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Wyatt Castillo RB, Nielsen SM, Chen E, Heald B, Ellsworth RE, Esplin ED, Tomlinson GE. Disparate Rates of Germline Variants in Cancer Predisposition Genes in African American/Black Compared With Non-Hispanic White Individuals Between 2015 and 2022. JCO Precis Oncol 2024; 8:e2300715. [PMID: 38991178 DOI: 10.1200/po.23.00715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/31/2024] [Indexed: 07/13/2024] Open
Abstract
PURPOSE African American/Black (AA/B) individuals are under-represented in genomic databases and thus less likely to receive definitive information from germline genetic testing (GGT) than non-Hispanic White (NHW) individuals. With nearly 500,000 AA/B and NHW individuals having undergone multigene panel testing (MGPT) for hereditary cancer risk at a single commercial laboratory, to our knowledge, we present the largest study to date investigating cancer GGT results in AA/B and NHW individuals. METHODS MGPT results from a retrospective cohort of AA/B (n = 48,684) and NHW (n = 444,831) patients were evaluated. Frequencies of pathogenic germline variants (PGVs) and variants of uncertain significance (VUS) were compared between AA/B and NHW individuals. Changes in frequency of VUS over time were determined. Pearson's chi-squared test was used to compare categorical variables among groups. All significance tests were two-tailed, and P < .05 was considered statistically significant. RESULTS Between 2015 and 2022, rates of VUS decreased 2.3-fold in AA/B and 1.8-fold in NHW individuals; however, frequencies of VUS and PGV remained significantly higher (46% v 32%; P < .0001) and lower (9% v 13%; P < .0001) in AA/B compared with NHW individuals. Rates of VUS in ATM, BRCA1, BRCA2, PALB2, and PMS2 were significantly higher in AA/B compared with NHW individuals, whereas rates of PGV in BRCA1, BRCA2, and PALB2 were higher in AA/B compared with NHW individuals (P < .001). CONCLUSION Despite reductions in VUS frequencies over time, disparities in definitive GGT results persist. Increasing inclusion of AA/B populations in both testing and research will further increase knowledge of genetic variants across these racial groups.
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Affiliation(s)
- Rachel B Wyatt Castillo
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
| | | | | | | | | | | | - Gail E Tomlinson
- Department of Pediatrics, UT Health San Antonio, San Antonio, TX
- Greehey Children's Cancer Research Institute, UT Health San Antonio, San Antonio, TX
- Mays Cancer Center, UT Health San Antonio, San Antonio, TX
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2
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Cragun D, Dean M, Baker D, Kelley M, Hooker G, Weidner A, Hunt P, Pal T. The Development and Evaluation of Novel Patient Educational Material for a Variant of Uncertain Significance (VUS) Result in Hereditary Cancer Genes. Curr Oncol 2024; 31:3361-3378. [PMID: 38920739 PMCID: PMC11202617 DOI: 10.3390/curroncol31060256] [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: 04/25/2024] [Revised: 05/30/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
A Variant of Uncertain Significance (VUS) is a difference in the DNA sequence with uncertain consequences for gene function. A VUS in a hereditary cancer gene should not change medical care, yet some patients undergo medical procedures based on their VUS result, highlighting the unmet educational needs among patients and healthcare providers. To address this need, we developed, evaluated, and refined novel educational materials to explain that while VUS results do not change medical care, it remains important to share any personal or family history of cancer with family members given that their personal and family medical history can guide their cancer risk management. We began by reviewing the prior literature and transcripts from interviews with six individuals with a VUS result to identify content and design considerations to incorporate into educational materials. We then gathered feedback to improve materials via a focus group of multidisciplinary experts and multiple rounds of semi-structured interviews with individuals with a VUS result. Themes for how to improve content, visuals, and usefulness were used to refine the materials. In the final round of interviews with an additional 10 individuals with a VUS result, materials were described as relatable, useful, factual, and easy to navigate, and also increased their understanding of cancer gene VUS results.
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Affiliation(s)
- Deborah Cragun
- College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Marleah Dean
- Department of Communication, University of South Florida, Tampa, FL 33620, USA
- Outcomes & Behavior Program, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - David Baker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Meghan Kelley
- Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Gillian Hooker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Anne Weidner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Paige Hunt
- College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
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3
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Horton RH, Macken WL, Pitceathly RDS, Lucassen AM. Discussion of off-target and tentative genomic findings may sometimes be necessary to allow evaluation of their clinical significance. JOURNAL OF MEDICAL ETHICS 2024; 50:295-298. [PMID: 37339848 PMCID: PMC11103297 DOI: 10.1136/jme-2023-109108] [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] [Received: 03/21/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
We discuss a case where clinical genomic investigation of muscle weakness unexpectedly found a genetic variant that might (or might not) predispose to kidney cancer. We argue that despite its off-target and uncertain nature, this variant should be discussed with the man who had the test, not because it is medical information, but because this discussion would allow the further clinical evaluation that might lead it to becoming so. We argue that while prominent ethical debates around genomics often take 'results' as a starting point and ask questions as to whether to look for and how to react to them, the construction of genomic results is fraught with ethical complexity, although often couched as a primarily technical problem. We highlight the need for greater focus on, and appreciation of, the ethical work undertaken daily by scientists and clinicians working in genomic medicine and discuss how public conversations around genomics need to adapt to prepare future patients for potentially uncertain and unexpected outcomes from clinical genomic tests.
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Affiliation(s)
- Rachel H Horton
- Clinical Ethics, Law and Society, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Centre for Personalised Medicine, St Anne's College, Oxford, UK
- Clinical Ethics, Law and Society, University of Southampton, Southampton, UK
| | - William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Anneke M Lucassen
- Clinical Ethics, Law and Society, Wellcome Trust Centre for Human Genetics, Oxford, UK
- Centre for Personalised Medicine, St Anne's College, Oxford, UK
- Clinical Ethics, Law and Society, University of Southampton, Southampton, UK
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4
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Roberts KJ, Chaves E, Ariza AJ, Thaker VV, Cho CC, Binns HJ. Exploring Genetic Testing for Rare Disorders of Obesity: Experience and Perspectives of Pediatric Weight Management Providers. Child Obes 2024. [PMID: 38227789 DOI: 10.1089/chi.2023.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Background: This study describes experiences and perspectives of pediatric weight management (PWM) providers on the implementation of genetic testing for rare causes of obesity. Methods: Purposive and snowball sampling recruited PWM providers via email to complete a 23-question survey with multiple choice and open-ended questions. Analyses include descriptive statistics, Fisher's exact test, one-way ANOVA with Tukey's post hoc test, and qualitative analysis. Results: Of the 55 respondents, 80% reported ordering genetic testing. Respondents were primarily physicians (82.8%) in practice for 11-20 years (42%), identified as female (80%), White (76.4%), and non-Hispanic (92.7%) and provided PWM care 1-4 half day sessions per week. Frequently reported patient characteristics that prompted testing did not vary by provider years of experience (YOE). These included obesity onset before age 6, hyperphagia, dysmorphic facies, and developmental delays. The number of patient characteristics that prompted testing varied by YOE (p = 0.03); respondents with 6-10 YOE indicated more patient characteristics than respondents with >20 YOE (mean 10.3 vs. mean 6.2). The reported primary benefit of testing was health information for patients/families; the primary drawback was the high number of indeterminate tests. Ethical concerns expressed were fear of increasing weight stigma, discrimination, and impact on insurance coverage. Respondents (42%) desired training and guidance on interpreting results and counseling patients and families. Conclusions: Most PWM providers reported genetic testing as an option for patient management. Provider training in genetics/genomics and research into provider and family attitudes on the genetics of obesity and the value of genetic testing are next steps to consider.
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Affiliation(s)
- Karyn J Roberts
- School of Nursing, College of Health Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Eileen Chaves
- Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Adolfo J Ariza
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Vidhu V Thaker
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chi C Cho
- School of Nursing, College of Health Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Helen J Binns
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
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5
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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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6
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Waung MW, Ma F, Wheeler AG, Zai CC, So J. The Diagnostic Landscape of Adult Neurogenetic Disorders. BIOLOGY 2023; 12:1459. [PMID: 38132285 PMCID: PMC10740572 DOI: 10.3390/biology12121459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Neurogenetic diseases affect individuals across the lifespan, but accurate diagnosis remains elusive for many patients. Adults with neurogenetic disorders often undergo a long diagnostic odyssey, with multiple specialist evaluations and countless investigations without a satisfactory diagnostic outcome. Reasons for these diagnostic challenges include: (1) clinical features of neurogenetic syndromes are diverse and under-recognized, particularly those of adult-onset, (2) neurogenetic syndromes may manifest with symptoms that span multiple neurological and medical subspecialties, and (3) a positive family history may not be present or readily apparent. Furthermore, there is a large gap in the understanding of how to apply genetic diagnostic tools in adult patients, as most of the published literature focuses on the pediatric population. Despite these challenges, accurate genetic diagnosis is imperative to provide affected individuals and their families guidance on prognosis, recurrence risk, and, for an increasing number of disorders, offer targeted treatment. Here, we provide a framework for recognizing adult neurogenetic syndromes, describe the current diagnostic approach, and highlight studies using next-generation sequencing in different neurological disease cohorts. We also discuss diagnostic pitfalls, barriers to achieving a definitive diagnosis, and emerging technology that may increase the diagnostic yield of testing.
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Affiliation(s)
- Maggie W. Waung
- Division of General Neurology, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | - Fion Ma
- Institute for Human Genetics, University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
| | - Allison G. Wheeler
- Institute for Human Genetics, University of California San Francisco School of Medicine, San Francisco, CA 94143, USA
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Clement C. Zai
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, Institute of Medical Science, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Joyce So
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, CA 94158, USA
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7
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Martorana D, Barili V, Uliana V, Ambrosini E, Riva M, De Sensi E, Luppi E, Messina C, Caleffi E, Pisani F, Percesepe A. Reassessment of the NF1 variants of unknown significance found during the 20-year activity of a genetics diagnostic laboratory. Eur J Med Genet 2023; 66:104847. [PMID: 37751797 DOI: 10.1016/j.ejmg.2023.104847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 07/05/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023]
Abstract
The finding of variants of uncertain significance (VUS) in the activity of a diagnostic genetic laboratory is a common issue, which is however provisional and needs to be periodically re-evaluated, due to the continuous advancements in our knowledge of the genetic diseases. Neurofibromatosis type 1, caused by the occurrence of heterozygous pathogenic NF1 variants, is a good model for studying the evolution of VUS, due to the widespread use of genetic testing for the disease, the constant enrichment of the international databases with NF1 variants and the full adult penetrance of the disease, which makes genotyping the parents a crucial step in the diagnostic workflow. The present study retrospectively reviewed and reinterpreted the genetic test results of NF1 in a diagnostic genetic laboratory in the period from January 1, 2000 to December 31, 2020. All the VUS were reinterpreted using the 2015 consensus standards and guidelines for the interpretation. Out of 589 NF1 genetic tests which were performed in the period, a total of 85 VUS were found and reinterpreted in 72 cases (84.7%): 21 (29.2%) were reclassified as benign/likely benign, whereas 51 (70.8%) were recoded as pathogenic/likely pathogenic with a significant trend distribution (Chi square test for trend p = 0.005). Synonymous VUS have mainly been reclassified as class 1 and 2 (7/8, 87.5%), whereas missense variants have been attributed to class 4 and 5 in 38 out of the 58 cases (65.5%). These findings underline an improvement in the classification of variants over time, suggesting that a reinterpretation of the genetic tests should be routinely performed to support the physicians in the clinical diagnosis of genetic diseases.
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Affiliation(s)
- Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy; CoreLAB Research Center, University Hospital of Parma, 43126, Italy
| | - Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Matteo Riva
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Elena Luppi
- Medical Genetics, University of Bologna, Italy
| | - Corinne Messina
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy
| | - Edoardo Caleffi
- Plastic Surgery, University Hospital of Parma, 43126, Parma, Italy
| | - Francesco Pisani
- Children's Neuropsychological Services, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Percesepe
- Medical Genetics, University Hospital of Parma, 43126, Parma, Italy; Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy.
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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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Núñez-Núñez ME, Lona-Reyes JC, López-Barragán B, Cruz-Osorio RM, Gutiérrez-Zepeda BM, Quintero-Ramos A, Becerra-Loaiza DS. Case Report: Characterization of known (c.607G>C) and novel (c.416C>G) ELANE mutations in two Mexican families with congenital neutropenia. Front Immunol 2023; 14:1194262. [PMID: 37795094 PMCID: PMC10547563 DOI: 10.3389/fimmu.2023.1194262] [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: 03/26/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023] Open
Abstract
The most common causes of congenital neutropenia are mutations in the ELANE (Elastase, Neutrophil Expressed) gene (19p13.3), mostly in exon 5 and the distal portion of exon 4, which result in different clinical phenotypes of neutropenia. Here, we report two pathogenic mutations in ELANE, namely, c.607G>C (p.Gly203Arg) and a novel variant c.416C>G (p.Pro139Arg), found in two Mexican families ascertained via patients with congenital neutropenia who responded positively to the granulocyte colony-stimulating factor (G-CSF) treatment. These findings highlight the usefulness of identifying variants in patients with inborn errors of immunity for early clinical management and the need to rule out mosaicism in noncarrier parents with more than one case in the family.
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Affiliation(s)
- María Enriqueta Núñez-Núñez
- Departamento de Alergia e Inmunología Clínica Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Juan Carlos Lona-Reyes
- Departamento de Infectología, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Brenda López-Barragán
- Departamento de Pediatría, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Rosa Margarita Cruz-Osorio
- Clínicas de Pediatría, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Departamento de Hemato-Oncología Pediátrica, Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Guadalajara, Mexico
| | - Bricia Melissa Gutiérrez-Zepeda
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Antonio Quintero-Ramos
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Investigación Biomédica 02, Hospital de Especialidades, Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | - Denisse Stephania Becerra-Loaiza
- Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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10
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Coad B, Joekes K, Rudnicka A, Frost A, Openshaw MR, Tatton-Brown K, Snape K. Evaluation of two Massive Open Online Courses (MOOCs) in genomic variant interpretation for the NHS workforce. BMC MEDICAL EDUCATION 2023; 23:540. [PMID: 37507729 PMCID: PMC10386229 DOI: 10.1186/s12909-023-04406-x] [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] [Received: 10/18/2022] [Accepted: 05/26/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND The implementation of the National Genomic Medicine Service in the UK has increased patient access to germline genomic testing. Increased testing leads to more genetic diagnoses but does result in the identification of genomic variants of uncertain significance (VUS). The rigorous process of interpreting these variants requires multi-disciplinary, highly trained healthcare professionals (HCPs). To meet this training need, we designed two Massive Open Online Courses (MOOCs) for HCPs involved in germline genomic testing pathways: Fundamental Principles (FP) and Inherited Cancer Susceptibility (ICS). METHODS An evaluation cohort of HCPs involved in genomic testing were recruited, with additional data also available from anonymous self-registered learners to both MOOCs. Pre- and post-course surveys and in-course quizzes were used to assess learner satisfaction, confidence and knowledge gained in variant interpretation. In addition, granular feedback was collected on the complexity of the MOOCs to iteratively improve the resources. RESULTS A cohort of 92 genomics HCPs, including clinical scientists, and non-genomics clinicians (clinicians working in specialties outside of genomics) participated in the evaluation cohort. Between baseline and follow-up, total confidence scores improved by 38% (15.2/40.0) (95% confidence interval [CI] 12.4-18.0) for the FP MOOC and 54% (18.9/34.9) (95%CI 15.5-22.5) for the ICS MOOC (p < 0.0001 for both). Of those who completed the knowledge assessment through six summative variant classification quizzes (V1-6), a mean of 79% of respondents classified the variants such that correct clinical management would be undertaken (FP: V1 (73/90) 81% Likely Pathogenic/Pathogenic [LP/P]; V2 (55/78) 70% VUS; V3 (59/75) 79% LP/P; V4 (62/72) 86% LP/LP. ICS: V5 (66/91) 73% VUS; V6 (76/88) 86% LP/P). A non-statistically significant higher attrition rate was seen amongst the non-genomics workforce when compared to genomics specialists for both courses. More participants from the non-genomics workforce rated the material as "Too Complex" (FP n = 2/7 [29%], ICS n = 1/5 [20%]) when compared to the specialist genomics workforce (FP n = 1/43 [2%], ICS n = 0/35 [0%]). CONCLUSIONS After completing one or both MOOCs, self-reported confidence in genomic variant interpretation significantly increased, and most respondents could correctly classify variants such that appropriate clinical management would be instigated. Genomics HCPs reported higher satisfaction with the level of content than the non-genomics clinicians. The MOOCs provided foundational knowledge and improved learner confidence, but should be adapted for different workforces to maximise the benefit for clinicians working in specialties outside of genetics.
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Affiliation(s)
- Beth Coad
- St George's University of London, London, UK.
| | | | | | - Amy Frost
- National Genomics Education, NHS England, London, UK
| | | | | | - Katie Snape
- St George's University of London, London, UK
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11
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Ahimaz P, Foltz JC, Ross MJ, Florido ME, Sebastin M, Yu JE. Exploring the role of genetic counselors in immunology: A study of immunologist and allergist perspectives. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:1939-1942.e2. [PMID: 36787825 DOI: 10.1016/j.jaip.2023.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/16/2023]
Affiliation(s)
- Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY; Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, NY.
| | - Jennah C Foltz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Meredith J Ross
- Division of Clinical Genetics, Department of Pediatrics, Columbia University, New York, NY
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY; Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Monisha Sebastin
- Division of Clinical Genetics, Department of Pediatrics, Montefiore Medical Center, New York, NY
| | - Joyce E Yu
- Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, Columbia University, New York, NY
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12
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Nguyen Dolphyn TT, Ormond KE, Weissman SM, Kim HJ, Reuter CM. Patient experiences with clinical confirmatory genetic testing after using direct-to-consumer raw DNA and third-party genetic interpretation services. Transl Behav Med 2023; 13:104-114. [PMID: 36327324 DOI: 10.1093/tbm/ibac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The availability of raw DNA and genetic interpretation tools allow individuals to access genetic health risk information, where analytical false-positives exist. Little is known about the experience of individuals who receive pathogenic or likely pathogenic variant(s) through raw DNA interpretation and follow-up with clinical confirmatory genetic testing. This qualitative study set out to describe the experiences of individuals who pursued clinical confirmatory genetic testing, including their perception of the process. Participants were recruited from social media and eligible if they discovered a potential pathogenic or likely pathogenic variant in a raw DNA interpretation report, completed clinical confirmatory genetic testing in the U.S., and provided documentation of those results. Individuals participated in semi-structured interviews, which were transcribed and inductively coded to identify themes. Of the 12 participants, 3 received clinical genetic testing results that confirmed pathogenic or likely pathogenic variants noted in raw DNA interpretation reports (confirmation positive), and 9 were not confirmed. Nearly all (n = 11) participants described emotional distress and information-seeking behavior as a coping mechanism after discovering a pathogenic or likely pathogenic variant in raw DNA interpretation. When pursuing confirmatory genetic testing, many (n = 9) faced challenges with finding knowledgeable healthcare providers and obtaining insurance coverage. Despite reporting concerns over raw DNA interpretation and a desire for more safeguards, almost all (n = 10) participants stated interest in using the service again. Overall, participants' experiences reveal they find personal utility in raw DNA interpretation results and provide insight into opportunities for patient and provider education.
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Affiliation(s)
- Tiffany T Nguyen Dolphyn
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA.,Stanford Medicine Clinical Genomics Program, Stanford School of Medicine, Stanford University, Stanford, California, 94305, USA
| | - Kelly E Ormond
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA.,Department of Genetics and Stanford Center for Biomedical Ethics, Stanford School of Medicine, Stanford University, Stanford, California, 94305, USA.,Health Ethics and Policy Lab, Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | | | - Helen J Kim
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA
| | - Chloe M Reuter
- Stanford Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, California, 94305, USA
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13
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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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Arbustini E, Behr ER, Carrier L, van Duijn C, Evans P, Favalli V, van der Harst P, Haugaa KH, Jondeau G, Kääb S, Kaski JP, Kavousi M, Loeys B, Pantazis A, Pinto Y, Schunkert H, Di Toro A, Thum T, Urtis M, Waltenberger J, Elliott P. Interpretation and actionability of genetic variants in cardiomyopathies: a position statement from the European Society of Cardiology Council on cardiovascular genomics. Eur Heart J 2022; 43:1901-1916. [PMID: 35089333 DOI: 10.1093/eurheartj/ehab895] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/03/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
This document describes the contribution of clinical criteria to the interpretation of genetic variants using heritable Mendelian cardiomyopathies as an example. The aim is to assist cardiologists in defining the clinical contribution to a genetic diagnosis and the interpretation of molecular genetic reports. The identification of a genetic variant of unknown or uncertain significance is a limitation of genetic testing, but current guidelines for the interpretation of genetic variants include essential contributions from clinical family screening that can establish a de novo assignment of the variant or its segregation with the phenotype in the family. A partnership between clinicians and patients helps to solve major uncertainties and provides reliable and clinically actionable information.
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Affiliation(s)
- Eloisa Arbustini
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elijah R Behr
- Cardiology Research Section and Cardiovascular Clinical Academic Group, Institute of Molecular and Clinical Sciences, St George's, University of London and St George's University Hospitals NHS Foundation Trust, London, UK
| | - Lucie Carrier
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Cornelia van Duijn
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Paul Evans
- Department of Infection, Immunity and Cardiovascular Disease, and INSIGNEO Institute, University of Sheffield, Sheffield S10 2RX, UK
| | | | - Pim van der Harst
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kristina Hermann Haugaa
- ProCardio Center for Innovation, Department of Cardiology, Oslo University Hospital, Rikshospitalet, Postboks 4950 Nydalen, Oslo 0424, Norway
- University of Oslo, Boks 1072 Blindern, Oslo 0316, Norway
| | - Guillaume Jondeau
- CNMR Syndrome de Marfan et apparentés, Member of VASCERN, AP-HP Hopital Bichat, Service de Cardiologie, 46 rue Henri Huchard, Paris 75018, France
- INSERM LVTS U1148, Paris 75018, France
- Université de Paris, Paris, France
| | - Stefan Kääb
- Medizinische Klinik und Poliklinik I, LMU University Hospital Munich, Munich, Germany
- German Center for Cardiovascular Research, Munich Heart Alliance, Munich, Germany
| | - Juan Pablo Kaski
- Institute of Cardiovascular Science, University College London, London, UK
- Centre for Inherited Cardiovascular Diseases, Great Ormond Street Hospital, London, UK
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bart Loeys
- Cardiogenomics, Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Antonis Pantazis
- The Royal Brompton and Harefield Hospitals, Part of Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Yigal Pinto
- Department of Experimental Cardiology, University of Amsterdam, Amsterdam University Medical Center, Meibergdreef 15, Amsterdam 1105 AZ, The Netherlands
| | - Heribert Schunkert
- Department of Cardiology, Deutsches Herzzentrum München, Technische Universität München, München, Germany
- Deutsches Zentrum für Herz- und Kreislaufforschung (DZHK), Munich Heart Alliance, Munich, Germany
| | - Alessandro Di Toro
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
- Fraunhofer Institute of Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - Mario Urtis
- Transplant Research Area and Centre for Inherited Cardiovascular Diseases, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Johannes Waltenberger
- Department of Cardiology and Cardiovascular Medicine, Medical Faculty, University of Münster, Münster, Germany
- Cardiovascular Medicine, Hirslanden Klinik Im Park, Seestrasse 220, Zürich 8027, Switzerland
| | - Perry Elliott
- Barts Heart Centre St Bartholomew's Hospital, London, UK
- Institute for Cardiovascular Science, University College London, London, UK
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15
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Dettwyler SA, Thull DL, McAuliffe PF, Steiman JG, Johnson RR, Diego EJ, Mai PL. Timely cancer genetic counseling and testing for young women with breast cancer: impact on surgical decision-making for contralateral risk-reducing mastectomy. Breast Cancer Res Treat 2022; 194:393-401. [PMID: 35596825 DOI: 10.1007/s10549-022-06619-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/25/2022] [Indexed: 01/02/2023]
Abstract
PURPOSE Genetic testing (GT) can identify individuals with pathogenic/likely pathogenic variants (PV/LPVs) in breast cancer (BC) predisposition genes, who may consider contralateral risk-reducing mastectomy (CRRM). We report on CRRM rates in young women newly diagnosed with BC who received GT through a multidisciplinary clinic. METHODS Clinical data were reviewed for patients seen between November 2014 and June 2019. Patients with non-metastatic, unilateral BC diagnosed at age ≤ 45 and completed GT prior to surgery were included. Associations between surgical intervention and age, BC stage, family history, and GT results were evaluated. RESULTS Of the 194 patients, 30 (15.5%) had a PV/LPV in a BC predisposition gene (ATM, BRCA1, BRCA2, CHEK2, NBN, NF1), with 66.7% in BRCA1 or BRCA2. Of 164 (84.5%) uninformative results, 132 (68%) were negative and 32 (16.5%) were variants of uncertain significance (VUS). Overall, 67 (34.5%) had CRRM, including 25/30 (83.3%) PV/LPV carriers and 42/164 (25.6%) non-carriers. A positive test result (p < 0.01) and significant family history were associated with CRRM (p = 0.02). For the 164 with uninformative results, multivariate analysis showed that CRRM was not associated with age (p = 0.23), a VUS, (p = 0.08), family history (p = 0.10), or BC stage (p = 0.11). CONCLUSION In this cohort of young women with BC, the identification of a PV/LPV in a BC predisposition gene and a significant family history were associated with the decision to pursue CRRM. Thus, incorporation of genetic services in the initial evaluation of young patients with a new BC could contribute to the surgical decision-making process.
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Affiliation(s)
- Shenin A Dettwyler
- UPMC Magee-Womens Hospital (Cancer Genetics Program), Pittsburgh, PA, USA. .,Currently at NYU Langone Health (The Pancreatic Cancer Center), New York, NY, USA.
| | - Darcy L Thull
- UPMC Magee-Womens Hospital (Cancer Genetics Program), Pittsburgh, PA, USA
| | | | - Jennifer G Steiman
- UPMC Magee-Womens Hospital (Magee-Womens Surgical Associates), Pittsburgh, PA, USA
| | - Ronald R Johnson
- UPMC Magee-Womens Hospital (Magee-Womens Surgical Associates), Pittsburgh, PA, USA
| | - Emilia J Diego
- UPMC Magee-Womens Hospital (Magee-Womens Surgical Associates), Pittsburgh, PA, USA
| | - Phuong L Mai
- University of Pittsburgh School of Medicine (Center for Clinical Genetics and Genomics), Pittsburgh, PA, USA
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16
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Recchia G, Lawrence ACE, Capacchione L, Freeman ALJ. Making BRCA1 genetic test reports easier to understand through user-centered design: A randomized trial. Genet Med 2022; 24:1684-1696. [PMID: 35522238 DOI: 10.1016/j.gim.2022.04.016] [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: 12/14/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Our objective was to apply a user-centered design process to identify phrases, graphics, and ways of communicating numerical risks that could be used to help patients understand their cancer risk and next steps on receiving BRCA1 genetic test results (positive, negative, and variants of uncertain significance). METHODS The first phase of the study, a user-centered design process, consisted of 4 rounds of interviews (N = 42, including 13 health care professionals and 16 patients having undergone BRCA testing). The second was a randomized, between-participants experimental study of 456 United Kingdom residents that compared the resulting reports to reports used in a United Kingdom national genomic laboratory hub. Outcomes were subjective and objective comprehension, communication efficacy, actionability, and perceived risk. RESULTS Subjective comprehension, communication efficacy, and actionability were all higher for the user-centered reports, with no difference in perceived risk. Comprehension of participants viewing user-centered reports was significantly better on 2 items, directionally (but not significantly) better on 6 items, and directionally (but not significantly) worse on 2 items. CONCLUSION Our results imply that user-centered design is a promising approach for developing materials about complex genetic risks. We suggest wordings that are likely to lead to improved comprehension when communicating BRCA-associated risks.
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Affiliation(s)
- Gabriel Recchia
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom.
| | - Alice C E Lawrence
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom
| | | | - Alexandra L J Freeman
- Winton Centre for Risk and Evidence Communication, Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, United Kingdom
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Bokkers K, Vlaming M, Engelhardt EG, Zweemer RP, van Oort IM, Kiemeney LALM, Bleiker EMA, Ausems MGEM. The Feasibility of Implementing Mainstream Germline Genetic Testing in Routine Cancer Care-A Systematic Review. Cancers (Basel) 2022; 14:cancers14041059. [PMID: 35205807 PMCID: PMC8870548 DOI: 10.3390/cancers14041059] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Germline genetic testing for patients with cancer can have important implications for treatment, preventive options, and for family members. In a mainstream genetic testing pathway, pre-test counseling is performed by non-genetic healthcare professionals, thereby making genetic testing more accessible to all patients who might benefit from it. These mainstream genetic testing pathways are being implemented in different hospitals around the world, and for different cancer types. It is important to evaluate how a mainstream genetic testing pathway can be made sustainable and if quality of genetic care is maintained. We show in this systematic review that it is feasible to incorporate a mainstream genetic testing pathway into routine cancer care while maintaining quality of care. A training procedure for non-genetic healthcare professionals and a close collaboration between genetics and other clinical departments are highly recommended to ensure sustainability. Abstract Background: Non-genetic healthcare professionals can provide pre-test counseling and order germline genetic tests themselves, which is called mainstream genetic testing. In this systematic review, we determined whether mainstream genetic testing was feasible in daily practice while maintaining quality of genetic care. Methods: PubMed, Embase, CINAHL, and PsychINFO were searched for articles describing mainstream genetic testing initiatives in cancer care. Results: Seventeen articles, reporting on 15 studies, met the inclusion criteria. Non-genetic healthcare professionals concluded that mainstream genetic testing was possible within the timeframe of a routine consultation. In 14 studies, non-genetic healthcare professionals completed some form of training about genetics. When referral was coordinated by a genetics team, the majority of patients carrying a pathogenic variant were seen for post-test counseling by genetic healthcare professionals. The number of days between cancer diagnosis and test result disclosure was always lower in the mainstream genetic testing pathway than in the standard genetic testing pathway (e.g., pre-test counseling at genetics department). Conclusions: Mainstream genetic testing seems feasible in daily practice with no insurmountable barriers. A structured pathway with a training procedure is desirable, as well as a close collaboration between genetics and other clinical departments.
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Affiliation(s)
- Kyra Bokkers
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
| | - Michiel Vlaming
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
| | - Ellen G. Engelhardt
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (E.G.E.); (E.M.A.B.)
| | - Ronald P. Zweemer
- Department of Gynecological Oncology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands;
| | - Inge M. van Oort
- Department of Urology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands; (I.M.v.O.); (L.A.L.M.K.)
| | - Lambertus A. L. M. Kiemeney
- Department of Urology, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands; (I.M.v.O.); (L.A.L.M.K.)
- Department for Health Evidence, Radboud University Medical Center, Geert Grooteplein Zuid 21, 6525 EZ Nijmegen, The Netherlands
| | - Eveline M. A. Bleiker
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; (E.G.E.); (E.M.A.B.)
- Department of Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- Family Cancer Clinic, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands; (K.B.); (M.V.)
- Correspondence: ; Tel.: +31-88-75-538-00
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18
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Szymaniak BM, Facchini LA, Kelsten MF, Cheng HH, Morgans AK. Operationalizing Genetic Testing in the Care of Patients with Prostate Cancer. Urol Oncol 2022. [DOI: 10.1007/978-3-030-89891-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Carter AB, Abruzzo LV, Hirschhorn JW, Jones D, Jordan DC, Nassiri M, Ogino S, Patel NR, Suciu CG, Temple-Smolkin RL, Zehir A, Roy S. Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group. J Mol Diagn 2021; 24:1-17. [PMID: 34656760 DOI: 10.1016/j.jmoldx.2021.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 02/09/2023] Open
Abstract
The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results. The Association for Molecular Pathology Electronic Health Record Working Group was convened to assess the challenges and opportunities and to recommend solutions on ways to resolve current problems associated with the display and use of genomic data in electronic health records.
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Affiliation(s)
- Alexis B Carter
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Children's Healthcare of Atlanta, Atlanta, Georgia.
| | - Lynne V Abruzzo
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Julie W Hirschhorn
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Medical University of South Carolina, Charleston, South Carolina
| | - Dan Jones
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; The Ohio State University Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, Columbus, Ohio
| | | | - Mehdi Nassiri
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Shuji Ogino
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Brigham & Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Nimesh R Patel
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, Rhode Island
| | - Christopher G Suciu
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Institute for Informatics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Ahmet Zehir
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Somak Roy
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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20
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Buckenmaier SS, Mollica MA, Freedman A, Kent EE, de Moor JS. Information Sources Used by Oncologists to Understand Multi-marker Tumor Panel Tests for Cancer Patients. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2021; 36:1105-1114. [PMID: 32415436 DOI: 10.1007/s13187-020-01742-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Precision medicine using multi-marker tumor panel (MMTP) testing can help inform cancer treatment decisions. Oncologists' knowledge of these tests and their ability to find up-to-date information about their application in clinical care is essential. This study aimed to (1) describe information sources used by oncologists to learn about new genomic tests and (2) examine characteristics associated with the use of each information source. The National Cancer Institute's National Survey of Precision Medicine in Cancer Treatment surveyed a nationally representative sample of oncologists about MMTP testing. We examined the use of 11 information sources among oncologists that reported using MMTP tests (n = 1222). Bivariate analyses were used to examine whether information sources differed by oncologist- and practice-level characteristics and type of MMTP test. Most oncologists reported using peer-reviewed medical literature (88.8%), scientific conferences (87.9%), and medical professional societies (83.8%) to learn about MMTPs. In contrast, government websites, FDA inserts, and foundation resources were each used by < 36% of oncologists. The use of information sources differed by oncologist and practice characteristics. For example, a greater percentage of oncologists with an academic affiliation used peer-reviewed medical literature and scientific conferences, as compared to those without an academic affiliation (p = 0.006). As the number and type of MMTP tests increase, providing oncologists with current information about their appropriate application is essential. Further understanding of how oncologists use specific information sources may improve the dissemination and effective implementation of new MMTPs and help tailor educational interventions based on provider characteristics.
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Affiliation(s)
- Susan S Buckenmaier
- Division of Cancer Control and Population Sciences, Healthcare Delivery Research Program, Outcomes Research Branch, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892-9762, USA.
| | - Michelle A Mollica
- Division of Cancer Control and Population Sciences, Healthcare Delivery Research Program, Outcomes Research Branch, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892-9762, USA
| | - Andrew Freedman
- Division of Cancer Control and Population Sciences, Epidemiology and Genomics Research Program, Clinical and Translational Epidemiology Branch, 9609 Medical Center Drive, Bethesda, MD, 20892-9762, USA
| | - Erin E Kent
- Department of Health Policy and Management, University of North Carolina, Chapel Hill, NC, USA
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Janet S de Moor
- Division of Cancer Control and Population Sciences, Healthcare Delivery Research Program, 9609 Medical Center Drive, Bethesda, MD, 20892-9762, USA
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21
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Sarquella-Brugada G, Fernandez-Falgueras A, Cesar S, Arbelo E, Coll M, Perez-Serra A, Puigmulé M, Iglesias A, Alcalde M, Vallverdú-Prats M, Fiol V, Ferrer-Costa C, Del Olmo B, Picó F, Lopez L, García-Alvarez A, Jordà P, Tiron de Llano C, Toro R, Grassi S, Oliva A, Brugada J, Brugada R, Campuzano O. Clinical impact of rare variants associated with inherited channelopathies: a 5-year update. Hum Genet 2021; 141:1579-1589. [PMID: 34546463 PMCID: PMC9522753 DOI: 10.1007/s00439-021-02370-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022]
Abstract
A proper interpretation of the pathogenicity of rare variants is crucial before clinical translation. Ongoing addition of new data may modify previous variant classifications; however, how often a reanalysis is necessary remains undefined. We aimed to extensively reanalyze rare variants associated with inherited channelopathies originally classified 5 years ago and its clinical impact. In 2016, rare variants identified through genetic analysis were classified following the American College of Medical Genetics and Genomics’ recommendations. Five years later, we have reclassified the same variants following the same recommendations but including new available data. Potential clinical implications were discussed. Our cohort included 49 cases of inherited channelopathies diagnosed in 2016. Update show that 18.36% of the variants changed classification mainly due to improved global frequency data. Reclassifications mostly occurred in minority genes associated with channelopathies. Similar percentage of variants remain as deleterious nowadays, located in main known genes (SCN5A, KCNH2 and KCNQ1). In 2016, 69.38% of variants were classified as unknown significance, but now, 53.06% of variants are classified as such, remaining the most common group. No management was modified after translation of genetic data into clinics. After 5 years, nearly 20% of rare variants associated with inherited channelopathies were reclassified. This supports performing periodic reanalyses of no more than 5 years since last classification. Use of newly available data is necessary, especially concerning global frequencies and family segregation. Personalized clinical translation of rare variants can be crucial to management if a significant change in classification is identified.
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Affiliation(s)
- Georgia Sarquella-Brugada
- Medical Science Department, School of Medicine, University of Girona, C/ Emili Grahit 77, 17003, Girona, Catalunya, Spain.,Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Anna Fernandez-Falgueras
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Cardiology Service, Hospital Josep Trueta, University of Girona, Girona, Spain
| | - Sergi Cesar
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Elena Arbelo
- Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Mónica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Alexandra Perez-Serra
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Marta Puigmulé
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Mireia Alcalde
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | | | - Victoria Fiol
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | | | - Bernat Del Olmo
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ferran Picó
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Laura Lopez
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ana García-Alvarez
- Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Paloma Jordà
- Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | | | - Rocío Toro
- Medicine Department, School of Medicine, Cádiz, Spain
| | - Simone Grassi
- Institute of Public Health, Section Legal Medicine, Catholic University, Rome, Italy
| | - Antonio Oliva
- Institute of Public Health, Section Legal Medicine, Catholic University, Rome, Italy
| | - Josep Brugada
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.,Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Ramon Brugada
- Medical Science Department, School of Medicine, University of Girona, C/ Emili Grahit 77, 17003, Girona, Catalunya, Spain. .,Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain. .,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain. .,Cardiology Service, Hospital Josep Trueta, University of Girona, Girona, Spain.
| | - Oscar Campuzano
- Medical Science Department, School of Medicine, University of Girona, C/ Emili Grahit 77, 17003, Girona, Catalunya, Spain. .,Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain. .,Centro de Investigación Biomédica en Red. Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
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22
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Makhnoon S, Bednar EM, Krause KJ, Peterson SK, Lopez-Olivo MA. Clinical management among individuals with variant of uncertain significance in hereditary cancer: A systematic review and meta-analysis. Clin Genet 2021; 100:119-131. [PMID: 33843052 PMCID: PMC8672382 DOI: 10.1111/cge.13966] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 12/01/2022]
Abstract
Improper medical use of variant of uncertain significance (VUS) remains a concern in hereditary cancer genetic testing. The goal of this study was to assess the association between pathogenic and likely pathogenic (P/LP), VUS, and benign and likely benign (B/LB) genetic test results and cancer-related surgical and screening management. Systematic searches of Medline, Embase, EBSCO CINAHL Plus, and PsycINFO were conducted from 1946 to August 26, 2020. Eligible studies included individuals with cancer genetic test result and surgical or screening management outcomes. We reviewed 885 abstracts and 22 studies that reported relevant surgical and screening outcomes were included. Meta-analysis revealed significantly higher surgical rates among individuals with P/LP than among those with VUS for therapeutic mastectomy with contralateral prophylactic mastectomy (OR = 7.35, 95% CI, 4.14-13.64), prophylactic mastectomy (OR = 3.05, 95% CI, 1.5-6.19), and oophorectomy (OR = 6.46, 95% CI, 3.64-11.44). There were no significant differences in therapeutic mastectomy, or breast conservation or lumpectomy rates between individuals with P/LP and VUS, or in any outcomes between patients with VUS and B/LB. Studies evaluating screening outcomes were limited, and results were conflicting. Comprehensive analysis do not indicate that a significant number of individuals with VUS results undergo inappropriate clinical management.
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Affiliation(s)
- Sukh Makhnoon
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Erica M. Bednar
- Clinical Cancer Genetics and the Cancer Prevention and Control Platform, Moon Shots Program, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kate J. Krause
- Research Medical Library, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Susan K. Peterson
- Department of Behavioral Science, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria A. Lopez-Olivo
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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23
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Berrios C, Hurley EA, Willig L, Thiffault I, Saunders C, Pastinen T, Goggin K, Farrow E. Challenges in genetic testing: clinician variant interpretation processes and the impact on clinical care. Genet Med 2021; 23:2289-2299. [PMID: 34257423 DOI: 10.1038/s41436-021-01267-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/24/2023] Open
Abstract
PURPOSE Efforts have been made to standardize laboratory variant interpretation, but clinicians are ultimately tasked with clinical correlation and application of genetic test results in patient care. This study aimed to explore processes clinicians utilize when reviewing and returning genetic test results, and how they impact patient care. METHODS Medical geneticists, genetic counselors, and nongenetics clinicians from two Midwestern states completed surveys (n = 98) and in-depth interviews (n = 29) on practices of reviewing and returning genetic test results. Retrospective chart review (n = 130) examined discordant interpretations and the impact on care. RESULTS Participants reported variable behaviors in both reviewing and returning results based on factors such as confidence, view of role, practice setting, and relationship with the lab. Providers did not report requesting changes to variant classifications from laboratories, but indicated relaying conflicting classifications to patients in some cases. Chart reviews revealed medically impactful differences in interpretation between laboratories and clinicians in 18 (13.8%) records. CONCLUSION Clinician practices for reviewing and integrating genetic test results into patient care vary within and between specialties and impact patient care. Strategies to better incorporate both laboratory and clinician expertise into interpretation of genetic results could result in improved care across providers and settings.
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Affiliation(s)
- Courtney Berrios
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA. .,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.
| | - Emily A Hurley
- University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Health Services and Outcomes Research, Children's Mercy Hospital, Kansas City, MO, USA.,University of Kansas Medical Center, Kansas City, MO, USA
| | - Laurel Willig
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Nephrology, Children's Mercy Hospital, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Carol Saunders
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Kathy Goggin
- University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Health Services and Outcomes Research, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Pharmacy, Kansas City, MO, USA
| | - Emily Farrow
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City School of Medicine, Kansas City, MO, USA.,Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA
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24
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Pediatric Oncologists' Experiences Returning and Incorporating Genomic Sequencing Results into Cancer Care. J Pers Med 2021; 11:jpm11060570. [PMID: 34207141 PMCID: PMC8235493 DOI: 10.3390/jpm11060570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 11/27/2022] Open
Abstract
Pediatric oncologists’ perspectives around returning and incorporating tumor and germline genomic sequencing (GS) results into cancer care are not well-described. To inform optimization of cancer genomics communication, we assessed oncologists’ experiences with return of genomic results (ROR), including their preparation/readiness for ROR, collaboration with genetic counselors (GCs) during ROR, and perceived challenges. The BASIC3 study paired pediatric oncologists with GCs to return results to patients’ families. We thematically analyzed 24 interviews with 12 oncologists at two post-ROR time points. Oncologists found pre-ROR meetings with GCs and geneticists essential to interpreting patients’ reports and communicating results to families. Most oncologists took a collaborative ROR approach where they discussed tumor findings and GCs discussed germline findings. Oncologists perceived many roles for GCs during ROR, including answering families’ questions and describing information in lay language. Challenges identified included conveying uncertain information in accessible language, limits of oncologists’ genetics expertise, and navigating families’ emotional responses. Oncologists emphasized how GCs’ and geneticists’ support was essential to ROR, especially for germline findings. GS can be successfully integrated into cancer care, but to account for the GC shortage, alternative ROR models and access to genetics resources will be needed to better support families and avoid burdening oncologists.
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25
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Richmond CM, James PA, Pantaleo SJ, Chong B, Lunke S, Tan TY, Macciocca I. Clinical and laboratory reporting impact of ACMG-AMP and modified ClinGen variant classification frameworks in MYH7-related cardiomyopathy. Genet Med 2021; 23:1108-1115. [PMID: 33568804 DOI: 10.1038/s41436-021-01107-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/29/2022] Open
Abstract
PURPOSE ClinGen provides gene-specific guidance for interpretation of sequence variants in MYH7. We assessed laboratory and clinical impact of reclassification by the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) and ClinGen recommendations in 43 MYH7 variants reported by a diagnostic laboratory between 2013 and 2017. METHODS Fifty-two proband reports containing MYH7 variants were reinterpreted by original ACMG-AMP and ClinGen guidelines. Evidence items were compared across schemes and reasons for classification differences recorded. Laboratory impact was assessed by number of recommended report reissues, and reclassifications coded as clinically "actionable" or "equivalent." Available pedigrees were reviewed to describe projected cascade impact. RESULTS ClinGen produced a higher proportion of diagnostic classifications (65% of variants) compared with ACMG-AMP (54%) and fewer variants of uncertain significance (30% versus 42%). ClinGen classification resulted in actionable changes in 18% of variants with equal upgrades and downgrades from original report. ClinGen's revisions to PM1 and PS4 contributed to classification differences in 21% and 19% of variants respectively. Each classification change per proband report impacted, on average, 3.1 cascade reports with a further 6.3 first- and second-degree relatives potentially available for genotyping per family. CONCLUSION ClinGen's gene-specific criteria provide expert-informed guidance for interpretation of MYH7 sequence variants. Periodic re-evaluation improves diagnostic confidence and should be considered by clinical and laboratory teams.
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Affiliation(s)
- Christopher M Richmond
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, QLD, Australia.,School of Medicine, Griffith University, Gold Coast, QLD, Australia
| | - Paul A James
- Genomic Medicine Department, Royal Melbourne Hospital, Melbourne, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia
| | - Sarah-Jane Pantaleo
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,University of Melbourne, Parkville, VIC, Australia.
| | - Ivan Macciocca
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.
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26
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Menke C, Nagaraj CB, Dawson B, He H, Tawde S, Wakefield EG. Understanding and interpretation of a variant of uncertain significance (VUS) genetic test result by pediatric providers who do not specialize in genetics. J Genet Couns 2021; 30:1559-1569. [PMID: 33969574 DOI: 10.1002/jgc4.1422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/09/2022]
Abstract
The advancement of genetic testing technologies has allowed for better diagnosis and management of patients, but also results in more variants of uncertain significance (VUSs) due to the increased number of genes being analyzed. There are more genetic tests available and more providers who do not specialize in genetics ordering genetic testing, but few studies examining how providers who do not specialize in genetics interpret VUSs. This study surveyed pediatric providers at a midwestern pediatric care center who do not specialize in genetics about their understanding of a mock genetic test report with a VUS result and whether their understanding of the result was associated with experience ordering genetic tests. Participants' preferences about content of the report and steps taken to understand the result were also examined. Of the 51 participants, 33% correctly answered both knowledge questions about the VUS result: one asking them to interpret the result and one asking them how they would explain the result to the patient. There was no association between answering both knowledge questions correctly and types of previous genetic tests ordered (p > .1 for 8 types of genetic tests), having received a genetic test report with a VUS result (p = .58), having referred patients to a genetics professional (p = .74), or feeling comfortable discussing a positive, negative, or VUS genetic test result (p > .4). This suggests that having previous experience ordering genetic tests does not contribute to the participants' knowledge about a variant of uncertain significance. Most participants reported that the amount of information in each section of the mock report was adequate. Participants were likely to reference multiple resources to better understand a VUS result, including published literature (82%), gene-specific databases (67%), and colleagues (63%). While these results cannot be generalized to all institutions, institutions can use the two knowledge questions to determine participants' understanding of genetic test results. This will help healthcare institutions determine methods that will best aide their providers who order genetic testing but do not specialize in genetics in learning more about the genetic testing process and better utilize results to improve patient care.
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Affiliation(s)
- Chelsea Menke
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chinmayee B Nagaraj
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian Dawson
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hua He
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sanjukta Tawde
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Genetic Services Laboratory, University of Chicago, Chicago, IL, USA
| | - Emily G Wakefield
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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27
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Friend P, Dickman E, Calzone K. Using a Genomics Taxonomy: Facilitating Patient Care Safety and Quality in the Era of Precision Oncology. Clin J Oncol Nurs 2021; 25:205-209. [PMID: 33739339 DOI: 10.1188/21.cjon.205-209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Oncology nurses need to be competent in the ever-expanding application of genomics in cancer care, and understanding foundational terms is necessary. A landscape analysis of Oncology Nursing Society (ONS) materials, a literature review, and expert opinion revealed inconsistencies and varying use of genomic terms, some of which are outdated. In response, the ONS Genomics Taxonomy was built to address inaccuracies and discrepancies in terms and to be an accessible resource for oncology nurses. The taxonomy is a living document that is updated to reflect evolving science and evidence and serves to diminish confusion, improve genomic literacy, and assist oncology nurses in providing safe genomic care.
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28
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Brown EE. The genetic counselor's role in management of patients with dyslipidemia. Curr Opin Lipidol 2021; 32:83-88. [PMID: 33492006 DOI: 10.1097/mol.0000000000000732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE OF REVIEW The role of genetic testing in diagnosis and management of dyslipidemias continues to grow. Consequently, it is increasingly important for patients to have access to clinicians who have expertise in medical genetics and the psychological implications related to this type of testing. Often a lipidologist has had limited training in this regard, and this review explores the role of the genetic counselor to fill this gap. RECENT FINDINGS Genetic counselors are key members of the healthcare team, and their specialized training in medical genetics and counseling allows them to fill this professional knowledge gap within the lipid clinic. SUMMARY With the continued emphasis on precision medicine, the utility of genetic testing for dyslipidemias will continue to grow. This will in turn increase the demand for provider expertise in medical genetics and counseling around these complex issues. Integrating a genetic counselor within the lipid clinic provides an ideal management scenario providing patients and families with access to not only medical information but also emotional support regarding their hereditary condition.
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Affiliation(s)
- Emily E Brown
- Center for Inherited Heart Disease, Division of Cardiology, Johns Hopkins University, Baltimore, Maryland, USA
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29
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Hori A, Ai T, Isshiki M, Motoi Y, Yano K, Tabe Y, Hattori N, Miida T. Novel Variants in the CLCN1, RYR2, and DCTN1 Found in Elderly Japanese Dementia Patients: A Case Series. Geriatrics (Basel) 2021; 6:geriatrics6010014. [PMID: 33562224 PMCID: PMC7931039 DOI: 10.3390/geriatrics6010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/18/2021] [Accepted: 02/04/2021] [Indexed: 11/16/2022] Open
Abstract
Dementia has an enormous impact on medical and financial resources in aging societies like Japan. Diagnosis of dementia can be made by physical and mental examinations, imaging tests, and findings of high abnormal proteins in cerebrospinal fluids. In addition, genetic tests can be performed in neurodegenerative diseases such as Alzheimer’s disease (AD), frontotemporal dementia (FTD), and Parkinson’s disease (PD). In this case series, we presented three cases of dementia with unknown causes who carry novel variants in the genes associated with neurodegenerative diseases. Three patients (Patients 1, 2, and 6) were found by screening 18 dementia patients using a gene panel including 63 genes. The age of onset for Patient 1 was 74 years old, and his father had PD and mother had AD. The age of onset for Patient 2 was 75 years old, and her mother had AD. The age of onset for Patient 6 was 83 years old, and her father, two sisters, and daughter had dementia. The Mini-Mental State Examination produced results of 20, 15, and 22, respectively. The suspected diagnosis by neurological examinations and imaging studies for Patients 1 and 2 was AD, and for Patient 6 was FTD. Patient 1 was treated with donepezil; Patient 2 was treated with donepezil and memantine; and Patient 6 was treated with donepezil, galantamine, and rivastigmine. The three rare variants identified were: CLCN1, encoding a chloride channel, c.2848G>A:p.Glu950Lys (Patient 1); RYR2, encoding a calcium releasing ryanodine receptor, c.13175A>G:p.Lys4392Arg (Patient 2); and DCTN1, encoding a subunit of dynactin, c. 3209G>A:p.Arg1070Gln (Patient 6). The detected variants were interpreted according to the American College of Medical Genetics (ACMG) guidelines. The minor allele frequency for each variant was 0.025%, 0.023%, and 0.0004% in East Asians, respectively. The DCTN1 variant found in Patient 6 might be associated with FTD. Although none of them were previously reported in dementia patients, all variants were classified as variants of unknown significance (VUS). Our report suggests that results of genetic tests in elderly patients with dementia need to be carefully interpreted. Further data accumulation of genotype–phenotype relationships and development of appropriate functional models are warranted.
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Affiliation(s)
- Atsushi Hori
- Center for Genomic and Regenerative Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (A.H.); (K.Y.)
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (M.I.); (Y.T.); (T.M.)
| | - Tomohiko Ai
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (M.I.); (Y.T.); (T.M.)
- Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Correspondence: or
| | - Miwa Isshiki
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (M.I.); (Y.T.); (T.M.)
| | - Yumiko Motoi
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (Y.M.); (N.H.)
| | - Kouji Yano
- Center for Genomic and Regenerative Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (A.H.); (K.Y.)
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (M.I.); (Y.T.); (T.M.)
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (Y.M.); (N.H.)
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo 113-8424, Japan; (M.I.); (Y.T.); (T.M.)
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30
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Kassem N, Stout LA, Hunter C, Schneider B, Radovich M. Precision Prevention: The Current State and Future of Genomically Guided Cancer Prevention. JCO Precis Oncol 2020; 4:96-108. [PMID: 35050732 DOI: 10.1200/po.19.00278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The identification of cancer-predisposing germline variants has potentially substantial clinical impact for patients and their families. Although management guidelines have been proposed for some genes, guidelines for other genes are lacking. This review focuses on the current surveillance and management guidelines for the most common hereditary cancer syndromes and discusses some of the most pivotal studies supporting the available guidelines. We also highlight the gaps in the identification of germline carriers, the cascade testing of at-risk relatives, and the challenges impeding the proper follow-up and optimal management of pathogenic germline carriers. The anticipated surge in the number of identified germline carriers, deficient management guidelines, poor cascade testing uptake, and long-term follow-up necessitate the development of multidisciplinary clinics as an obligatory step toward the improvement of cancer prevention.
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Affiliation(s)
- Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Cynthia Hunter
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Bryan Schneider
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
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31
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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32
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Makhnoon S, Mork M, Arun B, Volk RJ, Peterson SK. Perceptions of provider's epistemic authority in response to variant of uncertain significance-related recommendations. J Genet Couns 2020; 30:10.1002/jgc4.1337. [PMID: 33090616 PMCID: PMC8026756 DOI: 10.1002/jgc4.1337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 01/04/2023]
Abstract
Uncertain genetic information such as variants of uncertain significance (VUS) is often encountered by patients in clinical cancer genetic testing. Although healthcare providers facilitate patient's understanding of VUS-associated empirical risk and its medical implications, patients' understanding and perceptions of risk often differ and may be based on subjective evaluations such as their perception of provider's epistemic authority (EA). This study examines the hypothesis that individuals attribute greater EA to genetic counselors (GCs) (compared to gastrointestinal oncologists) and to providers who recommend more active VUS-related recommendations (compared to inactive). In a factorial experiment, 652 adult participants recruited on Amazon Mechanical Turk were block-randomized to read one of 10 different types of VUS-related scenarios in the context of colon cancer (5 recommendation types × 2 provider types). GCs were attributed higher EA than gastrointestinal oncologists (p = <.001). Active recommendations (comprehensive, check back, wrong) were attributed lower EA (M = 3.67, SD = 0.79) compared to the inactive (stand by, disregard) (M = 3.89, SD = 0.67) (p-value = <.001). The wrong recommendation was attributed lowest EA compared to the four correct recommendations (mean difference = -0.34, -0.45, -0.35, and -0.44, respectively; p = .002), which, when dropped from the analysis, showed no difference between the correct active and inactive recommendations (3.78 vs. 3.89, p = .095). The higher EA attributed to GCs is encouraging and possibly explained by increased public awareness of the genetic counseling profession. The lack of difference in EA attributed to various correct, yet incomplete forms of VUS-related recommendation indicates that individuals may be unaware of and thus completely rely on providers for complex medical topics like VUS. Communicating VUS-related uncertainty warrants caution and further research to elucidate best practices and outcomes.
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Affiliation(s)
- Sukh Makhnoon
- Department of Behavioral Science, MD Anderson Cancer Center, Houston Texas
| | - Maureen Mork
- Department of Clinical Cancer Genetics, MD Anderson Cancer Center, Houston Texas
| | - Banu Arun
- Department of Clinical Cancer Genetics, MD Anderson Cancer Center, Houston Texas
| | - Robert J Volk
- Department of Health Services Research, MD Anderson Cancer Center, Houston Texas
| | - Susan K Peterson
- Department of Behavioral Science, MD Anderson Cancer Center, Houston Texas
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Reid S, Spalluto LB, Pal T. Strategies to enhance identification of hereditary breast cancer gene carriers. Expert Rev Mol Diagn 2020; 20:861-865. [PMID: 32856489 PMCID: PMC7606636 DOI: 10.1080/14737159.2020.1816829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sonya Reid
- Vanderbilt University Medical Center, Nashville TN, USA
| | - Lucy B. Spalluto
- Vanderbilt University Medical Center, Nashville TN, USA,Veterans Health Administration – Tennessee Valley Healthcare System Geriatric Research, Education and Clinical Center (GRECC), Nashville, TN, USA
| | - Tuya Pal
- Vanderbilt University Medical Center, Nashville TN, USA
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34
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The Application of Next-Generation Sequencing (NGS) in Neonatal-Onset Urea Cycle Disorders (UCDs): Clinical Course, Metabolomic Profiling, and Genetic Findings in Nine Chinese Hyperammonemia Patients. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5690915. [PMID: 32934962 PMCID: PMC7479453 DOI: 10.1155/2020/5690915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022]
Abstract
During Jan. 2016–Dec. 2019, nine Chinese patients from eight unrelated families were diagnosed with neonatal-onset UCDs by targeted panel sequencing or whole-exome sequencing (WES). Their clinical manifestations, biochemical features, 180-day-age outcomes, and molecular genetic characteristics were reviewed retrospectively. NGS-based tests revealed 7 patients diagnosed with ornithine transcarbamylase deficiency (OTCD) and 2 with carbamoylphosphate synthetase I deficiency (CPS1D). The spectrum of the clinical presentation of nine affected individuals progressed from unspecific symptoms like poor feeding to somnolence, coma, and death. All patients presented with an acute hyperammonemia. The most robust metabolic pattern in OTCD was hyperglutaminemic hyperammonemia with high concentration of urine orotic acid, and it was reported in six patients. Of ten variants found on the OTC gene and CPS1 gene, 3 were novel: (c.176T>C (p.L59P)) in the OTC gene, c.2938G>A (p.G980S) and c.3734T>A (p.L1245H) in the CPS1 gene. There was a high mortality rate of 77.78% (7/9) for all the defects combined. An OTC-deficient male and a CPS1-deficient female survived from episodes of hyperammonemia. Although prompt recognition of UCD and the use of alternative pathway therapy in addition to provision of appropriate nutrition and dialysis improved survival, the overall outcomes for the neonatal-onset type are poor in China.
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35
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Atwal PS, Midei M, Adams D, Fay A, Heerinckx F, Milner P. The infantile neuroaxonal dystrophy rating scale (INAD-RS). Orphanet J Rare Dis 2020; 15:195. [PMID: 32727524 PMCID: PMC7392694 DOI: 10.1186/s13023-020-01479-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background INAD is an autosomal recessive neurogenetic disorder caused by biallelic pathogenic variants in PLA2G6. The downstream enzyme, iPLA2, plays a critical role in cell membrane homeostasis by helping to regulate levels of phospholipids. The clinical presentation occurs between 6 months and 3 years with global developmental regression, hypotonia, and progressive spastic tetraparesis. Progression is often rapid, resulting in severe spasticity, visual impairment, and cognitive decline, with many children not surviving past the first decade of life. To date, no accepted tool for assessing the severity of INAD exists; other commonly used scales (e.g. CHOP-INTEND, Modified Ashworth, Hammersmith Functional Motor Scale) do not accurately gauge the current severity of INAD, nor are they sensitive/specific enough to monitor disease progression. Finally, these other scales are not appropriate, because they do not address the combination of CNS, peripheral nerve, and visual pathology that occurs in children with INAD. Methods We have developed and validated a structured neurological examination for INAD (scored out of 80). The examination includes six main categories of pediatric developmental evaluation: 1) gross motor-and-truncal-stability skills, 2) fine motor skills, 3) bulbar function, 4) ocular function, 5) temporo-frontal function, and, 6) Functional evaluation of the autonomic nervous system. A cohort of patients diagnosed with INAD were followed prospectively to validate the score against disease severity and disease progression. Results We show significant correlation between the total neurological assessment score and months since symptom onset with a statistically significant (p = 6.7 × 10− 07) correlation between assessment score and disease onset. As hypothesized, the coefficient of months-since-symptom-onset is strongly negative, indicating a negative correlation between total score and months since symptom onset. Conclusion We have developed and validated a novel neurological assessment score in INAD that demonstrates strong correlation with disease severity and disease progression.
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Affiliation(s)
| | | | - Darius Adams
- Atlantic Medical Group, Morris Township, NJ, USA
| | - Alexander Fay
- University of California San Francisco (UCSF), San Francisco, CA, USA
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36
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Halverson CME, Connors LM, Wessinger BC, Clayton EW, Wiesner GL. Patient perspectives on variant reclassification after cancer susceptibility testing. Mol Genet Genomic Med 2020; 8:e1275. [PMID: 32329193 PMCID: PMC7336756 DOI: 10.1002/mgg3.1275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/17/2020] [Accepted: 04/02/2020] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Little is known about the impact of reclassification on patients' perception of medical uncertainty or trust in genetics-based clinical care. METHODS Semistructured telephone interviews were conducted with 20 patients who had received a reclassified genetic test result related to hereditary cancer. All participants had undergone genetic counseling and testing for cancer susceptibility at Vanderbilt-Ingram Cancer Center Hereditary Cancer Clinic within the last six years. RESULTS Most of the participants did not express distress related to the variant reclassification and only a minority expressed a decrease in trust in medical genetics. However, recall of the new interpretation was limited, even though all participants were recontacted by letter, phone, or clinic visit. CONCLUSION Reclassification of genetic tests is an important issue in modern healthcare because changes in interpretation have the potential to alter previously recommended management. Participants in this study did not express strong feelings of mistrust or doubt about their genetic evaluation. However, there was a low level of comprehension and information retention related to the updated report. Future research can build on this study to improve communication with patients about their reclassified results.
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Affiliation(s)
- Colin M E Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA.,Regenstrief Institute, Indianapolis, IN, USA
| | | | | | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,School of Law, Vanderbilt University, Nashville, TN, USA
| | - Georgia L Wiesner
- Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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37
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Campuzano O, Sarquella-Brugada G, Fernandez-Falgueras A, Coll M, Iglesias A, Ferrer-Costa C, Cesar S, Arbelo E, García-Álvarez A, Jordà P, Toro R, Tiron de Llano C, Grassi S, Oliva A, Brugada J, Brugada R. Reanalysis and reclassification of rare genetic variants associated with inherited arrhythmogenic syndromes. EBioMedicine 2020; 54:102732. [PMID: 32268277 PMCID: PMC7136601 DOI: 10.1016/j.ebiom.2020.102732] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/11/2020] [Accepted: 03/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Accurate interpretation of rare genetic variants is a challenge for clinical translation. Updates in recommendations for rare variant classification require the reanalysis and reclassification. We aim to perform an exhaustive re-analysis of rare variants associated with inherited arrhythmogenic syndromes, which were classified ten years ago, to determine whether their classification aligns with current standards and research findings. Methods In 2010, the rare variants identified through genetic analysis were classified following recommendations available at that time. Nowadays, the same variants have been reclassified following current American College of Medical Genetics and Genomics recommendations. Findings Our cohort included 104 cases diagnosed with inherited arrhythmogenic syndromes and 17 post-mortem cases in which inherited arrhythmogenic syndromes was cause of death. 71.87% of variants change their classification. While 65.62% of variants were classified as likely pathogenic in 2010, after reanalysis, only 17.96% remain as likely pathogenic. In 2010, 18.75% of variants were classified as uncertain role but nowadays 60.15% of variants are classified of unknown significance. Interpretation Reclassification occurred in more than 70% of rare variants associated with inherited arrhythmogenic syndromes. Our results support the periodical reclassification and personalized clinical translation of rare variants to improve diagnosis and adjust treatment. Funding Obra Social "La Caixa Foundation" (ID 100010434, LCF/PR/GN16/50290001 and LCF/PR/GN19/50320002), Fondo Investigacion Sanitaria (FIS PI16/01203 and FIS, PI17/01690), Sociedad Española de Cardiología, and “Fundacio Privada Daniel Bravo Andreu”.
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Affiliation(s)
- Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Biochemistry and Molecular Genetics Department, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain.
| | - Georgia Sarquella-Brugada
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Anna Fernandez-Falgueras
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Mónica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Carles Ferrer-Costa
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain
| | - Sergi Cesar
- Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Elena Arbelo
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Ana García-Álvarez
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Paloma Jordà
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Rocío Toro
- Medicine Department, School of Medicine, Cadiz, Spain
| | | | - Simone Grassi
- Section Legal Medicine, Institute of Public Health, Catholic University, Rome, Italy
| | - Antonio Oliva
- Section Legal Medicine, Institute of Public Health, Catholic University, Rome, Italy
| | - Josep Brugada
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Arrhythmias Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain; Arrhythmias Unit, Hospital Clinic, University of Barcelona-IDIBAPS, Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, C/ Dr Castany s/n, Parc Hospitalari Martí i Julià (M-2), 17190 Salt (Girona), Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain; Cardiology Service, Hospital Josep Trueta, University of Girona, Girona, Spain.
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Clift K, Macklin S, Halverson C, McCormick JB, Abu Dabrh AM, Hines S. Patients' views on variants of uncertain significance across indications. J Community Genet 2020; 11:139-145. [PMID: 31432391 PMCID: PMC7062975 DOI: 10.1007/s12687-019-00434-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
As genomic sequencing expands into more areas of patient care, an increasing number of patients learn of the variants of uncertain significance (VUSs) that they carry. Understanding the potential psychosocial consequences of the disclosure of a VUS can help inform pre- and post-test counseling discussions. Medical uncertainty in general elicits a variety of responses from patients, particularly in the growing field of medical genetics and genomics. It is important to consider patients' responses to the ambiguous nature of VUSs across different indications and situational contexts. Genetic counselors and other providers ordering genetic testing should be prepared for the possibility of their patients' misinterpretation of such results. Pre-test counseling should include a discussion of the possibility of VUSs and what it would mean for the patient's care and its potential psychosocial impacts. When a VUS is found, post-test counseling should include additional education and a discussion of the variant's implications and medical management recommendations based on the results. These discussions may help temper subjective interpretations, unrealistic views, and decisional regret.
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Affiliation(s)
- Kristin Clift
- Mayo Clinic Center for Individualized Medicine, Jacksonville, FL, USA.
| | - Sarah Macklin
- Mayo Clinic Department of Clinical Genomics, Jacksonville, FL, USA
| | - Colin Halverson
- Center for Bioethics, Indiana University School of Medicine, Indianapolis, IN, USA
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Roberts ME, Susswein LR, Janice Cheng W, Carter NJ, Carter AC, Klein RT, Hruska KS, Marshall ML. Ancestry-specific hereditary cancer panel yields: Moving toward more personalized risk assessment. J Genet Couns 2020; 29:598-606. [PMID: 32227564 DOI: 10.1002/jgc4.1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/20/2020] [Accepted: 02/23/2020] [Indexed: 12/11/2022]
Abstract
Healthcare disparities in genomic medicine are well described. Despite some improvements, we continue to see fewer individuals of African American, Asian, and Hispanic ancestry undergo genetic counseling and testing compared to those of European ancestry. It is well established that variant of uncertain significance (VUS) rates are higher among non-European ancestral groups undergoing multi-gene hereditary cancer panel testing. However, pathogenic variant (PV) yields, and genomic data in general, are often reported in aggregate and derived from cohorts largely comprised of individuals of European ancestry. We performed a retrospective review of clinical and ancestral data for individuals undergoing multi-gene hereditary cancer panel testing to determine ancestry-specific PV and VUS rates. An ancestry other than European was reported in 29,042/104,851 (27.7%) of individuals. Compared to Europeans (9.4%), individuals of Middle Eastern ancestry were more likely to test positive for one or more pathogenic variants (12.1%, p = .0025), while African Americans were less likely (7.9%, p < .0001). Asian and Middle Eastern individuals were most likely (34.8% and 33.2%, respectively) to receive a report with an overall classification of VUS, while individuals of Ashkenazi Jewish and European ancestry were least likely (17.1% and 20.4%, respectively). These data suggest that in addition to higher VUS rates, there may be ancestry-specific PV yields. Providing aggregate data derived from cohorts saturated with European individuals does not adequately reflect genetic testing outcomes in minority groups, and interrogation of ancestry-specific data is a step toward a more personalized risk assessment.
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Affiliation(s)
| | | | - Wanchun Janice Cheng
- BioReference Laboratories, Inc., Elmwood Park, New Jersey.,Sarah Lawrence College, Genetic Counseling Program, Bronxville, New York
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40
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McGill BC, Wakefield CE, Hetherington K, Munro LJ, Warby M, Lau L, Tyrrell V, Ziegler DS, O’Brien TA, Marshall GM, Malkin D, Hansford JR, Tucker KM, Vetsch J. "Balancing Expectations with Actual Realities": Conversations with Clinicians and Scientists in the First Year of a High-Risk Childhood Cancer Precision Medicine Trial. J Pers Med 2020; 10:E9. [PMID: 32075154 PMCID: PMC7151613 DOI: 10.3390/jpm10010009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Precision medicine is changing cancer care and placing new demands on oncology professionals. Precision medicine trials for high-risk childhood cancer exemplify these complexities. We assessed clinicians' (n = 39) and scientists' (n = 15) experiences in the first year of the PRecISion Medicine for Children with Cancer (PRISM) trial for children and adolescents with high-risk cancers, through an in-depth semi-structured interview. We thematically analysed participants' responses regarding their professional challenges, and measured oncologists' knowledge of genetics and confidence with somatic and germline molecular test results. Both groups described positive early experiences with PRISM but were cognisant of managing parents' expectations. Key challenges for clinicians included understanding and communicating genomic results, balancing biopsy risks, and drug access. Most oncologists rated 'good' knowledge of genetics, but a minority were 'very confident' in interpreting (25%), explaining (34.4%) and making treatment recommendations (18.8%) based on somatic genetic test results. Challenges for scientists included greater emotional impact of their work and balancing translational outputs with academic productivity. Continued tracking of these challenges across the course of the trial, while assessing the perspectives of a wider range of stakeholders, is critical to drive the ongoing development of a workforce equipped to manage the demands of paediatric precision medicine.
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Affiliation(s)
- Brittany C. McGill
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
| | - Claire E. Wakefield
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
| | - Kate Hetherington
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
| | - Lachlan J. Munro
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
| | - Meera Warby
- Hereditary Cancer Centre, Department of Medical Oncology, Prince of Wales Hospital, Randwick 2031, Australia; (M.W.); (K.M.T.)
- Prince of Wales Clinical School, UNSW Sydney, Sydney 2052, Australia
| | - Loretta Lau
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia;
- Children’s Cancer Institute, UNSW Sydney, Kensington 2750, Australia;
| | - Vanessa Tyrrell
- Children’s Cancer Institute, UNSW Sydney, Kensington 2750, Australia;
| | - David S. Ziegler
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia;
- Children’s Cancer Institute, UNSW Sydney, Kensington 2750, Australia;
| | - Tracey A. O’Brien
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia;
| | - Glenn M. Marshall
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia;
- Children’s Cancer Institute, UNSW Sydney, Kensington 2750, Australia;
| | - David Malkin
- Division of Haematology/Oncology, Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada;
| | - Jordan R. Hansford
- Children’s Cancer Centre, Royal Children’s Hospital, Melbourne 3052, Australia;
- Division of Cancer, Murdoch Children’s Research Institute, Melbourne 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne 3010, Australia
- Department of Paediatrics, Monash University, Melbourne 3800, Australia
| | - Katherine M. Tucker
- Hereditary Cancer Centre, Department of Medical Oncology, Prince of Wales Hospital, Randwick 2031, Australia; (M.W.); (K.M.T.)
- Prince of Wales Clinical School, UNSW Sydney, Sydney 2052, Australia
| | - Janine Vetsch
- School of Women’s and Children’s Health, UNSW Medicine, UNSW Sydney, Sydney 2052, Australia; (C.E.W.); (K.H.); (L.J.M.); (L.L.); (D.S.Z.); (T.A.O.); (J.V.)
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick 2031, Australia
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Makhnoon S, Peterson SK. Variant of Uncertain Significance-Related Uncertainty in Breast Cancer Genomics. CURRENT BREAST CANCER REPORTS 2020. [DOI: 10.1007/s12609-020-00351-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots". Genet Med 2020; 22:825-830. [PMID: 31911673 PMCID: PMC7200594 DOI: 10.1038/s41436-019-0740-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose Guidelines for variant interpretation incorporate variant hotspots in critical functional domains as evidence for pathogenicity (e.g., PM1 and PP2), but do not use “coldspots,” that is, regions without essential functions that tolerate variation, as evidence a variant is benign. To improve variant classification we evaluated BRCA1 and BRCA2 missense variants reported in ClinVar to identify regions where pathogenic missenses are extremely infrequent, defined as coldspots. Methods We used Bayesian approaches to model variant classification in these regions. Results BRCA1 exon 11 (~60% of the coding sequence), and BRCA2 exons 10 and 11 (~65% of the coding sequence), are coldspots. Of 89 pathogenic (P) or likely pathogenic (LP) missense variants in BRCA1, none are in exon 11 (odds <0.01, 95% confidence interval [CI] 0.0–0.01). Of 34 P or LP missense variants in BRCA2, none are in exons 10–11 (odds <0.01, 95% CI 0.0–0.01). More than half of reported missense variants of uncertain significance (VUS) in BRCA1 and BRCA2 are in coldspots (3115/5301 = 58.8%). Reclassifying these 3115 VUS as likely benign would substantially improve variant classification. Conclusion In BRCA1 and BRCA2 coldspots, missense variants are very unlikely to be pathogenic. Classification schemes that incorporate coldspots can reduce the number of VUS and mitigate risks from reporting benign variation as VUS.
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Clift KE, Macklin SK, Hines SL. Patients with pathogenic variants for breast cancer other than BRCA1 and BRCA2: qualitative interviews about health care experiences. Hered Cancer Clin Pract 2020; 17:32. [PMID: 31890060 PMCID: PMC6916015 DOI: 10.1186/s13053-019-0132-6] [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: 07/29/2019] [Accepted: 12/09/2019] [Indexed: 11/10/2022] Open
Abstract
Background Genetic testing for hereditary cancer syndromes has been revolutionized by next-generation sequencing, which allows for simultaneous review of numerous genes. Multigene panels are regularly offered to patients because of their scope and decreased cost and turnaround time. However, many genes included on larger panels have not been studied as extensively as BRCA1 and BRCA2 (BRCA1/2), and their clinical effects are often not as well established. Methods We identified patients who received positive test results for pathogenic variants of breast cancer genes from January 2012 through May 2018. We mailed a survey and conducted qualitative interviews to explore the personal and health care experiences of patients with pathogenic variants of BRCA1/2 and patients with "other" (ie, non-BRCA1/2 or PALB2; PTEN; ATM; TP53; NBM, RAD51C; MSH6) variants. We compared the experiences of these patients. Results Fifty-nine out of 128 individuals responded to the survey (46%). Thirty-two patients had BRCA1/2 variants, and 27 had other variants. (49 women and 10 men; median [range] age, 63 [34-87] years). We interviewed 21 patients (17 women and 4 men; median [range] age, 59.6 [34-82] years). Of the interview participants, ten patients had BRCA1/2 variants, and 11 had non-BRCA1/2 variants. Patients reported receiving poor information about their genetic test results, and they often educated their physicians about their results. Some patients believed that they had been ignored or "brushed off" by health care professionals because non-BRCA1/2 genes are less understood outside the genetics research community. Patients with BRCA1/2 variants had similar problems with health care providers, despite increased awareness and established guidelines about BRCA1/2. Conclusions Research is required to understand the clinical significance and proper management of diseases attributable to newly characterized hereditary cancer genes. Additional evaluation of patient and provider education should be at the forefront of efforts to improve patient care.
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Affiliation(s)
- Kristin E Clift
- 1Center for Individualized Medicine, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
| | - Sarah K Macklin
- 2Department of Clinical Genomics, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
| | - Stephanie L Hines
- 3Internal Medicine, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
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Lee HCH, Lau WL, Ko CH, Lee KC, Cheng FY, Wong S, Woo YH, Mak CM. Flexi-Myo Panel Strategy: Genomic Diagnoses of Myopathies and Muscular Dystrophies by Next-Generation Sequencing. Genet Test Mol Biomarkers 2019; 24:99-104. [PMID: 30907627 DOI: 10.1089/gtmb.2018.0185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aims: Muscle disorders are clinically and genetically heterogeneous. Investigations, including plasma creatine kinase, electromyography, and nerve conduction velocity studies are often nonspecific, whereas muscle biopsy might be limited by sampling bias and variable histopathology. Next-generation sequencing is now generally considered an important diagnostic tool for muscle disorders, with decreased costs and improved diagnostic yield. Inclusion of a large number of genes in the analysis might, however, generate a large number of ambiguous results and create unnecessary confusion for clinicians and patients. Methods: An ethnic Chinese patient presented at age 10 with tip-toe walking. Upon examination the patient had a waddling gait, a tight Achilles tendon with pes cavus. A muscle biopsy showed the presence of minicores with disruption of the myofibrillary network and Z-bands. Sequencing was performed using the Flexi-Myo panel, which provides coverage for 85 myopathic genes. Reporting of sequencing results was decided by the responsible chemical pathologists based on the available clinical and genetic information. Results: A previously identified heterozygous in-frame deletion was detected in MYH7, which confirmed the diagnosis of Laing myopathy. No variants of uncertain significance required reporting. Conclusion: We describe the effectiveness of our Flexi-Myo panel approach for the diagnosis of muscle disorders, which confirmed diagnosis of Laing myopathy in what had been a clinically ambiguous presentation. This approach enables efficient genomic testing for muscle diseases in adults and children with satisfactory diagnostic yield and sufficient sensitivity, whereas avoiding the reporting of ambiguous results. Similar strategies might also be implemented for other groups of disorders.
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Affiliation(s)
| | - Wai-Ling Lau
- Department of Paediatrics and Adolescent Medicine, Caritas Medical Centre, Hong Kong, China
| | - Chun-Hung Ko
- Department of Paediatrics and Adolescent Medicine, Caritas Medical Centre, Hong Kong, China
| | - Kam-Cheong Lee
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Fung-Yip Cheng
- Department of Clinical Pathology, Caritas Medical Centre, Hong Kong, China
| | - Shun Wong
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China.,Pathology Department, St. Paul's Hospital, Hong Kong, China
| | - Yip-Hin Woo
- Department of Radiology, Caritas Medical Centre, Hong Kong, China
| | - Chloe Miu Mak
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
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Preferences of women with epithelial ovarian cancer for aspects of genetic testing. GYNECOLOGIC ONCOLOGY RESEARCH AND PRACTICE 2019; 6:1. [PMID: 30693090 PMCID: PMC6341581 DOI: 10.1186/s40661-019-0066-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/14/2019] [Indexed: 01/13/2023]
Abstract
Background Although genetic testing is recommended for women with epithelial ovarian cancer (EOC), little is known about patient preferences for various testing options. We measured relative preferences for attributes of testing in women with EOC referred for genetic counseling. Methods Subjects were recruited to participate in a discrete-choice-experiment survey to elicit preferences for attributes of genetic testing: out-of-pocket cost ($0, $100, $250, or $1000), probability of a deleterious mutation (60, 80%, or 88%), probability of a variant of uncertain significance (VUS) result (5, 20%, or 40%), sample requirements (blood or saliva), and turn-around time (1, 2 or 4 weeks). Subjects viewed educational videos followed by a series of choices between pairs of constructed genetic tests with varying attribute levels. Random-parameters logit was used to estimate preference weights for attribute levels. Relative importance weights and money-equivalent values were calculated. Results Ninety-four patients were enrolled; 68 (76.4%) presented for genetic counseling. Test cost was the most important attribute to subjects (importance weight = 41 out of 100) followed by probability to detect deleterious mutations (36) and probability of a VUS result (20). Sample requirements and turnaround time did not drive test choices. Subjects were willing to pay an additional $155 and $70 for incremental 5% improvements in the probability to detect deleterious mutations and probability of a VUS result. At genetics consultation, 55/68 (80.9%) subjects chose multigene testing. Conclusions Low out-of-pocket cost, high probability of detecting deleterious mutations and high probability of a VUS result are preferred by patients with EOC considering genetic testing. Electronic supplementary material The online version of this article (10.1186/s40661-019-0066-8) contains supplementary material, which is available to authorized users.
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Cohen SA, Bradbury A, Henderson V, Hoskins K, Bednar E, Arun BK. Genetic Counseling and Testing in a Community Setting: Quality, Access, and Efficiency. Am Soc Clin Oncol Educ Book 2019; 39:e34-e44. [PMID: 31099680 DOI: 10.1200/edbk_238937] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
There is an increasing need for genetic counseling and testing for individuals diagnosed with cancer, as treatment may be affected by the results. In addition, the identification of individuals before a diagnosis of cancer allows for optimal surveillance and early detection and prevention of cancer. With the recognition that as much as 10% of all cancers are hereditary, there is a growing need to improve access to genetic counseling and genetic testing, both before and at the time of diagnosis. This article focuses on models of identifying at-risk patients, including underserved communities; providing genetic counseling and testing in community practices; using telehealth; and collaborating with nongenetics health care providers and technological solutions to maximize efficiency and access.
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Affiliation(s)
- Stephanie A Cohen
- 1 Cancer Genetics Risk Assessment Program, Ascension St. Vincent, Indianapolis, IN
| | - Angela Bradbury
- 2 Department of Medicine, Division of Hematology-Oncology, Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, PA
| | | | - Kent Hoskins
- 3 The University of Illinois at Chicago, Chicago, IL
| | - Erica Bednar
- 4 The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Banu K Arun
- 4 The University of Texas MD Anderson Cancer Center, Houston, TX
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Outcomes of 92 patient-driven family studies for reclassification of variants of uncertain significance. Genet Med 2018; 21:1435-1442. [PMID: 30374176 DOI: 10.1038/s41436-018-0335-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/28/2018] [Indexed: 01/30/2023] Open
Abstract
PURPOSE Family studies are an important but underreported source of information for reclassification of variants of uncertain significance (VUS). We evaluated outcomes of a patient-driven framework that offered familial VUS reclassification analysis to any adult with any clinically ascertained VUS from any laboratory in the United States. METHODS With guidance from FindMyVariant.org, participants recruited their own relatives for study participation. We genotyped relatives, calculated quantitative cosegregation likelihood ratios, and evaluated variant classifications using Tavtigian's unified framework for Bayesian analysis with American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria. We report participation and VUS reclassification rates from the 50 families enrolled for at least one year and reclassification results for 112 variants from the larger 92-family cohort. RESULTS For the 50-family cohort, 6.7 relatives per family were invited to participate and 67% of relatives returned samples for genotyping. Sixty-one percent of VUS were reclassified, 84% of which were classified as benign or likely benign. Genotyping relatives identified a de novo variant, phase variants, and relatives with phenotypes highly specific for or incompatible with specific classifications. CONCLUSIONS Motivated families can contribute to successful VUS reclassification at substantially higher rates than those previously published. Clinical laboratories could consider offering family studies to all patients with VUS.
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