, Baker C, Weir MA, Connaughton DM. Reclassification of Genetic Testing Results: A Case Report Demonstrating the Need for Structured Re-Evaluation of Genetic Findings. Can J Kidney Health Dis 2024; 11:20543581241242562. [PMID: 38623282 PMCID: PMC11017705 DOI: 10.1177/20543581241242562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/01/2024] [Indexed: 04/17/2024] Open
Abstract
Rationale Alport Syndrome (AS) is a progressive genetic condition characterized by chronic kidney disease (CKD), hearing loss, and eye abnormalities. It is caused by mutations in the genes COL4A3, COL4A4, and COL4A5. Heterozygous mutations in COL4A4 and COL4A3 cause autosomal dominant Alport Syndrome (ADAS), and a spectrum of phenotypes ranging from asymptomatic hematuria to CKD, with variable extra-renal features. In the past, heterozygous mutations in these genes were thought to be benign, however recent studies show that about 30% of patients can progress to CKD, and 15% can progress to end stage kidney disease (ESKD). Presenting Concerns We present a case of a woman who was noted to have microscopic hematuria pre-living kidney donation. Genetic testing revealed a heterozygous variant of uncertain significance (VUS) in the COL4A4 gene. VUSs are medically nonactionable findings and data show that VUSs can be detected in 41% of all patients who undergo clinical genetic testing. VUSs frustrate clinicians and patients alike. Although they cannot be used in medical decision-making, data suggest that reanalysis can result in the reclassification of a VUS over time. Diagnosis Post-donation, the index patient had a higher than anticipated rise in serum creatinine, raising a concern for possible intrinsic kidney disease. Kidney biopsy was deemed high risk in the setting of a unilateral kidney thereby limiting possible diagnostic intervention to determine the cause of disease. Intervention Re-evaluation of prior genetic testing results and reassessment of the previously identified VUS in COL4A4 was performed 5-years post-donation. These analyses, along with the addition of new phenotypic data and extended pedigree data, resulted in the reclassification of the previously identified VUS to a likely pathogenic variant. Outcomes This case demonstrates the importance of structured, periodic re-evaluation of genetic testing results. With the ever-changing landscape of genetics in medicine, the interpretation of a VUS can be dynamic and therefore warrant caution in living kidney donor evaluations. Studies have shown that about 10% of VUSs can be upgraded to a pathogenic classification after an 18- to 36-month interval. Structured re-evaluation of genomic testing results has not yet been integrated into clinical practice and poses a unique challenge in living kidney donation. Novel findings This case report highlights the variability of the ADAS phenotype caused by pathogenic heterozygous variants in the type 4 collagen genes. It supports the nomenclature change from a benign hematuria phenotype to ADAS, particularly when additional risk factors such as proteinuria, focal segmental glomerulosclerosis or glomerular basement membrane changes on kidney biopsy are present, or as in this case, evidence of disease in other family members.
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Affiliation(s)
- Clara Schott
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western, London, ON, Canada
| | - Samantha Colaiacovo
- Division of Medical Genetics, Department of Pediatrics, Victoria Hospital, London Health Science Center, ON, Canada
| | - Cadence Baker
- Division of Nephrology, Department of Medicine, University Hospital, London Health Sciences Centre, ON, Canada
| | - Matthew A. Weir
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western, London, ON, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, University of Western, London, ON, Canada
| | - Dervla M. Connaughton
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western, London, ON, Canada
- Division of Nephrology, Department of Medicine, University Hospital, London Health Sciences Centre, ON, Canada
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Sabatello M, Bakken S, Chung WK, Cohn E, Crew KD, Kiryluk K, Kukafka R, Weng C, Appelbaum PS. Return of polygenic risk scores in research: Stakeholders' views on the eMERGE-IV study. HGG ADVANCES 2024; 5:100281. [PMID: 38414240 PMCID: PMC10950748 DOI: 10.1016/j.xhgg.2024.100281] [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] [Received: 08/24/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Research on polygenic risk scores (PRSs) for common, genetically complex chronic diseases aims to improve health-related predictions, tailor risk-reducing interventions, and improve health outcomes. Yet, the study and use of PRSs in clinical settings raise equity, clinical, and regulatory challenges that can be greater for individuals from historically marginalized racial, ethnic, and other minoritized communities. As part of the National Human Genome Research Institute-funded Electronic Medical Records and Genomics IV Network, we conducted online focus groups with patients/community members, clinicians, and members of institutional review boards to explore their views on key issues, including PRS research, return of PRS results, clinical translation, and barriers and facilitators to health behavioral changes in response to PRS results. Across stakeholder groups, our findings indicate support for PRS development and a strong interest in having PRS results returned to research participants. However, we also found multi-level barriers and significant differences in stakeholders' views about what is needed and possible for successful implementation. These include researcher-participant interaction formats, health and genomic literacy, and a range of structural barriers, such as financial instability, insurance coverage, and the absence of health-supporting infrastructure and affordable healthy food options in poorer neighborhoods. Our findings highlight the need to revisit and implement measures in PRS studies (e.g., incentives and resources for follow-up care), as well as system-level policies to promote equity in genomic research and health outcomes.
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Affiliation(s)
- Maya Sabatello
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University, New York, NY, USA; Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, New York, NY, USA.
| | - Suzanne Bakken
- School of Nursing and Department of Biomedical Informatic, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth Cohn
- Northwell Health 600 Community Drive, Manhasset, NY, USA
| | - Katherine D Crew
- Department of Medicine and Epidemiology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Rita Kukafka
- Departments of Biomedical Informatics and Sociomedical Sciences, Columbia University, New York, NY 10032, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University, New York, NY 10032, USA
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Watts G, Newson AJ. Reconsidering reinterpretation: response to commentaries. JOURNAL OF MEDICAL ETHICS 2023; 49:824-825. [PMID: 37802639 DOI: 10.1136/jme-2023-109615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Affiliation(s)
- Gabriel Watts
- Faculty of Medicine and Health, School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
| | - Ainsley J Newson
- Faculty of Medicine and Health, School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
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7
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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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8
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Chen E, Facio FM, Aradhya KW, Rojahn S, Hatchell KE, Aguilar S, Ouyang K, Saitta S, Hanson-Kwan AK, Capurro NN, Takamine E, Jamuar SS, McKnight D, Johnson B, Aradhya S. Rates and Classification of Variants of Uncertain Significance in Hereditary Disease Genetic Testing. JAMA Netw Open 2023; 6:e2339571. [PMID: 37878314 PMCID: PMC10600581 DOI: 10.1001/jamanetworkopen.2023.39571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
Importance Variants of uncertain significance (VUSs) are rampant in clinical genetic testing, frustrating clinicians, patients, and laboratories because the uncertainty hinders diagnoses and clinical management. A comprehensive assessment of VUSs across many disease genes is needed to guide efforts to reduce uncertainty. Objective To describe the sources, gene distribution, and population-level attributes of VUSs and to evaluate the impact of the different types of evidence used to reclassify them. Design, Setting, and Participants This cohort study used germline DNA variant data from individuals referred by clinicians for diagnostic genetic testing for hereditary disorders. Participants included individuals for whom gene panel testing was conducted between September 9, 2014, and September 7, 2022. Data were analyzed from September 1, 2022, to April 1, 2023. Main Outcomes and Measures The outcomes of interest were VUS rates (stratified by age; clinician-reported race, ethnicity, and ancestry groups; types of gene panels; and variant attributes), percentage of VUSs reclassified as benign or likely benign vs pathogenic or likely pathogenic, and enrichment of evidence types used for reclassifying VUSs. Results The study cohort included 1 689 845 individuals ranging in age from 0 to 89 years at time of testing (median age, 50 years), with 1 203 210 (71.2%) female individuals. There were 39 150 Ashkenazi Jewish individuals (2.3%), 64 730 Asian individuals (3.8%), 126 739 Black individuals (7.5%), 5539 French Canadian individuals (0.3%), 169 714 Hispanic individuals (10.0%), 5058 Native American individuals (0.3%), 2696 Pacific Islander individuals (0.2%), 4842 Sephardic Jewish individuals (0.3%), and 974 383 White individuals (57.7%). Among all individuals tested, 692 227 (41.0%) had at least 1 VUS and 535 385 (31.7%) had only VUS results. The number of VUSs per individual increased as more genes were tested, and most VUSs were missense changes (86.6%). More VUSs were observed per sequenced gene in individuals who were not from a European White population, in middle-aged and older adults, and in individuals who underwent testing for disorders with incomplete penetrance. Of 37 699 unique VUSs that were reclassified, 30 239 (80.2%) were ultimately categorized as benign or likely benign. A mean (SD) of 30.7 (20.0) months elapsed for VUSs to be reclassified to benign or likely benign, and a mean (SD) of 22.4 (18.9) months elapsed for VUSs to be reclassified to pathogenic or likely pathogenic. Clinical evidence contributed most to reclassification. Conclusions and Relevance This cohort study of approximately 1.6 million individuals highlighted the need for better methods for interpreting missense variants, increased availability of clinical and experimental evidence for variant classification, and more diverse representation of race, ethnicity, and ancestry groups in genomic databases. Data from this study could provide a sound basis for understanding the sources and resolution of VUSs and navigating appropriate next steps in patient care.
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Affiliation(s)
- Elaine Chen
- Invitae Corporation, San Francisco, California
| | | | | | | | | | | | | | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Nicole Nakousi Capurro
- School of Medicine, University of Valparaíso, Valparaíso, Chile
- Facultad de Medicina, Universidad Andrés Bello, Viña del Mar, Chile
| | - Eriko Takamine
- Department of Medical Genetics, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Saumya Shekhar Jamuar
- Genetics Service, KK Women’s and Children’s Hospital, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | | | | | - Swaroop Aradhya
- Invitae Corporation, San Francisco, California
- Department of Pathology, Stanford University, Stanford, California
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9
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Hanson H, Astiazaran-Symonds E, Amendola LM, Balmaña J, Foulkes WD, James P, Klugman S, Ngeow J, Schmutzler R, Voian N, Wick MJ, Pal T, Tischkowitz M, Stewart DR. Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100870. [PMID: 37490054 PMCID: PMC10623578 DOI: 10.1016/j.gim.2023.100870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE Although the role of CHEK2 germline pathogenic variants in cancer predisposition is well known, resources for managing CHEK2 heterozygotes in clinical practice are limited. METHODS An international workgroup developed guidance on clinical management of CHEK2 heterozygotes informed by peer-reviewed publications from PubMed. RESULTS Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines. Risk-reducing mastectomy should be guided by personalized risk estimates and shared decision making. Colorectal and prostate cancer surveillance should be considered based on assessment of family history. For CHEK2 heterozygotes who develop cancer, no specific targeted medical treatment is recommended at this time. CONCLUSION Systematic prospective data collection is needed to establish the spectrum of CHEK2-associated cancer risks and to determine yet-unanswered questions, such as the outcomes of surveillance, response to cancer treatment, and survival after cancer diagnosis.
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Affiliation(s)
- Helen Hanson
- Southwest Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD; Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | | | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Susan Klugman
- Division of Reproductive & Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rita Schmutzler
- Center of Integrated Oncology (CIO), University of Cologne, Cologne, Germany; Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Nicoleta Voian
- Providence Genetic Risk Clinic, Providence Cancer Institute, Portland, OR
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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10
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Knox JBL, Svendsen MN. The fertility of moral ambiguity in precision medicine. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2023; 26:465-476. [PMID: 37280471 PMCID: PMC10243698 DOI: 10.1007/s11019-023-10160-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 06/08/2023]
Abstract
Although precision medicine cuts across a large spectrum of professions, interdisciplinary and cross-sectorial moral deliberation has yet to be widely enacted, let alone formalized in this field. In a recent research project on precision medicine, we designed a dialogical forum (i.e. 'the Ethics Laboratory') giving interdisciplinary and cross-sectorial stakeholders an opportunity to discuss their moral conundrums in concert. We organized and carried out four Ethics Laboratories. In this article, we use Simone de Beauvoir's concept of moral ambiguity as a lens to frame the participants' experience with fluid moral boundaries. By framing our approach through this concept we are able to elucidate irremediable moral issues that are collectively underexplored in the practice of precision medicine. Moral ambiguity accentuates an open and free space where different types of perspectives converge and can inform each other. Based on our study, we identified two dilemmas, or thematic interfaces, in the interdisciplinary moral deliberations which unfolded in the Ethics Laboratories: (1) the dilemma between the individual and the collective good; and (2) the dilemma between care and choice. Through our investigation of these dilemmas, we show how Beauvoir's concept of moral ambiquity not only serves as a fertile catalyst for greater moral awareness but, furthermore, how the concept can become an indispensable part of the practices of and the discourse about precision medicine.
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Affiliation(s)
- Jeanette Bresson Ladegaard Knox
- Department of Public Health, University of Copenhagen, Øster Farimagsgade 5, Building, 1014 Copenhagen, Denmark
- University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mette Nordahl Svendsen
- Department of Public Health, University of Copenhagen, Øster Farimagsgade 5, Building, 1014 Copenhagen, Denmark
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11
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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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12
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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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13
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Halley MC, Olson NW. Blurred Boundaries: Toward an Expanded Ethics of Research and Clinical Care. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:5-9. [PMID: 38410998 DOI: 10.1080/15265161.2023.2224148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
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14
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Vears DF, Savulescu J, Christodoulou J, Wall M, Newson AJ. Are We Ready for Whole Population Genomic Sequencing of Asymptomatic Newborns? Pharmgenomics Pers Med 2023; 16:681-691. [PMID: 37415831 PMCID: PMC10321326 DOI: 10.2147/pgpm.s376083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
The introduction of genomic sequencing technologies into routine newborn screening programs in some form is not only inevitable but also already occurring in some settings. The question is therefore not "if" but "when and how" genomic newborn screening (GNBS) should be implemented. In April 2022, the Centre for Ethics of Paediatric Genomics held a one-day symposium exploring ethical issues relating to the use of genomic sequencing in a range of clinical settings. This review article synthesises the panel discussion and presents both the potential benefits of wide-scale implementation of genomic newborn screening, as well as its practical and ethical issues, including obtaining appropriate consent, and health system implications. A more in-depth understanding of the barriers associated with implementing genomic newborn screening is critical to the success of GNBS programs, both from a practical perspective and also in order to maintain public trust in an important public health initiative.
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Affiliation(s)
- Danya F Vears
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Julian Savulescu
- Chen Su Lan Centennial Professor in Medical Ethics, Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Visiting Professorial Fellow in Biomedical Ethics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Distinguished Visiting Professor in Law, Melbourne University, Carlton, Victoria, Australia
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK
| | - John Christodoulou
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Service, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Ainsley J Newson
- Faculty of Medicine & Health, Sydney School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
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15
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Makhnoon S, Davidson E, Shirts B, Arun B, Shete S. Practices and Views of US Oncologists and Genetic Counselors Regarding Patient Recontact After Variant Reclassification: Results of a Nationwide Survey. JCO Precis Oncol 2023; 7:e2300079. [PMID: 37384863 PMCID: PMC10581618 DOI: 10.1200/po.23.00079] [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: 02/16/2023] [Revised: 04/26/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
PURPOSE Over a 5-year or 10-year period, between 6% and 15% of germline cancer genetic variants undergo reclassification. Up-to-date interpretation can clarify a variant's clinical significance and guide patient management. As the frequency of reclassifications increase, the issue of whether, how, when, and which providers should recontact patients with information about reclassification becomes important. However, the field lacks research evidence and definitive guidance from professional organizations about how providers should recontact patients. We compared the perspectives of US oncologists and cancer genetic counselors (GCs) to describe their practices and views regarding recontact. MATERIALS AND METHODS We developed a survey using themes identified from semistructured interviews with oncologists and GCs and administered it in a national sample of oncologists and GCs between July and September 2022. RESULTS In total, 634 respondents completed the survey including 349 oncologists and 285 GCs. On frequency of recontacting patients with reclassified results, 40% of GCs reported recontacting often compared with 12.5% of oncologists. Neither group reported recording patient preference for recontact on electronic medical record (EMR). Both groups agreed that all reclassified variants, even those that do not affect clinical management, should be returned to patients. They also reported that recontact via EMR messages, mailed letters, and phone calls from GC assistants were more suitable for downgrades. By contrast, face-to-face meetings and phone calls were preferred for upgrades. Remarkably, oncologists were more likely to endorse face-to-face return of results and were more likely to endorse return through a nongenetics provider compared to GCs. CONCLUSION These data on current recontact practices and opinions provide a foundation for developing guidelines with explicit recommendations on patient recontact that can help maximize clinical effect while considering provider preferences for recontact within resource-constrained genomic practice settings.
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Affiliation(s)
- Sukh Makhnoon
- Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX
| | - Elenita Davidson
- Department of Behavioral Science, UT MD Anderson Cancer Center, Houston, TTX
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Banu Arun
- Clinical Cancer Genetics, UT MD Anderson Cancer Center, Houston, TX
| | - Sanjay Shete
- Department of Epidemiology, UT MD Anderson Cancer Center, Houston, TX
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16
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Appelbaum PS, Berger SM, Brokamp E, Brown HS, Burke W, Clayton EW, Evans BJ, Hamid R, Marchant GE, Martin DM, O'Connor BC, Pagán JA, Parens E, Roberts JL, Rowe J, Schneider J, Siegel K, Veenstra DL, Chung WK. Practical considerations for reinterpretation of individual genetic variants. Genet Med 2023; 25:100801. [PMID: 36748709 PMCID: PMC10408279 DOI: 10.1016/j.gim.2023.100801] [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: 08/29/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
With the growing use of genetic testing in medicine, the question of when genetic findings should be reinterpreted in light of new data has become inescapable. The generation of population and disease-specific data, development of computational tools, and new understandings of the relationship of specific genes to disorders can all trigger changes in variant classification that may have important implications for patients and the clinicians caring for them. This is a particular concern for patients from groups underrepresented in current reference datasets, since they have higher rates of uncertain findings. Here we identify the challenges to implementing a systematic approach to variant reinterpretation and propose solutions. In particular, we address (a) the infrastructure needed to support implementation of systematic variant reinterpretation, (b) the issues around obtaining consent from patients for reinterpretation, (c) the process for triggering reinterpretation, (d) pathways for the flow of reinterpreted data, (e) considerations for how to cover the costs of reinterpretation, and (f) practical issues related to implementation of processes and policies that address these issues, including the importance of a fixed duration during which there is an expectation that variants will be reinterpreted.
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Affiliation(s)
- Paul S Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY
| | - Sara M Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Elly Brokamp
- Vanderbilt Genomics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Henry Shelton Brown
- Management, Policy and Community Health, UT Health School of Public Health, University of Texas Health Science Center at Houston, Austin Regional Campus, Austin, TX
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN; Center for Biomedical Ethics and Society, School of Law, Vanderbilt University, Nashville, TN
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Wertheim College of Engineering, University of Florida, Gainesville, FL
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Gary E Marchant
- Center for Law, Science & Innovation, Sandra Day O'Connor School of Law, Arizona State University, Phoenix, AZ
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, MI
| | | | - José A Pagán
- Department of Public Health Policy and Management, School of Global Public Health, New York University, New York, NY
| | - Erik Parens
- Hastings Center Initiative in Bioethics, The Hastings Center, Garrison, NY
| | - Jessica L Roberts
- Health Law & Policy Institute Humanities, University of Houston Law Center, Houston, TX; College of Medicine, University of Houston, Houston, TX
| | - John Rowe
- Department of Health Policy and Management, Mailman School of Public Health, Columbia University, New York, NY
| | | | - Karolynn Siegel
- Department of Sociomedical Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - David L Veenstra
- The Comparative Health Outcomes, Policy and Economics (CHOICE) Institute, School of Pharmacy, University of Washington, Seattle, WA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY.
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17
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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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18
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Appelbaum PS, Burke W, Parens E, Roberts J, Berger S, Chung WK. Cases in Precision Medicine: Is There an Obligation to Return Reinterpreted Genetic Results to Former Patients? Ann Intern Med 2023; 176:563-567. [PMID: 36972543 PMCID: PMC10413009 DOI: 10.7326/m22-3682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Interpretation of many genetic test results can change over time as new data accumulate. Hence, physicians who order genetic tests may subsequently receive revised reports with important implications for patients' medical treatment-even for patients who are no longer in their care. Several of the ethical principles underlying medical practice suggest an obligation to reach out to former patients with this information. Discharging that obligation can be accomplished, at a minimum, by attempting to contact the former patient with their last known contact information.
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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
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA
| | | | - Jessica Roberts
- Health Law & Policy Institute, University of Houston Law Center, Houston, TX
| | - Sara Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY
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19
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Makhnoon S, Levin B, Ensinger M, Mattie K, Volk RJ, Zhao Z, Mendoza T, Shete S, Samiian L, Grana G, Grainger A, Arun B, Shirts BH, Peterson SK. A multicenter study of clinical impact of variant of uncertain significance reclassification in breast, ovarian and colorectal cancer susceptibility genes. Cancer Med 2023; 12:2875-2884. [PMID: 36426404 PMCID: PMC9939195 DOI: 10.1002/cam4.5202] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/30/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Clinical interpretation of genetic test results is complicated by variants of uncertain significance (VUS) that have an unknown impact on health but can be clarified through reclassification. There is little empirical evidence regarding VUS reclassification in oncology care settings, including the prevalence and outcomes of reclassification, and racial/ethnic differences. METHODS This was a retrospective analysis of persons with and without a personal history of cancer carrying VUS (with or without an accompanying pathogenic or likely pathogenic [P/LP] variant) in breast, ovarian, and colorectal cancer predisposition genes seen at four cancer care settings (in Texas, Florida, Ohio, and New Jersey) between 2013 and 2019. RESULTS In 2715 individuals included in the study, 3261 VUS and 313 P/LP variants were reported; 8.1% of all individuals with VUS experienced reclassifications and rates varied significantly among cancer care settings from 4.81% to 20.19% (overall p < 0.001). Compared to their prevalence in the overall sample, reclassification rates for Black individuals were higher (13.6% vs. 19.0%), whereas the rates for Asian individuals were lower (6.3% vs. 3.5%) and rates for White and Hispanic individuals were proportional. Two-year prevalence of VUS reclassification remained steady between 2014 and 2019. Overall, 11.3% of all reclassified VUS resulted in clinically actionable findings and 4.6% subsequently changed individuals' clinical managements. CONCLUSIONS The findings from this large multisite study suggest that VUS reclassification alters clinical management, has implications for precision cancer prevention, and highlights the need for implementing practices and solutions for efficiently returning reinterpreted genetic test results.
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Affiliation(s)
- Sukh Makhnoon
- Department of Behavioral ScienceUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Brooke Levin
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | | | - Kristin Mattie
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | - Robert J. Volk
- Department of Health Services ResearchUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Tito Mendoza
- Department of Symptoms researchUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Sanjay Shete
- Division of Cancer Prevention and Population SciencesUT MD Anderson Cancer CenterHoustonTexasUSA
| | | | - Generosa Grana
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | | | - Banu Arun
- Clinical Cancer GeneticsUT MD Anderson Cancer CenterHoustonTexasUSA
| | | | - Susan K. Peterson
- Department of Behavioral ScienceUT MD Anderson Cancer CenterHoustonTexasUSA
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20
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Clabout T, Maes L, Acke F, Wuyts W, Van Schil K, Coucke P, Janssens S, De Leenheer E. Negative Molecular Diagnostics in Non-Syndromic Hearing Loss: What Next? Genes (Basel) 2022; 14:genes14010105. [PMID: 36672845 PMCID: PMC9859074 DOI: 10.3390/genes14010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Congenital hearing loss has an impact on almost every facet of life. In more than 50% of cases, a genetic cause can be identified. Currently, extensive genetic testing is available, although the etiology of some patients with obvious familial hearing loss remains unknown. We selected a cohort of mutation-negative patients to optimize the diagnostic yield for genetic hearing impairment. In this retrospective study, 21 patients (17 families) with negative molecular diagnostics for non-syndromic hearing loss (gene panel analysis) were included based on a positive family history with a similar type of hearing loss. Additional genetic testing was performed using a whole exome sequencing panel (WESHL panel v2.0) in four families with the strongest likelihood of genetic hearing impairment. In this cohort (n = 21), the severity of hearing loss was most commonly moderate (52%). Additional genetic testing revealed pathogenic copy number variants in the STRC gene in two families. In summary, regular re-evaluation of hearing loss patients with presumably genetic etiology after negative molecular diagnostics is recommended, as we might miss newly discovered deafness genes. The switch from gene panel analysis to whole exome sequencing or whole genome sequencing for the testing of congenital hearing loss seems promising.
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Affiliation(s)
- Thomas Clabout
- Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Laurence Maes
- Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Frederic Acke
- Department of Otorhinolaryngology, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
| | - Kristof Van Schil
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Prins Boudewijnlaan 43, B-2650 Edegem, Belgium
| | - Paul Coucke
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Els De Leenheer
- Department of Otorhinolaryngology, Ghent University Hospital, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
- Correspondence: ; Tel.: +32-93322332
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21
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Atzeni R, Massidda M, Fotia G, Uva P. VariantAlert: A web-based tool to notify updates in genetic variant annotations. Hum Mutat 2022; 43:1808-1815. [PMID: 36300680 PMCID: PMC10091775 DOI: 10.1002/humu.24495] [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: 04/13/2022] [Revised: 10/06/2022] [Accepted: 10/25/2022] [Indexed: 01/24/2023]
Abstract
The reinterpretation of variants based on updated annotations is part of the routine work of research laboratories: the more data is collected about a specific variant, the higher the probability to reinterpret its classification. To support this task, we developed VariantAlert, a web-based tool to help researchers and clinicians to be constantly informed about changes in variant annotations extracted from multiple sources. VariantAlert provides daily re-annotation of variants using external resources accessed through application programming interface, such as MyVariant.info providing in turn links to gnomAD, catalogue of somatic mutations In cancer (COSMIC), ClinVar, CIViC, and many others. Researchers and clinicians can submit one or more lists of variants. If a change is detected for the annotation of a variant due to the upgrade of the underlying resource (e.g., change in gnomAD allele frequency, presence in COSMIC database, change in ClinVar classification) the user is notified by email and updated annotations are stored on the web-site. VariantAlert is freely available at https://github.com/next-crs4/VariantAlert. Installation and deployment are easy thanks to the use of the Docker platform. A Makefile allows you to easily bootstrap VariantAlert. VariantAlert is also available as a web service at https://variant-alert.crs4.it/.
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Affiliation(s)
- Rossano Atzeni
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Science and Technology Park Polaris, Pula, Italy
| | - Matteo Massidda
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Science and Technology Park Polaris, Pula, Italy
| | - Giorgio Fotia
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Science and Technology Park Polaris, Pula, Italy
| | - Paolo Uva
- Clinical Bioinformatics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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22
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Outram SM, Brown J, Ackerman SL. The social value of genomic sequencing for disadvantaged families facing rare disease. Soc Sci Med 2022; 314:115465. [PMID: 36279794 DOI: 10.1016/j.socscimed.2022.115465] [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: 05/06/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
This study explores parental expectations and value-making processes in respect to pediatric clinical genomic sequencing for socially disadvantaged families. Drawing on interviews and ethnographic observations with parents of children with undiagnosed physical and/or intellectual differences seeking to find whether these differences have a genetic etiology, we explore expectations and parental assessments of the value of genomic sequencing within the context of an ongoing research study. We demonstrate how the value of sequencing to parents goes well beyond finding diagnostic results or receiving prescriptive guidance as to the best care and treatment of their child; instead, value is co-created by parents, clinicians, and genetic counsellors throughout the enrollment and return of results process. Parents in our study found that clinicians and genetic counsellors repeatedly reenforce that parents need to lower their expectations and be prepared to wait for genetic science to provide more definitive answers. At the same time, parents experience that clinical teams validate parents for having made a good choice in their undertaking of genomic sequencing and, no matter the result, that they are not to blame for their child's symptoms. The experience of many parents (although not all) is that genomic science reduces or removes their sense of guilt for their child's condition, providing a platform that affirms them as "good parents." Moreover, rather than being voiceless and isolated, socially disadvantaged parents who enter into diagnostic sequencing find themselves in a familial-biosocial framework wherein they are co-partners in a socially and biologically authoritative vision of the future.
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Affiliation(s)
- S M Outram
- Program in Bioethics, Institute for Health & Aging, University of California, San Francisco, CA, USA.
| | - Jeh Brown
- Program in Bioethics, Institute for Health & Aging, University of California, San Francisco, CA, USA
| | - S L Ackerman
- Department of Social & Behavioral Sciences, University of California, San Francisco, CA, USA
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23
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Postel MD, Culver JO, Ricker C, Craig DW. Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum. Hum Mutat 2022; 43:1590-1608. [PMID: 35510381 PMCID: PMC9560997 DOI: 10.1002/humu.24394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
While whole-genome and exome sequencing have transformed our collective understanding of genetics' role in disease pathogenesis, there are certain conditions and populations for whom DNA-level data fails to identify the underlying genetic etiology. Specifically, patients of non-White race and non-European ancestry are disproportionately affected by "variants of unknown/uncertain significance" (VUS), limiting the scope of precision medicine for minority patients and perpetuating health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret from DNA data alone. RNA analysis can illuminate the consequences of VUS, thereby allowing for their reclassification as pathogenic versus benign. Here we review the critical role transcriptome analysis plays in clarifying VUS in both neoplastic and non-neoplastic diseases.
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Affiliation(s)
- Mackenzie D. Postel
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Julie O. Culver
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Charité Ricker
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Keck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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24
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Newey PJ. Approach to the patient with a variant of uncertain significance on genetic testing. Clin Endocrinol (Oxf) 2022; 97:400-408. [PMID: 35996232 DOI: 10.1111/cen.14818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/29/2022]
Abstract
Establishing a genetic diagnosis may lead to major health benefits for the patient and their wider family, but is dependent on the accurate interpretation of test results. The processes of variant interpretation are by their nature imprecise such that the potential for uncertain test results (i.e., variant(s) of uncertain significance [VUS]) are an inevitable consequence of genomic testing. With an increased responsibility for diagnostic testing in the hands of the specialty physician (e.g., endocrinologist) rather than clinical geneticist, it is essential that they are familiar with the possible outcomes of testing including an understanding of the VUS category. While uncertainty is endemic to many aspects of clinical medicine, receiving a VUS result may pose a considerable challenge to both the clinician and the patient. In this article, a framework to support decision-making when confronted with a VUS variant is provided, focusing on the key components of the genetic testing pathway. This highlights the importance of assessing the VUS result in the context of the clinical presentation and genetic testing strategy, the value of multidisciplinary team working and ensuring good communication with the patient.
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Affiliation(s)
- Paul J Newey
- Division of Molecular and Clinical Medicine, Ninewells Hospital & Medical School, University of Dundee, Dundee, Scotland, UK
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25
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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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26
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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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Rahimzadeh V, Friedman JM, de Wert G, Knoppers BM. Exome/Genome-Wide Testing in Newborn Screening: A Proportionate Path Forward. Front Genet 2022; 13:865400. [PMID: 35860465 PMCID: PMC9289115 DOI: 10.3389/fgene.2022.865400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Population-based newborn screening (NBS) is among the most effective public health programs ever launched, improving health outcomes for newborns who screen positive worldwide through early detection and clinical intervention for genetic disorders discovered in the earliest hours of life. Key to the success of newborn screening programs has been near universal accessibility and participation. Interest has been building to expand newborn screening programs to also include many rare genetic diseases that can now be identified by exome or genome sequencing (ES/GS). Significant declines in sequencing costs as well as improvements to sequencing technologies have enabled researchers to elucidate novel gene-disease associations that motivate possible expansion of newborn screening programs. In this paper we consider recommendations from professional genetic societies in Europe and North America in light of scientific advances in ES/GS and our current understanding of the limitations of ES/GS approaches in the NBS context. We invoke the principle of proportionality—that benefits clearly outweigh associated risks—and the human right to benefit from science to argue that rigorous evidence is still needed for ES/GS that demonstrates clinical utility, accurate genomic variant interpretation, cost effectiveness and universal accessibility of testing and necessary follow-up care and treatment. Confirmatory or second-tier testing using ES/GS may be appropriate as an adjunct to conventional newborn screening in some circumstances. Such cases could serve as important testbeds from which to gather data on relevant programmatic barriers and facilitators to wider ES/GS implementation.
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Affiliation(s)
- Vasiliki Rahimzadeh
- Stanford Center for Biomedical Ethics, Stanford University, Stanford, CA, United States
- *Correspondence: Vasiliki Rahimzadeh,
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Guido de Wert
- Department of Health, Ethics and Society, Maastricht University, Maastricht, Netherlands
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Burke W, Parens E, Chung WK, Berger SM, Appelbaum PS. The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review. Ann Intern Med 2022; 175:994-1000. [PMID: 35436152 PMCID: PMC10555957 DOI: 10.7326/m21-4109] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic tests expand diagnostic and screening opportunities but also identify genetic variants of uncertain clinical significance (VUSs). Only a minority of VUSs are likely to prove pathogenic when later reassessed, but resolution of the uncertainty is rarely timely. That uncertainty adds complexity to clinical decision making and can result in harms and costs to patients and the health care system, including the time-consuming analysis required to interpret a VUS and the potential for unnecessary treatment and adverse psychological effects. Current efforts to improve variant interpretation will help reduce the scope of the problem, but the high prevalence of rare and novel variants in the human genome points to VUSs as an ongoing challenge. Additional strategies can help mitigate the potential harms of VUSs, including testing protocols that limit identification or reporting of VUSs, subclassification of VUSs according to the likelihood of pathogenicity, routine family-based evaluation of variants, and enhanced counseling efforts. All involve tradeoffs, and the appropriate balance of measures is likely to vary for different test uses and clinical settings. Cross-specialty deliberation and public input could contribute to systematic and broadly supported policies for managing VUSs.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, WA, USA
| | | | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sara M. Berger
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul S. Appelbaum
- Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
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Johnson LM, Mandrell BN, Li C, Lu Z, Gattuso J, Harrison LW, Mori M, Ouma AA, Pritchard M, Sharp KMH, Nichols KE. Managing Pandora's Box: Familial Expectations around the Return of (Future) Germline Results. AJOB Empir Bioeth 2022; 13:152-165. [PMID: 35471132 DOI: 10.1080/23294515.2022.2063994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Pediatric oncology patients are increasingly being offered germline testing to diagnose underlying cancer predispositions. Meanwhile, as understanding of variant pathogenicity evolves, planned reanalysis of genomic results has been suggested. Little is known regarding the types of genomic information that parents and their adolescent children with cancer prefer to receive at the time of testing or their expectations around the future return of genomic results. METHODS Parents and adolescent children with cancer eligible for genomic testing for cancer predisposition were surveyed regarding their attitudes and expectations for receiving current and future germline results (ClinicalTrials.gov Identifier: NCT02530658). RESULTS All parents (100%) desired to learn about results for treatable or preventable conditions, with 92.4% wanting results even when there is no treatment or prevention. Parents expressed less interest in receiving uncertain results for themselves (88.3%) than for their children (95.3%). Most parents (95.9%) and adolescents (87.9%) believed that providers have a responsibility to share new or updated germline results indefinitely or at any point during follow-up care. Fewer parents (67.5%) indicated that they would want results if their child was deceased: 10.3% would not want to be contacted, 19.3% were uncertain. CONCLUSIONS Expectations for return of new or updated genomic results are high among pediatric oncology families, although up to one third of parents have reservations about receiving such information in the event of their child's death. These results underscore the importance of high-quality pre-and post-test counseling, conducted by individuals trained in consenting around genomic testing to elicit family preferences and align expectations around the return of germline results.
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Affiliation(s)
- Liza-Marie Johnson
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Belinda N Mandrell
- Department of Pediatrics, Division of Nursing Research, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chen Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhaohua Lu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jami Gattuso
- Department of Pediatrics, Division of Nursing Research, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lynn W Harrison
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Motomi Mori
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Annastasia A Ouma
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michele Pritchard
- Department of Pediatrics, Division of Nursing Research, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, TN, USA
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30
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Fischer CG, Pallavajjala A, Jiang L, Anagnostou V, Tao J, Adams E, Eshleman JR, Gocke CD, Lin MT, Platz EA, Xian RR. Artificial intelligence-assisted serial analysis of clinical cancer genomics data identifies changing treatment recommendations and therapeutic targets. Clin Cancer Res 2022; 28:2361-2372. [PMID: 35312750 DOI: 10.1158/1078-0432.ccr-21-4061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/15/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Given the pace of predictive biomarker and targeted therapy development, it is unknown if repeat annotation of the same next-generation sequencing data can identify additional clinically actionable targets that could be therapeutically leveraged. In this study, we sought to determine the predictive yield of serial re-analysis of clinical tumor sequencing data. EXPERIMENTAL DESIGN Using artificial intelligence (AI)-assisted variant annotation, we retrospectively re-analyzed sequencing data from 2,219 cancer patients from a single academic medical center at 3-month intervals totaling 9 months in 2020. The yield of serial re-analysis was assessed by the proportion of patients with improved strength of therapeutic recommendations. RESULTS 1,775 patients (80%) had {greater than or equal to}1 potentially clinically actionable mutation at baseline, including 243 (11%) patients who had an alteration targeted by an FDA-approved drug for their cancer type. By month nine, the latter increased to 458 (21%) patients mainly due to a single pan-cancer agent directed against tumors with high tumor mutation burden. Within this timeframe, 67 new therapies became available and 45 were no longer available. Variant pathogenicity classifications also changed leading to changes in treatment recommendations for 124 patients (6%). CONCLUSIONS Serial re-annotation of tumor sequencing data improved the strength of treatment recommendations (based on level of evidence) in a mixed cancer cohort and showed substantial changes in available therapies and variant classifications. These results suggest a role for repeat analysis of tumor sequencing data in clinical practice, which can be streamlined with AI support.
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Affiliation(s)
| | | | - LiQun Jiang
- Johns Hopkins Medical Institutions, United States
| | - Valsamo Anagnostou
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jessica Tao
- Johns Hopkins Medical Institutions, United States
| | - Emily Adams
- Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | | | | | - Ming-Tseh Lin
- The Johns Hopkins School of Medicine, Baltimore, United States
| | - Elizabeth A Platz
- Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Rena R Xian
- Johns Hopkins Medical Institutions, Baltimore, MD, United States
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31
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Leung ML, Ji J, Baker S, Buchan JG, Sivakumaran TA, Krock BL, Hutchins R, Bayrak-Toydemir P, Pfeifer J, Cremona ML, Funke B, Santani AB. A Framework of Critical Considerations in Clinical Exome Reanalyses by Clinical and Laboratory Standards Institute. J Mol Diagn 2022; 24:177-188. [PMID: 35074075 DOI: 10.1016/j.jmoldx.2021.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
Exome reanalysis is useful for providing molecular diagnoses for previously uninformative samples. However, challenges exist in implementing a practical solution for clinicians and laboratories. This study complements the current literature by providing practical considerations for patient-level and cohort-level reanalyses. The Clinical and Laboratory Standards Institute assembled the Document Development Committee and an interpretation working group that developed the framework for reevaluation of exome-based data. We describe two distinct but complementary approaches toward exome reanalyses: clinician-initiated patient-level reanalysis, and laboratory-initiated cohort-level reanalysis. We highlight the advantages and constraints for both approaches, and provide a high-level conceptual guide for ordering clinicians and laboratories through the critical decision pathways. Because clinical exome sequencing continues to be the standard of care in genetics, exome reanalysis would be critical in increasing the overall diagnostic yield. A systematic guide will facilitate the efficient adoption of reevaluation of exome data for laboratories, health care professionals, genetic counselors, and clinicians.
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Affiliation(s)
- Marco L Leung
- Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Jianling Ji
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California; Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Samuel Baker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jillian G Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Theru A Sivakumaran
- Division of Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, Arizona
| | | | | | - Pinar Bayrak-Toydemir
- Department of Pathology, The University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - John Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | | | | | - Avni B Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania; Veritas Genetics, Boston, Massachusetts.
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Zouk H, Yu W, Oza A, Hawley M, Vijay Kumar PK, Koch C, Mahanta LM, Harley JB, Jarvik GP, Karlson EW, Leppig KA, Myers MF, Prows CA, Williams MS, Weiss ST, Lebo MS, Rehm HL. Reanalysis of eMERGE phase III sequence variants in 10,500 participants and infrastructure to support the automated return of knowledge updates. Genet Med 2022; 24:454-462. [PMID: 34906510 PMCID: PMC10128874 DOI: 10.1016/j.gim.2021.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The clinical genomics knowledgebase is dynamic with variant classifications changing as newly identified cases, additional population data, and other evidence become available. This is a challenge for the clinical laboratory because of limited resource availability for variant reassessment. METHODS Throughout the Electronic Medical Records and Genomics phase III program, clinical sites associated with the Mass General Brigham/Broad sequencing center received automated, real-time notifications when reported variants were reclassified. In this study, we summarized the nature of these reclassifications and described the proactive reassessment framework we used for the Electronic Medical Records and Genomics program data set to identify variants most likely to undergo reclassification. RESULTS Reanalysis of 1855 variants led to the reclassification of 2% (n = 45) of variants, affecting 0.6% (n = 67) of participants. Of these reclassifications, 78% (n = 35) were high-impact changes affecting reportability, with 8 variants downgraded from likely pathogenic/pathogenic to variants of uncertain significance (VUS) and 27 variants upgraded from VUS to likely pathogenic/pathogenic. Most upgraded variants (67%) were initially classified as VUS-Favor Pathogenic, highlighting the benefit of VUS subcategorization. The most common reason for reclassification was new published case data and/or functional evidence. CONCLUSION Our results highlight the importance of periodic sequence variant reevaluation and the need for automated approaches to advance routine implementation of variant reevaluations in clinical practice.
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Affiliation(s)
- Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Andrea Oza
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Prathik K Vijay Kumar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA
| | - John B Harley
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH; US Department of Veteran Affairs Medical Center, Cincinnati, OH
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | | | | | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; University of Cincinnati College of Medicine, Cincinnati, OH
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Scott T Weiss
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.
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33
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Marshall JL, Peshkin BN, Yoshino T, Vowinckel J, Danielsen HE, Melino G, Tsamardinos I, Haudenschild C, Kerr DJ, Sampaio C, Rha SY, FitzGerald KT, Holland EC, Gallagher D, Garcia-Foncillas J, Juhl H. OUP accepted manuscript. Oncologist 2022; 27:272-284. [PMID: 35380712 PMCID: PMC8982374 DOI: 10.1093/oncolo/oyab048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Corresponding author: John L. Marshall, MD, The Ruesch Center for the Cure of Gastrointestinal Cancers, Frederick P. Smith Endowed Chair, Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road, Washington, DC 20007, USA. Tel: +1 202 444 2223;
| | - Beth N Peshkin
- Georgetown University, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | | | - Håvard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Radiumhospitalet, Montebello, Oslo, Norway
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Ioannis Tsamardinos
- JADBio Gnosis DA, N. Plastira 100, Science and Technology Park of Crete and Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, Heraklion, GR, Greece
| | | | - David J Kerr
- Nuffield Division of Clinical and Laboratory Sciences, Level 4, Academic Block, John Radcliffe Infirmary, Headington, Oxford, UK
| | | | - Sun Young Rha
- Yonsei Cancer Center, Yonsei University College of Medicine, Seodaemun-Ku, Seoul, Korea
| | - Kevin T FitzGerald
- Department of Medical Humanities in the School of Medicine, Creighton University, Omaha, NE, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Gallagher
- St. James’s Hospital/Trinity College Dublin, St. Raphael’s House, Dublin, Ireland
| | - Jesus Garcia-Foncillas
- Cancer Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain
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Mensah NE, Sabir AH, Bond A, Roworth W, Irving M, Davies AC, Ahn JW. Automated reanalysis application to assist in detecting novel gene–disease associations after genome sequencing. Genet Med 2021; 24:811-820. [DOI: 10.1016/j.gim.2021.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 08/31/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
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35
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Fragmented responsibility: views of Israeli HCPs regarding patient recontact following variant reclassification. J Community Genet 2021; 13:13-18. [PMID: 34609721 PMCID: PMC8491183 DOI: 10.1007/s12687-021-00556-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
While genomic medicine is becoming an important part of patient care with an ever-increasing diagnostic yield, recontacting patients after reclassification of variants of uncertain clinical significance (VUSs) remains a major challenge. Although periodical reinterpretation of VUSs is highly desired, recontacting former patients with new classifications is commonly not fulfilled in practice. We draw on semi-structured interviews with 20 Israeli healthcare professionals and stakeholders involved in communicating the results of genome-wide sequencing to patients. Findings show agreement that an individual health care professional cannot address the task of recontacting patients after re-classification, and that responsibility should be shared among the medical specialties, laboratory scientists, as well as patients. In the absence of established guidelines, many respondents suggested that the patient should be informed about reclassification during a follow-up contact but they disagreed who should be responsible for informing the patient. HCPs agreed that the solution to this challenge involves a centralized automated database that is accessible, continuously updated, and facilitates retrospective as well as prospective flagging of reclassification for patients who can benefit from this information. National and international policies providing concrete guidelines on the optimal way to recontact patients with new valuable genomic information are needed.
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Brokamp E, Koziura ME, Phillips JA, Tang LA, Cogan JD, Rives LC, Robertson AK, Duncan L, Bican A, Peterson JF, Newman JH, Hamid R, Bastarache L. One is the loneliest number: genotypic matchmaking using the electronic health record. Genet Med 2021; 23:1830-1832. [PMID: 34230636 PMCID: PMC11140587 DOI: 10.1038/s41436-021-01179-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/05/2021] [Indexed: 01/02/2023] Open
Affiliation(s)
- Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leigh Anne Tang
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Josh F Peterson
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa Bastarache
- Center for Precision Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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37
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Matalonga L, Hernández-Ferrer C, Piscia D, Schüle R, Synofzik M, Töpf A, Vissers LELM, de Voer R, Tonda R, Laurie S, Fernandez-Callejo M, Picó D, Garcia-Linares C, Papakonstantinou A, Corvó A, Joshi R, Diez H, Gut I, Hoischen A, Graessner H, Beltran S. Solving patients with rare diseases through programmatic reanalysis of genome-phenome data. Eur J Hum Genet 2021; 29:1337-1347. [PMID: 34075210 PMCID: PMC8440686 DOI: 10.1038/s41431-021-00852-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/18/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022] Open
Abstract
Reanalysis of inconclusive exome/genome sequencing data increases the diagnosis yield of patients with rare diseases. However, the cost and efforts required for reanalysis prevent its routine implementation in research and clinical environments. The Solve-RD project aims to reveal the molecular causes underlying undiagnosed rare diseases. One of the goals is to implement innovative approaches to reanalyse the exomes and genomes from thousands of well-studied undiagnosed cases. The raw genomic data is submitted to Solve-RD through the RD-Connect Genome-Phenome Analysis Platform (GPAP) together with standardised phenotypic and pedigree data. We have developed a programmatic workflow to reanalyse genome-phenome data. It uses the RD-Connect GPAP's Application Programming Interface (API) and relies on the big-data technologies upon which the system is built. We have applied the workflow to prioritise rare known pathogenic variants from 4411 undiagnosed cases. The queries returned an average of 1.45 variants per case, which first were evaluated in bulk by a panel of disease experts and afterwards specifically by the submitter of each case. A total of 120 index cases (21.2% of prioritised cases, 2.7% of all exome/genome-negative samples) have already been solved, with others being under investigation. The implementation of solutions as the one described here provide the technical framework to enable periodic case-level data re-evaluation in clinical settings, as recommended by the American College of Medical Genetics.
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Affiliation(s)
- Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Hernández-Ferrer
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Davide Piscia
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Rebecca Schüle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research (HIH), University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Steven Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Daniel Picó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Carles Garcia-Linares
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Anastasios Papakonstantinou
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alberto Corvó
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ricky Joshi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Hector Diez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- European Reference Network for Rare Neurological Diseases, Tübingen, Germany
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain.
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38
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Doheny S. Recontacting in medical genetics: the implications of a broadening knowledge base. Hum Genet 2021; 141:1045-1051. [PMID: 34459979 PMCID: PMC9160136 DOI: 10.1007/s00439-021-02353-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
The practice of recontacting patients has a long history in medicine but emerged as an issue in genetics as the rapid expansion of knowledge and of testing capacity raised questions about whether, when and how to recontact patients. Until recently, the debate on recontacting has focussed on theoretical concerns of experts. The publication of empirical research into the views of patients, clinicians, laboratories and services in a number of countries has changed this. These studies have filled out, and altered our view of, this issue. Whereas debates on the duty to recontact have explored all aspects of recontact practice, recent contributions have been developing a more nuanced view of recontacting. The result is a narrowing of the scope of the duty, so that a norm on recontacting focuses on the practice of reaching out to discharged patients. This brings into focus the importance of the consent conversation, the resource implications of this duty, and the role of the patient in recontacting.
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Affiliation(s)
- Shane Doheny
- Cardiff University Institute of Cancer and Genetics, Cardiff, SGM, UK.
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39
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Haverfield EV, Esplin ED, Aguilar SJ, Hatchell KE, Ormond KE, Hanson-Kahn A, Atwal PS, Macklin-Mantia S, Hines S, Sak CWM, Tucker S, Bleyl SB, Hulick PJ, Gordon OK, Velsher L, Gu JYJ, Weissman SM, Kruisselbrink T, Abel C, Kettles M, Slavotinek A, Mendelsohn BA, Green RC, Aradhya S, Nussbaum RL. Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC Med 2021; 19:199. [PMID: 34404389 PMCID: PMC8371767 DOI: 10.1186/s12916-021-01999-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings. METHODS Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates' correction. RESULTS Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility. CONCLUSIONS This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.
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Affiliation(s)
| | | | | | | | - Kelly E Ormond
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Paldeep S Atwal
- Mayo Clinic, Jacksonville, FL, USA.,Atwal Clinic, Palm Beach, FL, USA.,PWNHealth, New York, NY, USA
| | | | | | | | | | | | | | - Ora K Gordon
- Providence Research Network, St John Cancer Institute, Los Angeles, CA, USA.,University of California, Los Angeles, CA, USA
| | | | | | - Scott M Weissman
- Genome Medical, San Francisco, CA, USA.,Chicago Genetic Consultants, Northbrook, IL, USA
| | | | | | | | - Anne Slavotinek
- University of California San Francisco, San Francisco, CA, USA
| | | | - Robert C Green
- Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA, 94103, USA.,Volunteer Faculty, University of California San Francisco, San Francisco, CA, USA
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40
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Wagner JK, Meyer MN. Genomic medicine and the "loss of chance" medical malpractice doctrine. HGG ADVANCES 2021; 2. [PMID: 34250511 PMCID: PMC8270012 DOI: 10.1016/j.xhgg.2021.100032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
As genomic medicine expands, interest in how medical malpractice law will apply to such questions as whether and when to return new or updated genomic results has grown. Given that access to some genomic results (such as those pertaining to minors or those for which scientific interpretations are unsettled) is delayed for years, the “loss of chance” (LOC) doctrine is of particular potential relevance. Yet it has received relatively little attention among scholars of law and genomics. We performed legal research to determine the status of this malpractice doctrine across the United States and consider its potential applicability to genomic medicine. We further examined known genomic medicine malpractices to assess whether this doctrine had yet been invoked in that context. We identified a trend toward adoption of the LOC doctrine, finding 29 states (58%) have adopted, 15 states (30%) have rejected, and six states (12%) have deferred or not yet addressed the doctrine. Attempts to invoke or apply the doctrine in the known genomic medical malpractice cases were also found. While our findings do not provide cause for substantial concern, the availability of the LOC medical malpractice doctrine is a potentially important factor to consider when making programmatic decisions for genomic medicine. Future research examining whether liability risks posed by this doctrine prompt defensive medicine practices would be useful.
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Affiliation(s)
- Jennifer K Wagner
- Center for Translational Bioethics and Health Care Policy, Geisinger, 100 N. Academy Ave., MC 30-42, Danville, PA 17822, USA
| | - Michelle N Meyer
- Center for Translational Bioethics and Health Care Policy, Geisinger, 100 N. Academy Ave., MC 30-42, Danville, PA 17822, USA.,Steele Institute for Health Innovation, Geisinger, 100 N. Academy Ave, Danville, PA 17822, USA
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41
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Abstract
Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA;
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42
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Abstract
PURPOSE OF REVIEW Perinatal disorders include stillbirth, congenital structural anomalies, and critical illnesses in neonates. The cause of these is often unknown despite a thorough clinical workup. Genetic diseases cause a significant portion of perinatal disorders. The purpose of this review is to describe recent advances in genetic testing of perinatal disorders of unknown cause and to provide a potential diagnostic strategy. RECENT FINDINGS Exome and genome sequencing (ES and GS) have demonstrated that significant portions of perinatal disorders are caused by genetic disease. However, estimates of the exact proportion have varied widely across fetal and neonatal cohorts and most of the genetic diagnoses found in recent studies have been unique to individual cases. Having a specific genetic diagnosis provides significant clinical utility, including improved prognostication of the outcome, tailored therapy, directed testing for associated syndromic manifestations, referral to appropriate subspecialists, family planning, and redirection of care. SUMMARY Perinatal disorders of unknown cause, with nonspecific presentations, are often caused by genetic diseases best diagnosed by ES or GS. Prompt diagnosis facilitates improved clinical care. Improvements in noninvasive sampling, variant interpretation, and population-level research will further enhance the clinical utility of genetic testing. VIDEO ABSTRACT http://links.lww.com/MOP/A61.
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Affiliation(s)
- Thomas Hays
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald J. Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, USA
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
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43
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Savarese M, Välipakka S, Johari M, Hackman P, Udd B. Is Gene-Size an Issue for the Diagnosis of Skeletal Muscle Disorders? J Neuromuscul Dis 2021; 7:203-216. [PMID: 32176652 PMCID: PMC7369045 DOI: 10.3233/jnd-190459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human genes have a variable length. Those having a coding sequence of extraordinary length and a high number of exons were almost impossible to sequence using the traditional Sanger-based gene-by-gene approach. High-throughput sequencing has partly overcome the size-related technical issues, enabling a straightforward, rapid and relatively inexpensive analysis of large genes. Several large genes (e.g. TTN, NEB, RYR1, DMD) are recognized as disease-causing in patients with skeletal muscle diseases. However, because of their sheer size, the clinical interpretation of variants in these genes is probably the most challenging aspect of the high-throughput genetic investigation in the field of skeletal muscle diseases. The main aim of this review is to discuss the technical and interpretative issues related to the diagnostic investigation of large genes and to reflect upon the current state of the art and the future advancements in the field.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Salla Välipakka
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland.,Neuromuscular Research Center, Tampere University and University Hospital, Tampere, Finland.,Department of Neurology, Vaasa Central Hospital, Vaasa, Finland
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44
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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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45
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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: 12] [Impact Index Per Article: 4.0] [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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46
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Perceptions of best practices for return of results in an international survey of psychiatric genetics researchers. Eur J Hum Genet 2020; 29:231-240. [PMID: 33011736 PMCID: PMC7532738 DOI: 10.1038/s41431-020-00738-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/02/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Many research sponsors and genetic researchers agree that some medically relevant genetic findings should be offered to participants. The scarcity of research specific to returning genetic results related to psychiatric disorders hinders the ability to develop ethically justified and empirically informed guidelines for responsible return of results for these conditions. We surveyed 407 psychiatric genetics researchers from 39 countries to examine their perceptions of challenges to returning individual results and views about best practices for the process of offering and returning results. Most researchers believed that disclosure of results should be delayed if a patient-participant is experiencing significant psychiatric symptoms. Respondents felt that there is little research on the impact of returning results to participants with psychiatric disorders and agreed that return of psychiatric genetics results to patient-participants may lead to discrimination by insurance companies or other third parties. Almost half of researchers believed results should be returned through a participant's treating psychiatrist, but many felt that clinicians lack knowledge about how to manage genetic research results. Most researchers thought results should be disclosed by genetic counselors or medical geneticists and in person; however, almost half also supported disclosure via telemedicine. This is the first global survey to examine the perspectives of researchers with experience working with this patient population and with these conditions. Their perspectives can help inform the development of much-needed guidelines to promote responsible return of results related to psychiatric conditions to patients with psychiatric disorders.
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47
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Roberts JL, Foulkes AL. GENETIC DUTIES. WILLIAM AND MARY LAW REVIEW 2020; 62:143-211. [PMID: 37654734 PMCID: PMC10471136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Most of our genetic information does not change, yet the results of our genetic tests might. Labs reclassify genetic variants in response to advances in genetic science. As a result, a person who took a test in 2010 could take the same test with the same lab in 2020 and get a different result. However, no legal duty requires labs or physicians to inform patients when a lab reclassifies a variant, even if the reclassification communicates clinically actionable information. This Article considers the need for such duties and their potential challenges. In so doing, it offers much-needed guidance to physicians and labs, who may face liability, and to courts, which will hear these cases.
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48
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Response to Faulkner et al. Genet Med 2020; 23:243. [PMID: 32873931 DOI: 10.1038/s41436-020-00955-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022] Open
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49
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Hays T, Groopman EE, Gharavi AG. Genetic testing for kidney disease of unknown etiology. Kidney Int 2020; 98:590-600. [PMID: 32739203 PMCID: PMC7784921 DOI: 10.1016/j.kint.2020.03.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/09/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
In many cases of chronic kidney disease, the cause of disease remains unknown despite a thorough nephrologic workup. Genetic testing has revolutionized many areas of medicine and promises to empower diagnosis and targeted management of such cases of kidney disease of unknown etiology. Recent studies using genetic testing have demonstrated that Mendelian etiologies account for approximately 20% of cases of kidney disease of unknown etiology. Although genetic testing has significant benefits, including tailoring of therapy, informing targeted workup, detecting extrarenal disease, counseling patients and families, and redirecting care, it also has important limitations and risks that must be considered.
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Affiliation(s)
- Thomas Hays
- Department of Pediatrics, Division of Neonatology and Perinatology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA; Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.
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Affiliation(s)
- Amy E Cyr
- Washington University School of Medicine, Box 8109, 660 South Euclid Avenue, Saint Louis, MO, 63110, USA.
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