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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Damiani G. Bayesian cost-effectiveness analysis of Whole genome sequencing versus Whole exome sequencing in a pediatric population with suspected genetic disorders. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2024; 25:999-1011. [PMID: 37975990 PMCID: PMC11283423 DOI: 10.1007/s10198-023-01644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Genetic diseases are medical conditions caused by sequence or structural changes in an individual's genome. Whole exome sequencing (WES) and whole genome sequencing (WGS) are increasingly used for diagnosing suspected genetic conditions in children to reduce the diagnostic delay and accelerating the implementation of appropriate treatments. While more information is becoming available on clinical efficacy and economic sustainability of WES, the broad implementation of WGS is still hindered by higher complexity and economic issues. The aim of this study is to estimate the cost-effectiveness of WGS versus WES and standard testing for pediatric patients with suspected genetic disorders. A Bayesian decision tree model was set up. Model parameters were retrieved both from hospital administrative datasets and scientific literature. The analysis considered a lifetime time frame and adopted the perspective of the Italian National Health Service (NHS). Bayesian inference was performed using the Markov Chain Monte Carlo simulation method. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI). The present analysis showed that implementing first-line WGS would be a cost-effective strategy, against the majority of the other tested alternatives at a threshold of €30,000-50,000, for diagnosing outpatient pediatric patients with suspected genetic disorders. According to the sensitivity analyses, the findings were robust to most assumption and parameter uncertainty. Lessons learnt from this modeling study reinforces the adoption of first-line WGS, as a cost-effective strategy, depending on actual difficulties for the NHS to properly allocate limited resources.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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2
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Abulí A, Antolín E, Borrell A, Garcia-Hoyos M, García Santiago F, Gómez Manjón I, Maíz N, González González C, Rodríguez-Revenga L, Valenzuena Palafoll I, Suela J. Guidelines for NGS procedures applied to prenatal diagnosis by the Spanish Society of Gynecology and Obstetrics and the Spanish Association of Prenatal Diagnosis. J Med Genet 2024; 61:727-733. [PMID: 38834294 DOI: 10.1136/jmg-2024-109878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
OBJECTIVE This document addresses the clinical application of next-generation sequencing (NGS) technologies for prenatal genetic diagnosis and aims to establish clinical practice recommendations in Spain to ensure uniformity in implementing these technologies into prenatal care. METHODS A joint committee of expert obstetricians and geneticists was created to review the existing literature on fetal NGS for genetic diagnosis and to make recommendations for Spanish healthcare professionals. RESULTS This guideline summarises technical aspects of NGS technologies, clinical indications in prenatal setting, considerations regarding findings to be reported, genetic counselling considerations as well as data storage and protection policies. CONCLUSIONS This document provides updated recommendations for the use of NGS diagnostic tests in prenatal diagnosis. These recommendations should be periodically reviewed as our knowledge of the clinical utility of NGS technologies, applied during pregnancy, may advance.
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Affiliation(s)
- Anna Abulí
- Clinical and Molecular Genetics, Vall d'Hebron University Hospital, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Eugenia Antolín
- Gynecology and Obstetrics, La Paz University Hospital, Madrid, Spain
| | - Antoni Borrell
- Gynecology and Obstetrics, Clinic Hospital of Barcelona, Barcelona, Spain
| | | | | | | | - Nerea Maíz
- Maternal-Fetal Medicine Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Obstetrics, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | - Laia Rodríguez-Revenga
- Biochemistry and Molecular Genetics, Clinic Hospital of Barcelona, Barcelona, Spain
- August Pi Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | | | - Javier Suela
- Genetics, Sanitas Central Laboratory, Alcobendas, Spain
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3
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Hammer-Hansen S, Stoltze U, Bartels E, Hansen TVO, Byrjalsen A, Tybjærg-Hansen A, Juul K, Schmiegelow K, Tfelt J, Bundgaard H, Wadt K, Diness BR. Actionability and familial uptake following opportunistic genomic screening in a pediatric cancer cohort. Eur J Hum Genet 2024; 32:846-857. [PMID: 38740897 PMCID: PMC11220050 DOI: 10.1038/s41431-024-01618-7] [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: 07/04/2023] [Revised: 04/02/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
The care for patients with serious conditions is increasingly guided by genomic medicine, and genomic medicine may equally transform care for healthy individual if genomic population screening is implemented. This study examines the medical impact of opportunistic genomic screening (OGS) in a cohort of patients undergoing comprehensive genomic germline DNA testing for childhood cancer, including the impact on their relatives. Medical actionability and uptake after cascade testing in the period following disclosure of OGS results was quantified. A secondary finding was reported to 19/595 (3.2%) probands primarily in genes related to cardiovascular and lipid disorders. After a mean follow up time of 1.6 years (Interquartile range (IQR): 0.57-1.92 yrs.) only 12 (63%) of these variants were found to be medically actionable. Clinical follow up or treatment was planned in 16 relatives, and as in the probands, the prescribed treatment was primarily betablockers or cholesterol lowering therapy. No invasive procedures or implantation of medical devices were performed in probands or relatives, and no reproductive counseling was requested. After an average of 1.6 years of follow-up 2.25 relatives per family with an actionable finding had been tested. This real-world experience of OGS grants new insight into the practical implementation effects and derived health care demands of genotype-first screening. The resulting health care effect and impact on demand for genetic counseling and workup in relatives extends beyond the effect in the probands.
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Affiliation(s)
- Sophia Hammer-Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Stoltze
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Emil Bartels
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Anne Tybjærg-Hansen
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Klaus Juul
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatric and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Jacob Tfelt
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Forensic Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Henning Bundgaard
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Department of Cardiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Rode Diness
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, Faculty of Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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4
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Malcikova J, Pavlova S, Baliakas P, Chatzikonstantinou T, Tausch E, Catherwood M, Rossi D, Soussi T, Tichy B, Kater AP, Niemann CU, Davi F, Gaidano G, Stilgenbauer S, Rosenquist R, Stamatopoulos K, Ghia P, Pospisilova S. ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update. Leukemia 2024; 38:1455-1468. [PMID: 38755420 PMCID: PMC11217004 DOI: 10.1038/s41375-024-02267-x] [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: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
In chronic lymphocytic leukemia (CLL), analysis of TP53 aberrations (deletion and/or mutation) is a crucial part of treatment decision-making algorithms. Technological and treatment advances have resulted in the need for an update of the last recommendations for TP53 analysis in CLL, published by ERIC, the European Research Initiative on CLL, in 2018. Based on the current knowledge of the relevance of low-burden TP53-mutated clones, a specific variant allele frequency (VAF) cut-off for reporting TP53 mutations is no longer recommended, but instead, the need for thorough method validation by the reporting laboratory is emphasized. The result of TP53 analyses should always be interpreted within the context of available laboratory and clinical information, treatment indication, and therapeutic options. Methodological aspects of introducing next-generation sequencing (NGS) in routine practice are discussed with a focus on reliable detection of low-burden clones. Furthermore, potential interpretation challenges are presented, and a simplified algorithm for the classification of TP53 variants in CLL is provided, representing a consensus based on previously published guidelines. Finally, the reporting requirements are highlighted, including a template for clinical reports of TP53 aberrations. These recommendations are intended to assist diagnosticians in the correct assessment of TP53 mutation status, but also physicians in the appropriate understanding of the lab reports, thus decreasing the risk of misinterpretation and incorrect management of patients in routine practice whilst also leading to improved stratification of patients with CLL in clinical trials.
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Affiliation(s)
- Jitka Malcikova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Mark Catherwood
- Haematology Department, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Hematopoietic and Leukemic Development, UMRS_938, Sorbonne University, Paris, France
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnon P Kater
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | | | - Frederic Davi
- Sorbonne Université, Paris, France
- Department of Hematology, Hôpital Pitié-Salpêtière, AP-HP, Paris, France
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Paolo Ghia
- Università Vita-Salute San Raffaele, Milan, Italy.
- Strategic Research Program on CLL, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic.
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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5
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Brauneck A, Schmalhorst L, Weiss S, Baumbach L, Völker U, Ellinghaus D, Baumbach J, Buchholtz G. Legal aspects of privacy-enhancing technologies in genome-wide association studies and their impact on performance and feasibility. Genome Biol 2024; 25:154. [PMID: 38872191 PMCID: PMC11170858 DOI: 10.1186/s13059-024-03296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024] Open
Abstract
Genomic data holds huge potential for medical progress but requires strict safety measures due to its sensitive nature to comply with data protection laws. This conflict is especially pronounced in genome-wide association studies (GWAS) which rely on vast amounts of genomic data to improve medical diagnoses. To ensure both their benefits and sufficient data security, we propose a federated approach in combination with privacy-enhancing technologies utilising the findings from a systematic review on federated learning and legal regulations in general and applying these to GWAS.
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Affiliation(s)
- Alissa Brauneck
- Hamburg University Faculty of Law, University of Hamburg, Hamburg, Germany.
| | - Louisa Schmalhorst
- Hamburg University Faculty of Law, University of Hamburg, Hamburg, Germany
| | - Stefan Weiss
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Linda Baumbach
- Department of Health Economics and Health Services Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology (IKMB), Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Gabriele Buchholtz
- Hamburg University Faculty of Law, University of Hamburg, Hamburg, Germany
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6
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Go M, Shim SH. Genomic aspects in reproductive medicine. Clin Exp Reprod Med 2024; 51:91-101. [PMID: 38263590 PMCID: PMC11140259 DOI: 10.5653/cerm.2023.06303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 01/25/2024] Open
Abstract
Infertility is a complex disease characterized by extreme genetic heterogeneity, compounded by various environmental factors. While there are exceptions, individual genetic and genomic variations related to infertility are typically rare, often family-specific, and may serve as susceptibility factors rather than direct causes of the disease. Consequently, identifying the cause of infertility and developing prevention and treatment strategies based on these factors remain challenging tasks, even in the modern genomic era. In this review, we first examine the genetic and genomic variations associated with infertility, and subsequently summarize the concepts and methods of preimplantation genetic testing in light of advances in genome analysis technology.
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Affiliation(s)
- Minyeon Go
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
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7
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Dratch L, Owczarzak J, Mu W, Cousins KAQ, Massimo L, Grossman M, Erby L. The lived experience of reconstructing identity in response to genetic risk of frontotemporal degeneration and amyotrophic lateral sclerosis. J Genet Couns 2024; 33:515-527. [PMID: 37424394 PMCID: PMC10776796 DOI: 10.1002/jgc4.1749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/06/2023] [Accepted: 06/27/2023] [Indexed: 07/11/2023]
Abstract
With the increasing availability of predictive genetic testing for adult-onset neurodegenerative conditions, it is imperative that we better understand the impact of learning one's risk status. Frontotemporal degeneration (FTD) is the second most prevalent cause of early-onset dementia. About one-third of patients have an identifiable genetic etiology, and some genetic variants that cause FTD can also cause amyotrophic lateral sclerosis (ALS). To understand individuals' risk perception and broader experience of living at risk, we completed semi-structured telephone interviews with 14 asymptomatic adults who tested positive for a variant known to cause risk for FTD and/or ALS. We conducted a thematic analysis, and within the core topic of identity, we derived three themes: conceptualization of FTD and ALS as a threat to identity, enduring uncertainty and dread, and varying centrality of risk status to identity. FTD and ALS risk raised fundamental issues for participants related to the essence of personhood, challenged them to confront Cartesian dualism (the philosophy of mind-body separation), and exposed how time, relationships, and social roles have affected their understanding of the nature of the self. Our findings provide important insight into how being at genetic risk shapes an individual's identity. We conclude that genetic counseling interventions that allow for identity exploration, anticipatory guidance, and uncertainty management should be utilized when supporting persons at risk.
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Affiliation(s)
- Laynie Dratch
- Department of Neurology, University of Pennsylvania, Philadelphia, PA
| | - Jill Owczarzak
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Weiyi Mu
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD
| | | | - Lauren Massimo
- Department of Neurology, University of Pennsylvania, Philadelphia, PA
| | - Murray Grossman
- Department of Neurology, University of Pennsylvania, Philadelphia, PA
| | - Lori Erby
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD
- Center for Precision Health Research, NHGRI, NIH, Bethesda, MD
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8
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Martyn M, Lee L, Jan A, Lynch E, Weerasuriya R, Kanga-Parabia A, Gaff C. Evaluation of a two-step model of opportunistic genomic screening. Eur J Hum Genet 2024; 32:656-664. [PMID: 38528054 PMCID: PMC11153562 DOI: 10.1038/s41431-024-01592-0] [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: 01/18/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/27/2024] Open
Abstract
Increasing use of diagnostic genomic sequencing is pushing health services to confront the issue of opportunistic genomic screening (OGS). To date, OGS has been offered concomitant with diagnostic testing. In contrast, we piloted a service offering OGS after return of diagnostic testing results. Evaluation was designed to provide insights for future models of service and included patient surveys at three time points, semi-structured interviews with genetic counsellors (GCs) and a focus group with medical scientists. Uptake was relatively low: 83 of 200 patients approached (42%) attended the OGS service, with 81 accepting OGS. Whilst many who declined to attend the service cited practical barriers, others gave reasons that indicated this was a considered decision. Despite specific genetic counselling, one third of patients did not understand the scope of re-analysis. Yet after post-test counselling, all respondents with novel pathogenic additional findings (AF) understood the implications and reported relevant follow-up. Recall was high: five months after last contact, 75% recalled being offered OGS without prompting. GC interviews and patient survey responses provide insights into complexities that influence patient support needs, including diagnostic status and AF result type. There was no consensus among patients or professionals about when to offer OGS. There was a clear preference for multiple, flexible methods of information provision; achieving this whilst balancing patient support needs and resource requirements is a challenge requiring further investigation. Decisions about whether, when and how to offer OGS are complex; our study shows the two-step approach warrants further exploration.
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Affiliation(s)
- Melissa Martyn
- Melbourne Genomics Health Alliance, Parkville, VIC, 3052, Australia.
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3052, Australia.
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.
| | - Ling Lee
- Melbourne Genomics Health Alliance, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Alli Jan
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Central Coast Local Health District, NSW Health, Gosford, NSW, 2250, Australia
| | - Elly Lynch
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Victorian Clinical Genetics Services, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Rona Weerasuriya
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
- Australian Red Cross, 23-47 Villiers Street, North Melbourne, VIC, 3051, Australia
| | - Anaita Kanga-Parabia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Clara Gaff
- Melbourne Genomics Health Alliance, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
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9
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Brown CM, Amendola LM, Chandrasekhar A, Hagelstrom RT, Halter G, Kesari A, Thorpe E, Perry DL, Taft RJ, Coffey AJ. A framework for the evaluation and reporting of incidental findings in clinical genomic testing. Eur J Hum Genet 2024; 32:665-672. [PMID: 38565640 PMCID: PMC11153510 DOI: 10.1038/s41431-024-01575-1] [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: 10/16/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.
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Affiliation(s)
- Carolyn M Brown
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
| | - Laura M Amendola
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | | | | | - Gillian Halter
- Scripps MD Anderson Cancer Center, San Diego, CA, 92121, USA
| | - Akanchha Kesari
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina, Inc., San Diego, CA, 92122, USA.
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10
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Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
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Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Viora-Dupont E, Robert F, Chassagne A, Pélissier A, Staraci S, Sanlaville D, Edery P, Lesca G, Putoux A, Pons L, Cadenes A, Baurand A, Sawka C, Bertolone G, Spetchian M, Yousfi M, Salvi D, Gautier E, Vitobello A, Denommé-Pichon AS, Bruel AL, Tran Mau-Them F, Faudet A, Keren B, Labalme A, Chatron N, Abel C, Dupuis-Girod S, Poisson A, Buratti J, Mignot C, Afenjar A, Whalen S, Charles P, Heide S, Mouthon L, Moutton S, Sorlin A, Nambot S, Briffaut AS, Asensio ML, Philippe C, Thauvin-Robinet C, Héron D, Rossi M, Meunier-Bellard N, Gargiulo M, Peyron C, Binquet C, Faivre L. Expectations, needs and mid-term outcomes in people accessing to secondary findings from ES: 1st French mixed study (FIND Study). Eur J Hum Genet 2024:10.1038/s41431-024-01616-9. [PMID: 38802530 DOI: 10.1038/s41431-024-01616-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/29/2024] Open
Abstract
Generation and subsequently accessibility of secondary findings (SF) in diagnostic practice is a subject of debate around the world and particularly in Europe. The French FIND study has been set up to assess patient/parent expectations regarding SF from exome sequencing (ES) and to collect their real-life experience until 1 year after the delivery of results. 340 patients who had ES for undiagnosed developmental disorders were included in this multicenter mixed study (quantitative N = 340; qualitative N = 26). Three groups of actionable SF were rendered: predisposition to late-onset actionable diseases; genetic counseling; pharmacogenomics. Participants expressed strong interest in obtaining SF and a high satisfaction level when a SF is reported. The medical actionability of the SF reinforced parents' sense of taking action for their child and was seen as an opportunity. While we observed no serious psychological concerns, we showed that these results could have psychological consequences, in particular for late-onset actionable diseases SF, within families already dealing with rare diseases. This study shows that participants remain in favor of accessing SF despite the potential psychological, care, and lifestyle impacts, which are difficult to anticipate. The establishment of a management protocol, including the support of a multidisciplinary team, would be necessary if national policy allows the reporting of these data.
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Affiliation(s)
- Eléonore Viora-Dupont
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France.
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France.
| | - Françoise Robert
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Clinical Psychology Lab., Psychopathology, Psychoanalysis (EA4056, ED 261), University of Paris, Sorbonne Paris City, Paris, France
| | - Aline Chassagne
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of Sociology and Anthropology (LaSA, EA3189), University of Burgundy-Franche-Comté, Besançon, France
| | - Aurore Pélissier
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Stéphanie Staraci
- Genetics Department, Reference Center for Hereditary Cardiac Disorders, GH APHP, Paris, France
| | - Damien Sanlaville
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Patrick Edery
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Gaetan Lesca
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Audrey Putoux
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Linda Pons
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Amandine Cadenes
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Amandine Baurand
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Caroline Sawka
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Geoffrey Bertolone
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Myrtille Spetchian
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Meriem Yousfi
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Dominique Salvi
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Elodie Gautier
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Antonio Vitobello
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
| | | | - Ange-Line Bruel
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
| | | | - Anne Faudet
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Boris Keren
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Audrey Labalme
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Nicolas Chatron
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- Univ Lyon, Univ Lyon 1, CNRS, INSERM, Physiopathologie et Génétique du Neurone et du Muscle, UMR5261, U1315, Institut NeuroMyoGène, 69008, Lyon, France
| | - Carine Abel
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Sophie Dupuis-Girod
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
| | - Alice Poisson
- Reference Center for Rare Disorders with psychiatric expression C.H. Le Vinatier, Bron, France
- Equipe de recherche AESIO santé, unité de Sant Etienne, Clinique médico chirurgicale mutualiste, Saint Etienne, France
| | - Julien Buratti
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Cyril Mignot
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Alexandra Afenjar
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Sandra Whalen
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Perrine Charles
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Solveig Heide
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Linda Mouthon
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Sébastien Moutton
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Arthur Sorlin
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Sophie Nambot
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France
| | - Anne-Sophie Briffaut
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Marie-Laure Asensio
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | | | - Christel Thauvin-Robinet
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Genetics Department, Reference Center for Intellectual Disabilities, University Hospital, Dijon, France
| | - Delphine Héron
- Genetics Department, Reference Center for Developmental Disorders, GH APHP, Paris, France
| | - Massimiliano Rossi
- Genetics Department, Reference Center for Developmental Disorders, HCL, Bron, France
- INSERM U1028, CNRS UMR5292, CRNL, GENDEV Team, University of Claude Bernard Lyon 1, Bron, France
| | - Nicolas Meunier-Bellard
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Marcela Gargiulo
- Clinical Psychology Lab., Psychopathology, Psychoanalysis (EA4056, ED 261), University of Paris, Sorbonne Paris City, Paris, France
- Institute of myology, GH APHP, Paris, France
| | - Christine Peyron
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- Laboratory of economy (LEDi), University of Burgundy, Dijon, France
| | - Christine Binquet
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France
- CHU Dijon Bourgogne, INSERM, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, Dijon, France
| | - Laurence Faivre
- FHU TRANSLAD, GAD INSERM UMR 1231, University of Burgundy, Dijon, France.
- Genetics Department, Reference Center for Developmental Disorders, University Hospital, Dijon, France.
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12
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Cornel MC, van der Meij KRM, van El CG, Rigter T, Henneman L. Genetic Screening-Emerging Issues. Genes (Basel) 2024; 15:581. [PMID: 38790210 PMCID: PMC11121342 DOI: 10.3390/genes15050581] [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: 03/29/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
In many countries, some form of genetic screening is offered to all or part of the population, either in the form of well-organized screening programs or in a less formalized way. Screening can be offered at different phases of life, such as preconception, prenatal, neonatal and later in life. Screening should only be offered if the advantages outweigh the disadvantages. Technical innovations in testing and treatment are driving changes in the field of prenatal and neonatal screening, where many jurisdictions have organized population-based screening programs. As a result, a greater number and wider range of conditions are being added to the programs, which can benefit couples' reproductive autonomy (preconception and prenatal screening) and improve early diagnosis to prevent irreversible health damage in children (neonatal screening) and in adults (cancer and cascade screening). While many developments in screening are technology-driven, citizens may also express a demand for innovation in screening, as was the case with non-invasive prenatal testing. Relatively new emerging issues for genetic screening, especially if testing is performed using DNA sequencing, relate to organization, data storage and interpretation, benefit-harm ratio and distributive justice, information provision and follow-up, all connected to acceptability in current healthcare systems.
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Affiliation(s)
- Martina C. Cornel
- Section Community Genetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1100 DD Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1100 DD Amsterdam, The Netherlands
| | - Karuna R. M. van der Meij
- Section Community Genetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1100 DD Amsterdam, The Netherlands
| | - Carla G. van El
- Section Community Genetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1100 DD Amsterdam, The Netherlands
| | - Tessel Rigter
- Section Community Genetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1100 DD Amsterdam, The Netherlands
| | - Lidewij Henneman
- Section Community Genetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1007 MB Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1100 DD Amsterdam, The Netherlands
- Amsterdam Reproduction and Development Research Institute, 1100 DD Amsterdam, The Netherlands
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13
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Marshall DA, Hua N, Buchanan J, Christensen KD, Frederix GWJ, Goranitis I, Ijzerman M, Jansen JP, Lavelle TA, Regier DA, Smith HS, Ungar WJ, Weymann D, Wordsworth S, Phillips KA. Paving the path for implementation of clinical genomic sequencing globally: Are we ready? HEALTH AFFAIRS SCHOLAR 2024; 2:qxae053. [PMID: 38783891 PMCID: PMC11115369 DOI: 10.1093/haschl/qxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicolle Hua
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - James Buchanan
- Health Economics and Policy Research Unit, Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London E1 2AB, United Kingdom
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Geert W J Frederix
- Epidemiology and Health Economics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Australian Genomics, Parkville, Victoria 3052, Australia
| | - Maarten Ijzerman
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria 3000, Australia
- Erasmus School of Health Policy & Management, Eramus University Rotterdam, 3062 PA Rotterdam, The Netherlands
| | - Jeroen P Jansen
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, United States
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hadley S Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario M5T 3M6, Canada
| | - Deirdre Weymann
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health and NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Kathryn A Phillips
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
- Health Affairs Scholar Emerging & Global Health Policy, Health Affairs, Washington, DC 20036, United States
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14
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Amiel J, Héron D, Isidor B. [Exome, genome and incidental findings]. Med Sci (Paris) 2024; 40:377-380. [PMID: 38651963 DOI: 10.1051/medsci/2024029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Affiliation(s)
- Jeanne Amiel
- Service de Médecine génomique des maladies rares, hôpital Necker-Enfants Malades, Paris
| | - Delphine Héron
- UF de génétique clinique, APHP Sorbonne Université, hôpital Pitié-Salpêtrière, Paris
| | - Bertrand Isidor
- Service de génétique médicale, unité de génétique clinique, CHU de Nantes - Hôtel Dieu, Nantes
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15
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Nolan J, Buchanan J, Taylor J, Almeida J, Bedenham T, Blair E, Broadgate S, Butler S, Cazeaux A, Craft J, Cranston T, Crawford G, Forrest J, Gabriel J, George E, Gillen D, Haeger A, Hastings Ward J, Hawkes L, Hodgkiss C, Hoffman J, Jones A, Karpe F, Kasperaviciute D, Kovacs E, Leigh S, Limb E, Lloyd-Jani A, Lopez J, Lucassen A, McFarlane C, O'Rourke AW, Pond E, Sherman C, Stewart H, Thomas E, Thomas S, Thomas T, Thomson K, Wakelin H, Walker S, Watson M, Williams E, Ormondroyd E. Secondary (additional) findings from the 100,000 Genomes Project: Disease manifestation, health care outcomes, and costs of disclosure. Genet Med 2024; 26:101051. [PMID: 38131308 DOI: 10.1016/j.gim.2023.101051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The UK 100,000 Genomes Project offered participants screening for additional findings (AFs) in genes associated with familial hypercholesterolemia (FH) or hereditary cancer syndromes including breast/ovarian cancer (HBOC), Lynch, familial adenomatous polyposis, MYH-associated polyposis, multiple endocrine neoplasia (MEN), and von Hippel-Lindau. Here, we report disclosure processes, manifestation of AF-related disease, outcomes, and costs. METHODS An observational study in an area representing one-fifth of England. RESULTS Data were collected from 89 adult AF recipients. At disclosure, among 57 recipients of a cancer-predisposition-associated AF and 32 recipients of an FH-associated AF, 35% and 88%, respectively, had personal and/or family history evidence of AF-related disease. During post-disclosure investigations, 4 cancer-AF recipients had evidence of disease, including 1 medullary thyroid cancer. Six women with an HBOC AF, 3 women with a Lynch syndrome AF, and 2 individuals with a MEN AF elected for risk-reducing surgery. New hyperlipidemia diagnoses were made in 6 FH-AF recipients and treatment (re-)initiated for 7 with prior hyperlipidemia. Generating and disclosing AFs in this region cost £1.4m; £8680 per clinically significant AF. CONCLUSION Generation and disclosure of AFs identifies individuals with and without personal or familial evidence of disease and prompts appropriate clinical interventions. Results can inform policy toward secondary findings.
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Affiliation(s)
- Joshua Nolan
- Radcliffe Department of Medicine, University of Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, United Kingdom
| | - John Taylor
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joao Almeida
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Tina Bedenham
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Edward Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Suzanne Broadgate
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Samantha Butler
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Angela Cazeaux
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Judith Craft
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Treena Cranston
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Gillian Crawford
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Jamie Forrest
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; University of Manchester, Manchester, United Kingdom
| | - Jessica Gabriel
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Elaine George
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Donna Gillen
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Ash Haeger
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | | | - Lara Hawkes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Claire Hodgkiss
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Jonathan Hoffman
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Alan Jones
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Fredrik Karpe
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Dalia Kasperaviciute
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Erika Kovacs
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Sarah Leigh
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Limb
- Population Health Research Institute, St George's University of London, London, United Kingdom
| | - Anjali Lloyd-Jani
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Javier Lopez
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Anneke Lucassen
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Centre for Personalised Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Carlos McFarlane
- Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Anthony W O'Rourke
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Emily Pond
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Catherine Sherman
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Ellen Thomas
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Simon Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Tessy Thomas
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Thomson
- Oxford Genetic Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Hannah Wakelin
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Susan Walker
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Melanie Watson
- University Hospitals Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Eleanor Williams
- Genomics England, United Kingdom Department of Health and Social Care, United Kingdom
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, University of Oxford, United Kingdom; NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom.
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16
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Goranitis I, Meng Y, Martyn M, Best S, Bouffler S, Bombard Y, Gaff C, Stark Z. Eliciting parental preferences and values for the return of additional findings from genomic sequencing. NPJ Genom Med 2024; 9:10. [PMID: 38355752 PMCID: PMC10867021 DOI: 10.1038/s41525-024-00399-8] [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: 08/26/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Health economic evidence is needed to inform the design of high-value and cost-effective processes for returning genomic results from analyses for additional findings (AF). This study reports the results of a discrete-choice experiment designed to elicit preferences for the process of returning AF results from the perspective of parents of children with rare conditions and to estimate the value placed on AF analysis. Overall, 94 parents recruited within the Australian Genomics and Melbourne Genomics programmes participated in the survey, providing preferences in a total of 1128 choice scenarios. Statistically significant preferences were identified for the opportunity to change the choices made about AF; receiving positive AF in person from a genetic counsellor; timely access to a medical specialist and high-quality online resources; receiving automatic updates through a secure online portal if new information becomes available; and lower costs. For AF uptake rates ranging between 50-95%, the mean per person value from AF analysis was estimated at AU$450-$1700 (US$300-$1140). The findings enable the design of a value-maximising process of analysis for AF in rare-disease genomic sequencing.
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Affiliation(s)
- Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.
- Australian Genomics, Melbourne, VIC, Australia.
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.
| | - Yan Meng
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa Martyn
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Stephanie Best
- Australian Genomics, Melbourne, VIC, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Victorian Comprehensive Cancer Centre Alliance, Melbourne, VIC, Australia
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sophie Bouffler
- Australian Genomics, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, Canada
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Melbourne Genomics Health Alliance, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC, Australia
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
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17
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Friedman JM, Bombard Y, Carleton B, Issa AM, Knoppers B, Plon SE, Rahimzadeh V, Relling MV, Williams MS, van Karnebeek C, Vears D, Cornel MC. Should secondary pharmacogenomic variants be actively screened and reported when diagnostic genome-wide sequencing is performed in a child? Genet Med 2024; 26:101033. [PMID: 38007624 DOI: 10.1016/j.gim.2023.101033] [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: 04/24/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023] Open
Abstract
This white paper was prepared by the Global Alliance for Genomics and Health Regulatory and Ethics Work Stream's Pediatric Task Team to review and provide perspective with respect to ethical, legal, and social issues regarding the return of secondary pharmacogenomic variants in children who have a serious disease or developmental disorder and are undergoing exome or genome sequencing to identify a genetic cause of their condition. We discuss actively searching for and reporting pharmacogenetic/genomic variants in pediatric patients, different methods of returning secondary pharmacogenomic findings to the patient/parents and/or treating clinicians, maintaining these data in the patient's health record over time, decision supports to assist using pharmacogenetic results in future treatment decisions, and sharing information in public databases to improve the clinical interpretation of pharmacogenetic variants identified in other children. We conclude by presenting a series of points to consider for clinicians and policymakers regarding whether, and under what circumstances, routine screening and return of pharmacogenomic variants unrelated to the indications for testing is appropriate in children who are undergoing genome-wide sequencing to assist in the diagnosis of a suspected genetic disease.
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Affiliation(s)
- Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Bruce Carleton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Division of Translational Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pharmaceutical Outcomes Programme, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Amalia M Issa
- Personalized Precision Medicine & Targeted Therapeutics, Springfield, MA; Health Policy, University of the Sciences, Philadelphia, PA; Pharmaceutical Sciences, University of the Sciences, Philadelphia, PA; Family Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Sharon E Plon
- Department of Pediatrics, Texas Children's Cancer and Hematology Center, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Vasiliki Rahimzadeh
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Mary V Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Clara van Karnebeek
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam University Medical Centers, Amsterdam, The Netherlands; United for Metabolic Diseases, The Netherlands; Radboud Center for Mitochondrial and Metabolic Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danya Vears
- University of Melbourne, Carlton, Melbourne, Australia; Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martina C Cornel
- Department of Human Genetics and Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands
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18
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Koster R, Schipper LJ, Giesbertz NAA, van Beek D, Mendeville M, Samsom KG, Rosenberg EH, Hogervorst FBL, Roepman P, Boelens MC, Bosch LJW, van den Berg JG, Meijer GA, Voest EE, Cuppen E, Ruijs MWG, van Wezel T, van der Kolk L, Monkhorst K. Impact of genetic counseling strategy on diagnostic yield and workload for genome-sequencing-based tumor diagnostics. Genet Med 2024; 26:101032. [PMID: 38006283 DOI: 10.1016/j.gim.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
PURPOSE Genome sequencing (GS) enables comprehensive molecular analysis of tumors and identification of hereditary cancer predisposition. According to guidelines, directly determining pathogenic germline variants (PGVs) requires pretest genetic counseling, which is cost-ineffective. Referral for genetic counseling based on tumor variants alone could miss relevant PGVs and/or result in unnecessary referrals. METHODS We validated GS for detection of germline variants and simulated 3 strategies using paired tumor-normal GS data of 937 metastatic patients. In strategy-1, genetic counseling before tumor testing allowed direct PGV analysis. In strategy-2 and -3, germline testing and referral for post-test genetic counseling is based on tumor variants using Dutch (strategy-2) or Europen Society for Medical Oncology (ESMO) Precision Medicine Working Group (strategy-3) guidelines. RESULTS In strategy-1, PGVs would be detected in 50 patients (number-needed-to counsel; NTC = 18.7). In strategy-2, 86 patients would have been referred for genetic counseling and 43 would have PGVs (NTC = 2). In strategy-3, 94 patients would have been referred for genetic counseling and 32 would have PGVs (NTC = 2.9). Hence, 43 and 62 patients, respectively, were unnecessarily referred based on a somatic variant. CONCLUSION Both post-tumor test counseling strategies (2 and 3) had significantly lower NTC, and strategy-2 had the highest PGV yield. Combining pre-tumor test mainstreaming and post-tumor test counseling may maximize the clinically relevant PGV yield and minimize unnecessary referrals.
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Affiliation(s)
- Roelof Koster
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Luuk J Schipper
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Kris G Samsom
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Linda J W Bosch
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Gerrit A Meijer
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Tom van Wezel
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Kim Monkhorst
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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19
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Fernández-Castillejo S, Roig B, Melé M, Serrano S, Salvat M, Querol M, Brunet J, Pineda M, Cisneros A, Parada D, Badia J, Borràs J, Rodríguez-Balada M, Gumà J. Opportunistic genetic screening increases the diagnostic yield and is medically valuable for care of patients and their relatives with hereditary cancer. J Med Genet 2023; 61:69-77. [PMID: 37591735 PMCID: PMC10803988 DOI: 10.1136/jmg-2023-109389] [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: 05/10/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Multigene panel testing by next-generation sequencing (MGP-NGS) enables the detection of germline pathogenic or likely pathogenic variants (PVs/LPVs) in genes beyond those associated with a certain cancer phenotype. Opportunistic genetic screening based on MGP-NGS in patients with suspicion of hereditary cancer reveals these incidental findings (IFs). METHODS MGP-NGS was performed in patients who fulfilled the clinical criteria to undergo genetic testing according to the Catalan Health Service guidelines. Variants were classified following the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and the Cancer Variant Interpretation Group UK guidelines. RESULTS IFs were identified in 10 (1.22%) of the 817 patients who underwent MGP-NGS. The mean age at cancer diagnosis was 49.4±9.5 years. Three IFs (30.0%) were detected in PMS2, two (20.0%) in ATM and TP53 and one (10.0%) in MSH6, NTHL1 and VHL. Seven (70.0%) IFs were single-nucleotide substitutions, two (20.0%) were deletions and one (10.0%) was a duplication. Three (30.0) IFs were located in intronic regions, three (30.3%) were nonsense, two (20.0%) were frameshift and two (20.0%) were missense variations. Six (60.0%) IFs were classified as PVs and four (40.0%) as LPVs. CONCLUSIONS Opportunistic genetic screening increased the diagnostic yield by 1.22% in our cohort. Most of the identified IFs were present in clinically actionable genes (n=7; 70.0%), providing these families with an opportunity to join cancer early detection programmes, as well as secondary cancer prevention. IFs might facilitate the diagnosis of asymptomatic individuals and the early management of cancer once it develops.
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Affiliation(s)
- Sara Fernández-Castillejo
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Bàrbara Roig
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mireia Melé
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Sara Serrano
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mònica Salvat
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Montserrat Querol
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBGI, Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
| | - Adela Cisneros
- Hematology Department, ICO and Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - David Parada
- Pathology Molecular Unit, Department of Pathology, Hospital Universitari Sant Joan de Reus (HUSJR), Spain. Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Badia
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Borràs
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Marta Rodríguez-Balada
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Josep Gumà
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
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20
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Grauman Å, Ancillotti M, Veldwijk J, Mascalzoni D. Precision cancer medicine and the doctor-patient relationship: a systematic review and narrative synthesis. BMC Med Inform Decis Mak 2023; 23:286. [PMID: 38098034 PMCID: PMC10722840 DOI: 10.1186/s12911-023-02395-x] [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: 03/29/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The implementation of precision medicine is likely to have a huge impact on clinical cancer care, while the doctor-patient relationship is a crucial aspect of cancer care that needs to be preserved. This systematic review aimed to map out perceptions and concerns regarding how the implementation of precision medicine will impact the doctor-patient relationship in cancer care so that threats against the doctor-patient relationship can be addressed. METHODS Electronic databases (Pubmed, Scopus, Web of Science, Social Science Premium Collection) were searched for articles published from January 2010 to December 2021, including qualitative, quantitative, and theoretical methods. Two reviewers completed title and abstract screening, full-text screening, and data extraction. Findings were summarized and explained using narrative synthesis. RESULTS Four themes were generated from the included articles (n = 35). Providing information addresses issues of information transmission and needs, and of complex concepts such as genetics and uncertainty. Making decisions in a trustful relationship addresses opacity issues, the role of trust, and and physicians' attitude towards the role of precision medicine tools in decision-making. Managing negative reactions of non-eligible patients addresses patients' unmet expectations of precision medicine. Conflicting roles in the blurry line between clinic and research addresses issues stemming from physicians' double role as doctors and researchers. CONCLUSIONS Many findings have previously been addressed in doctor-patient communication and clinical genetics. However, precision medicine adds complexity to these fields and further emphasizes the importance of clear communication on specific themes like the distinction between genomic and gene expression and patients' expectations about access, eligibility, effectiveness, and side effects of targeted therapies.
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Affiliation(s)
- Å Grauman
- Centre for Research Ethics and Bioethics, Uppsala University, Box 564, Uppsala, SE-751 22, Sweden.
| | - M Ancillotti
- Centre for Research Ethics and Bioethics, Uppsala University, Box 564, Uppsala, SE-751 22, Sweden
| | - J Veldwijk
- Erasmus School of Health Policy & Management, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Erasmus Choice Modelling Centre, Erasmus University Rotterdam, Rotterdam, the Netherlands
| | - D Mascalzoni
- Centre for Research Ethics and Bioethics, Uppsala University, Box 564, Uppsala, SE-751 22, Sweden
- Erasmus Choice Modelling Centre, Erasmus University Rotterdam, Rotterdam, the Netherlands
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21
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Kuiper JML, Borry P, Vears DF, Van Esch H, Cornel MC, Van Hoyweghen I. Dealing with ambivalence in the practice of advanced genetic healthcare: towards an ethical choreography. Eur J Hum Genet 2023; 31:1387-1392. [PMID: 37592172 PMCID: PMC10689481 DOI: 10.1038/s41431-023-01436-3] [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: 02/17/2023] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
The implementation of next-generation sequencing (NGS) in diagnostic practice has stimulated ongoing debates on how to construct and perform "good" genomic care. Our multi-sited qualitative fieldwork at two large European centres for human genetics (CHGs) revealed tangible ambivalence in beliefs, norms, and actions in the enactment of NGS practices across sites stemming from differing expectations, interests, demands, and tensions. First, ambivalence was present around the boundaries of clinical diagnostic genetic care. The overlap between research and clinical work and diagnostics and screening led to ambivalence around "best" practices and norms concerning whom to offer NGS testing and how far to take testing. Secondly, the clinical value of NGS results, especially VUS and unsolicited findings, was ambivalently valued, resulting in an inconsistent approach towards these types of findings. Thirdly, ambivalence was recognized in applying guidelines in the reality of clinical practice. The ambivalence we encountered was often not made explicit or acknowledged, causing a failure to benefit from its possibility to encourage reflexivity and change. We propose to facilitate a more explicit ethical choreography [27], where ethics and science are developed iteratively whilst welcoming different perspectives and disciplines. Pulling experiences and practices of ambivalence into the light can help to understand the points of tension in the values and internal logic in care practices within the CHGs and facilitate a more informed, transparent, and consciously chosen direction for genetic care.
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Affiliation(s)
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Danya F Vears
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Hilde Van Esch
- Center for Human genetics, University Hospitals Leuven, Leuven, Belgium
| | - Martina C Cornel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Human Genetics and Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
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22
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Deutsche Gesellschaft für Humangenetik e.V. (GfH). MED GENET-BERLIN 2023; 35:313-321. [PMID: 38841542 PMCID: PMC11006314 DOI: 10.1515/medgen-2023-2060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
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23
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Hartley T, Gillespie MK, Graham ID, Hayeems RZ, Li S, Sampson M, Boycott KM, Potter BK. Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations. Genet Med 2023; 25:100948. [PMID: 37551668 DOI: 10.1016/j.gim.2023.100948] [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: 03/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023] Open
Abstract
PURPOSE Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations. METHODS We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool. RESULTS We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores. CONCLUSION Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.
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Affiliation(s)
- Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; University of Ottawa, Ottawa, Ontario, Canada.
| | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Ian D Graham
- University of Ottawa, Ottawa, Ontario, Canada; The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Robin Z Hayeems
- Hospital for Sick Children, Toronto, Ontario, Canada; University of Toronto, Toronto, Ontario, Canada
| | - Sheena Li
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Margaret Sampson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada; University of Ottawa, Ottawa, Ontario, Canada; Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
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24
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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25
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Ormond KE, Blasimme A, Vayena E. Ethical Aspects of Pediatric Genetic Care: Testing and Treatment. Pediatr Clin North Am 2023; 70:1029-1046. [PMID: 37704345 DOI: 10.1016/j.pcl.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Pediatric health care providers caring for patients and families with genetic disease will encounter a range of ethical issues. These include traditional pediatric health care issues, such as surrogate decision making and end-of-life care. Genetic testing raises the importance of informed consent for potential risks that move beyond the oft discussed physical risks and into longer term concepts such as psychological impact, privacy and potential discrimination. Predictive testing in childhood also raises questions of whether the child has an autonomy interest in delaying testing until they have decision making capacity to do so on their own. And finally, treatments including gene therapies and gene editing, may raise issues of identity for families dealing with genetic disease.
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Affiliation(s)
- Kelly E Ormond
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland; Department of Genetics and Stanford Center for Biomedical Ethics, Stanford University School of Medicine.
| | - Alessandro Blasimme
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland
| | - Effy Vayena
- Department of Health Sciences and Technology, Health Ethics & Policy Lab, ETH Zurich. Hottingerstrasse 10, Zurich 8092, Switzerland
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26
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McGurk KA, Zhang X, Theotokis P, Thomson K, Harper A, Buchan RJ, Mazaika E, Ormondroyd E, Wright WT, Macaya D, Pua CJ, Funke B, MacArthur DG, Prasad SK, Cook SA, Allouba M, Aguib Y, Yacoub MH, O'Regan DP, Barton PJR, Watkins H, Bottolo L, Ware JS. The penetrance of rare variants in cardiomyopathy-associated genes: A cross-sectional approach to estimating penetrance for secondary findings. Am J Hum Genet 2023; 110:1482-1495. [PMID: 37652022 PMCID: PMC10502871 DOI: 10.1016/j.ajhg.2023.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Understanding the penetrance of pathogenic variants identified as secondary findings (SFs) is of paramount importance with the growing availability of genetic testing. We estimated penetrance through large-scale analyses of individuals referred for diagnostic sequencing for hypertrophic cardiomyopathy (HCM; 10,400 affected individuals, 1,332 variants) and dilated cardiomyopathy (DCM; 2,564 affected individuals, 663 variants), using a cross-sectional approach comparing allele frequencies against reference populations (293,226 participants from UK Biobank and gnomAD). We generated updated prevalence estimates for HCM (1:543) and DCM (1:220). In aggregate, the penetrance by late adulthood of rare, pathogenic variants (23% for HCM, 35% for DCM) and likely pathogenic variants (7% for HCM, 10% for DCM) was substantial for dominant cardiomyopathy (CM). Penetrance was significantly higher for variant subgroups annotated as loss of function or ultra-rare and for males compared to females for variants in HCM-associated genes. We estimated variant-specific penetrance for 316 recurrent variants most likely to be identified as SFs (found in 51% of HCM- and 17% of DCM-affected individuals). 49 variants were observed at least ten times (14% of affected individuals) in HCM-associated genes. Median penetrance was 14.6% (±14.4% SD). We explore estimates of penetrance by age, sex, and ancestry and simulate the impact of including future cohorts. This dataset reports penetrance of individual variants at scale and will inform the management of individuals undergoing genetic screening for SFs. While most variants had low penetrance and the costs and harms of screening are unclear, some individuals with highly penetrant variants may benefit from SFs.
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Affiliation(s)
- Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Kate Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Harper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Erica Mazaika
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William T Wright
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, Northern Ireland, UK
| | | | - Chee Jian Pua
- National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sanjay K Prasad
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Stuart A Cook
- MRC London Institute of Medical Sciences, Imperial College London, London, UK; National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, UK; The Alan Turing Institute, London, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
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27
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Christian S, Dzwiniel T. Principles of Genetic Counseling in Inherited Heart Conditions. Card Electrophysiol Clin 2023; 15:229-239. [PMID: 37558294 DOI: 10.1016/j.ccep.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Cardiac genetic counseling is the process of helping individuals adapt to a personal diagnosis or family history of an inherited heart condition. The process is shown to benefit patients and includes specialized skills, such as counseling children and interpreting complex genetic results. Emerging areas include: evolving service delivery models for caring for patients and communicating risk to relatives, new areas of need including postmortem molecular autopsy, and new populations of individuals found to carry a likely pathogenic/pathogenic cardiac variant identified through genomic screening. This article provides an overview of the cardiac genetic counseling process and evolving areas in the field.
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Affiliation(s)
- Susan Christian
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.
| | - Tara Dzwiniel
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
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Leitsalu L, Reigo A, Palover M, Nikopensius T, Läll K, Krebs K, Reisberg S, Mägi R, Kals M, Alavere H, Nõukas M, Kolk A, Normet I, Tammesoo ML, Käärik E, Puusepp M, Metsalu K, Allik A, Milani L, Fischer K, Tõnisson N, Metspalu A. Lessons learned during the process of reporting individual genomic results to participants of a population-based biobank. Eur J Hum Genet 2023; 31:1048-1056. [PMID: 36192438 PMCID: PMC10474261 DOI: 10.1038/s41431-022-01196-6] [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: 04/29/2022] [Revised: 08/06/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
The return of individual genomic results (ROR) to research participants is still in its early phase, and insight on how individuals respond to ROR is scarce. Studies contributing to the evidence base for best practices are crucial before these can be established. Here, we describe a ROR procedure conducted at a population-based biobank, followed by surveying the responses of almost 3000 participants to a range of results, and discuss lessons learned from the process, with the aim of facilitating large-scale expansion. Overall, participants perceived the information that they received with counseling as valuable, even when the reporting of high risks initially caused worry. The face-to-face delivery of results limited the number of participants who received results. Although the participants highly valued this type of communication, additional means of communication need to be considered to improve the feasibility of large-scale ROR. The feedback collected sheds light on the value judgements of the participants and on potential responses to the receipt of genetic risk information. Biobanks in other countries are planning or conducting similar projects, and the sharing of lessons learned may provide valuable insight and aid such endeavors.
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Affiliation(s)
- Liis Leitsalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marili Palover
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tiit Nikopensius
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kristi Läll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kristi Krebs
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sulev Reisberg
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- STACC, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mart Kals
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Helene Alavere
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Margit Nõukas
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anneli Kolk
- Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Ivi Normet
- Family Medicine Center of Medicum, Tallinn, Estonia
| | - Mari-Liis Tammesoo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Käärik
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Mairo Puusepp
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kristjan Metsalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Annely Allik
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Current - Estonian Research Council, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Krista Fischer
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Mathematics and Statistics, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Tartu University Hospital, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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29
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Clayton EW, Tritell AM, Thorogood AM. Avoiding Liability and Other Legal Land Mines in the Evolving Genomics Landscape. Annu Rev Genomics Hum Genet 2023; 24:333-346. [PMID: 36630592 DOI: 10.1146/annurev-genom-100722-021725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This article reviews evolving legal implications for clinicians and researchers as genomics is used more widely in both the clinic and in translational research, reflecting rapid changes in scientific knowledge as well as the surrounding cultural and political environment. Professionals will face new and changing duties to make or act upon a genetic diagnosis, address direct-to-consumer genetic testing in patient care, consider the health implications of results for patients' family members, and recontact patients when test results change over time. Professional duties in reproductive genetic testing will need to be recalibrated in response to disruptive changes to reproductive rights in the United States. We also review the debate over who controls the flow of genetic information and who is responsible for its protection, considering the globally influential European Union General Data Protection Regulation and the rapidly evolving data privacy law landscape of the United States.
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Affiliation(s)
- Ellen Wright Clayton
- Department of Pediatrics and Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, Tennessee, USA;
- School of Law, Vanderbilt University, Nashville, Tennessee, USA;
| | - Alex M Tritell
- School of Law, Vanderbilt University, Nashville, Tennessee, USA;
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30
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Brunfeldt M, Kaare M, Saarinen I, Koskenvuo J, Kääriäinen H. Opt-in for secondary findings as part of diagnostic whole-exome sequencing: Real-life experience from an international diagnostic laboratory. Mol Genet Genomic Med 2023; 11:e2180. [PMID: 37025058 PMCID: PMC10422066 DOI: 10.1002/mgg3.2180] [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: 08/08/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Discussion about the risks and benefits of offering secondary findings as part of genome-wide diagnostics lacks real-life data. We studied the opt-in decisions of patients/families referred to whole exome study (WES) in Blueprint Genetics (BpG), a genetic testing company with customers in over 70 countries to receive secondary findings. Based on the American College of Medical Genetics (ACMG) recommendations for reporting secondary findings, BpG offered testing of specific actionable genes without additional charge for specimens submitted to WES diagnostics. METHODS Individuals could opt-in for a secondary findings analysis by using a separate electronic consent form. Data from BpG database of electronic consent forms was used for the analysis. RESULTS During the selected study period there were 3263 WES referrals, from which 2012 were index patients. About half of the individuals (50.4%) opted in to receiving secondary findings. Of patients who opted in, a secondary finding was detected for 2.7%, similar to other studies. We detected huge differences relating to opt-in between individuals from different countries; for instance, 90% of the 41 patients and their family members in Romania opted to receive secondary findings, while none of the 98 patients in Luxembourg chose that option. CONCLUSION Differences between sexes or between children and adults were small. This data offers one view to the interest of patients and family members to opt in to receiving secondary findings. Research is needed to understand the influence of factors like age, education etc. and possible participation in pre-test counseling to receiving/not receiving secondary findings.
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Affiliation(s)
| | - Milja Kaare
- Blueprint Genetics, a Quest Diagnostics CompanyEspooFinland
| | - Inka Saarinen
- Blueprint Genetics, a Quest Diagnostics CompanyEspooFinland
| | - Juha Koskenvuo
- Blueprint Genetics, a Quest Diagnostics CompanyEspooFinland
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31
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Kodida R, Reble E, Clausen M, Shickh S, Mighton C, Sam J, Forster N, Panchal S, Aronson M, Semotiuk K, Graham T, Silberman Y, Randall Armel S, McCuaig JM, Cohn I, Morel CF, Elser C, Eisen A, Carroll JC, Glogowski E, Schrader KA, Di Gioacchino V, Lerner-Ellis J, Kim RH, Bombard Y. A model for the return and referral of all clinically significant secondary findings of genomic sequencing. J Med Genet 2023; 60:733-739. [PMID: 37217257 DOI: 10.1136/jmg-2022-109091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Secondary findings (SFs) identified through genomic sequencing (GS) can offer a wide range of health benefits to patients. Resource and capacity constraints pose a challenge to their clinical management; therefore, clinical workflows are needed to optimise the health benefits of SFs. In this paper, we describe a model we created for the return and referral of all clinically significant SFs, beyond medically actionable results, from GS. As part of a randomised controlled trial evaluating the outcomes and costs of disclosing all clinically significant SFs from GS, we consulted genetics and primary care experts to determine a feasible workflow to manage SFs. Consensus was sought to determine appropriate clinical recommendations for each category of SF and which clinician specialist would provide follow-up care. We developed a communication and referral plan for each category of SFs. This involved referrals to specialised clinics, such as an Adult Genetics clinic, for highly penetrant medically actionable findings. Common and non-urgent SFs, such as pharmacogenomics and carrier status results for non-family planning participants, were directed back to the family physician (FP). SF results and recommendations were communicated directly to participants to respect autonomy and to their FPs to support follow-up of SFs. We describe a model for the return and referral of all clinically significant SFs to facilitate the utility of GS and promote the health benefits of SFs. This may serve as a model for others returning GS results transitioning participants from research to clinical settings.
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Affiliation(s)
- Rita Kodida
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Marc Clausen
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Salma Shickh
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Jordan Sam
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Nicole Forster
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
| | - Seema Panchal
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Kara Semotiuk
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Tracy Graham
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yael Silberman
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology & Toxicology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chantal F Morel
- Fred A. Litwin Family Centre in Genetic Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine Elser
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Eisen
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - June C Carroll
- Department of Family & Community Medicine, University of Toronto, Toronto, Ontario, Canada
- Granovsky Gluskin Family Medicine Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | | | - Kasmintan A Schrader
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Vanessa Di Gioacchino
- The Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Jordan Lerner-Ellis
- Pathology & Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, Ontario, Canada
| | - Raymond H Kim
- Division of Medical Oncology & Hematology, Princess Margaret Hospital Cancer Centre, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services & Policy Research Program, Li Ka Shing Knowledge Institute, St Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management & Evaluation, University of Toronto, Toronto, Ontario, Canada
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32
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Henkel J, Laner A, Locher M, Wohlfrom T, Neitzel B, Becker K, Neuhann T, Abicht A, Steinke-Lange V, Holinski-Feder E. Diagnostic yield and clinical relevance of expanded germline genetic testing for nearly 7000 suspected HBOC patients. Eur J Hum Genet 2023; 31:925-930. [PMID: 37188824 PMCID: PMC10400578 DOI: 10.1038/s41431-023-01380-2] [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: 10/11/2022] [Revised: 01/18/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Here we report the results of a retrospective germline analysis of 6941 individuals fulfilling the criteria necessary for genetic testing of hereditary breast- and ovarian cancer (HBOC) according to the German S3 or AGO Guidelines. Genetic testing was performed by next-generation sequencing using 123 cancer-associated genes based on the Illumina TruSight® Cancer Sequencing Panel. In 1431 of 6941 cases (20.6%) at least one variant was reported (ACMG/AMP classes 3-5). Of those 56.3% (n = 806) were class 4 or 5 and 43.7% (n = 625) were a class 3 (VUS). We defined a 14 gene HBOC core gene panel and compared this to a national and different internationally recommended gene panels (German Hereditary Breast and Ovarian Cancer Consortium HBOC Consortium, ClinGen expert Panel, Genomics England PanelsApp) in regard of diagnostic yield, revealing a diagnostic range of pathogenic variants (class 4/5) from 7.8 to 11.6% depending on the panel evaluated. With the 14 HBOC core gene panel having a diagnostic yield of pathogenic variants (class 4/5) of 10.8%. Additionally, 66 (1%) pathogenic variants (ACMG/AMP class 4 or 5) were found in genes outside the 14 HBOC core gene set (secondary findings) that would have been missed with the restriction to the analysis of HBOC genes. Furthermore, we evaluated a workflow for a periodic re-evaluation of variants of uncertain clinical significance (VUS) for the improvement of clinical validity of germline genetic testing.
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Affiliation(s)
- Jan Henkel
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
| | | | | | | | | | | | - Angela Abicht
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Friedrich-Baur-Institute, Department of Neurology, Klinikum der Universität, Ludwig-Maximilians-Universität, München, Germany
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, München, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, München, Germany.
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität, München, Germany.
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Bouffler SE, Lee L, Lynch F, Martyn M, Lynch E, Macciocca I, Curnow L, McCorkell G, Lunke S, Chong B, Marum JE, Delatycki M, Downie L, Goranitis I, Vears DF, Best S, Clausen M, Bombard Y, Stark Z, Gaff CL. Two-step offer and return of multiple types of additional genomic findings to families after ultrarapid trio genomic testing in the acute care setting: a study protocol. BMJ Open 2023; 13:e072999. [PMID: 37270192 DOI: 10.1136/bmjopen-2023-072999] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
INTRODUCTION As routine genomic testing expands, so too does the opportunity to look for additional health information unrelated to the original reason for testing, termed additional findings (AF). Analysis for many different types of AF may be available, particularly to families undergoing trio genomic testing. The optimal model for service delivery remains to be determined, especially when the original test occurs in the acute care setting. METHODS AND ANALYSIS Families enrolled in a national study providing ultrarapid genomic testing to critically ill children will be offered analysis for three types of AF on their stored genomic data: paediatric-onset conditions in the child, adult-onset conditions in each parent and reproductive carrier screening for the parents as a couple. The offer will be made 3-6 months after diagnostic testing. Parents will have access to a modified version of the Genetics Adviser web-based decision support tool before attending a genetic counselling appointment to discuss consent for AF. Parental experiences will be evaluated using qualitative and quantitative methods on data collected through surveys, appointment recordings and interviews at multiple time points. Evaluation will focus on parental preferences, uptake, decision support use and understanding of AF. Genetic health professionals' perspectives on acceptability and feasibility of AF will also be captured through surveys and interviews. ETHICS AND DISSEMINATION This project received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. Findings will be disseminated through peer-review journal articles and at conferences nationally and internationally.
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Affiliation(s)
| | - Ling Lee
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Fiona Lynch
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ivan Macciocca
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lisette Curnow
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Giulia McCorkell
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sebastian Lunke
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Justine E Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Martin Delatycki
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lilian Downie
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Ilias Goranitis
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, Melbourne Schoold of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Danya F Vears
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marc Clausen
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Zornitza Stark
- Australian Genomics Health Alliance, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
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Vears DF, Hallowell N, Bentzen HB, Ellul B, Nøst TH, Kerasidou A, Kerr SM, Th Mayrhofer M, Mežinska S, Ormondroyd E, Solberg B, Sand BW, Budin-Ljøsne I. A practical checklist for return of results from genomic research in the European context. Eur J Hum Genet 2023; 31:687-695. [PMID: 36949262 PMCID: PMC10250331 DOI: 10.1038/s41431-023-01328-6] [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: 09/12/2022] [Revised: 02/13/2023] [Accepted: 02/21/2023] [Indexed: 03/24/2023] Open
Abstract
An increasing number of European research projects return, or plan to return, individual genomic research results (IRR) to participants. While data access is a data subject's right under the General Data Protection Regulation (GDPR), and many legal and ethical guidelines allow or require participants to receive personal data generated in research, the practice of returning results is not straightforward and raises several practical and ethical issues. Existing guidelines focusing on return of IRR are mostly project-specific, only discuss which results to return, or were developed outside Europe. To address this gap, we analysed existing normative documents identified online using inductive content analysis. We used this analysis to develop a checklist of steps to assist European researchers considering whether to return IRR to participants. We then sought feedback on the checklist from an interdisciplinary panel of European experts (clinicians, clinical researchers, population-based researchers, biobank managers, ethicists, lawyers and policy makers) to refine the checklist. The checklist outlines seven major components researchers should consider when determining whether, and how, to return results to adult research participants: 1) Decide which results to return; 2) Develop a plan for return of results; 3) Obtain participant informed consent; 4) Collect and analyse data; 5) Confirm results; 6) Disclose research results; 7) Follow-up and monitor. Our checklist provides a clear outline of the steps European researchers can follow to develop ethical and sustainable result return pathways within their own research projects. Further legal analysis is required to ensure this checklist complies with relevant domestic laws.
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Affiliation(s)
- Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC, 3052, Australia.
- University of Melbourne, Parkville, VIC, 3052, Australia.
- Centre for Biomedical Ethics and Law, KU Leuven, Leuven, 3000, Belgium.
- Uehiro Centre for Practical Ethics, University of Oxford, Oxford, OX3 7RF, UK.
| | - Nina Hallowell
- Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield department of Population Health, University of Oxford, Oxford, OX3 7RF, UK
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bridget Ellul
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
- K. G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Faculty of Medicine and Health, NTNU, Norwegian University of Science and Technology, N- 7491, Trondheim, Norway
| | - Angeliki Kerasidou
- Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield department of Population Health, University of Oxford, Oxford, OX3 7RF, UK
| | - Shona M Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | | | - Signe Mežinska
- Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
| | - Elizabeth Ormondroyd
- Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre United Kingdom, University of Oxford, Oxford, UK
| | - Berge Solberg
- Department of Public Health and Nursing, The Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Isabelle Budin-Ljøsne
- Division of Climate and Environmental Health, Department of Food Safety, Norwegian Institute of Public Health, Oslo, Norway
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35
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Shickh S, Sebastian A, Clausen M, Mighton C, Elser C, Eisen A, Waldman L, Panchal S, Ward T, Carroll JC, Glogowski E, Schrader KA, Lerner-Ellis J, Kim RH, Thorpe KE, Bombard Y. Great expectations: patients' preferences for clinically significant results from genomic sequencing. Hum Genet 2023; 142:553-562. [PMID: 36943453 PMCID: PMC11249280 DOI: 10.1007/s00439-023-02543-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
We aimed to describe patient preferences for a broad range of secondary findings (SF) from genomic sequencing (GS) and factors driving preferences. We assessed preference data within a trial of the Genomics ADvISER, (SF decision aid) among adult cancer patients. Participants could choose from five categories of SF: (1) medically actionable; (2) polygenic risks; (3) rare diseases; (4) early-onset neurological diseases; and (5) carrier status. We analyzed preferences using descriptive statistics and drivers of preferences using multivariable logistic regression models. The 133 participants were predominantly European (74%) or East Asian or mixed ancestry (13%), female (90%), and aged > 50 years old (60%). The majority chose to receive SF. 97% (129/133) chose actionable findings with 36% (48/133) choosing all 5 categories. Despite the lack of medical actionability, participants were interested in receiving SF of polygenic risks (74%), carrier status (75%), rare diseases (59%), and early-onset neurologic diseases (53%). Older participants were more likely to be interested in receiving results for early-onset neurological diseases, while those exhibiting lower decisional conflict were more likely to select all categories. Our results highlight a disconnect between cancer patient preferences and professional guidelines on SF, such as ACMG's recommendations to only return medically actionable secondary findings. In addition to clinical evidence, future guidelines should incorporate patient preferences.
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Affiliation(s)
- Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Agnes Sebastian
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Marc Clausen
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada
| | - Christine Elser
- University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Larissa Waldman
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Marvelle Koffler Breast Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - Thomas Ward
- Zane Cohen Centre, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
| | - June C Carroll
- Ray D Wolfe Department of Family Medicine, Sinai Health, Toronto, ON, Canada
- Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jordan Lerner-Ellis
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Sinai Health, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Raymond H Kim
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network and Sinai Health, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kevin E Thorpe
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Applied Health Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health Toronto, 30 Bond Street, Toronto, ON, M5B 1W8, Canada.
- Ontario Institute for Cancer Research, Toronto, ON, Canada.
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36
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Kotnik U, Maver A, Peterlin B, Lovrecic L. Assessment of pathogenic variation in gynecologic cancer genes in a national cohort. Sci Rep 2023; 13:5307. [PMID: 37002323 PMCID: PMC10066348 DOI: 10.1038/s41598-023-32397-8] [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: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Population-based estimates of pathogenic variation burden in gynecologic cancer predisposition genes are a prerequisite for the development of effective precision public health strategies. This study aims to reveal the burden of pathogenic variants in a comprehensive set of clinically relevant breast, ovarian, and endometrial cancer genes in a large population-based study. We performed a rigorous manual classification procedure to identify pathogenic variants in a panel of 17 gynecologic cancer predisposition genes in a cohort of 7091 individuals, representing 0.35% of the general population. The population burden of pathogenic variants in hereditary gynecologic cancer-related genes in our study was 2.14%. Pathogenic variants in genes ATM, BRCA1, and CDH1 are significantly enriched and the burden of pathogenic variants in CHEK2 is decreased in our population compared to the control population. We have identified a high burden of pathogenic variants in several gynecologic cancer-related genes in the Slovenian population, most importantly in the BRCA1 gene.
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Affiliation(s)
- Urška Kotnik
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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37
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Alvarez-Mora MI, Rodríguez-Revenga L, Jodar M, Potrony M, Sanchez A, Badenas C, Oriola J, Villanueva-Cañas JL, Muñoz E, Valldeoriola F, Cámara A, Compta Y, Carreño M, Martí MJ, Sánchez-Valle R, Madrigal I. Implementation of Exome Sequencing in Clinical Practice for Neurological Disorders. Genes (Basel) 2023; 14:genes14040813. [PMID: 37107571 PMCID: PMC10137364 DOI: 10.3390/genes14040813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023] Open
Abstract
Neurological disorders (ND) are diseases that affect the brain and the central and autonomic nervous systems, such as neurodevelopmental disorders, cerebellar ataxias, Parkinson’s disease, or epilepsies. Nowadays, recommendations of the American College of Medical Genetics and Genomics strongly recommend applying next generation sequencing (NGS) as a first-line test in patients with these disorders. Whole exome sequencing (WES) is widely regarded as the current technology of choice for diagnosing monogenic ND. The introduction of NGS allows for rapid and inexpensive large-scale genomic analysis and has led to enormous progress in deciphering monogenic forms of various genetic diseases. The simultaneous analysis of several potentially mutated genes improves the diagnostic process, making it faster and more efficient. The main aim of this report is to discuss the impact and advantages of the implementation of WES into the clinical diagnosis and management of ND. Therefore, we have performed a retrospective evaluation of WES application in 209 cases referred to the Department of Biochemistry and Molecular Genetics of the Hospital Clinic of Barcelona for WES sequencing derived from neurologists or clinical geneticists. In addition, we have further discussed some important facts regarding classification criteria for pathogenicity of rare variants, variants of unknown significance, deleterious variants, different clinical phenotypes, or frequency of actionable secondary findings. Different studies have shown that WES implementation establish diagnostic rate around 32% in ND and the continuous molecular diagnosis is essential to solve the remaining cases.
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38
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Wagener R, Walter C, Surowy HM, Brandes D, Soura S, Alzoubi D, Yasin L, Fischer U, Dugas M, Borkhardt A, Brozou T. Noncancer-related Secondary Findings in a Cohort of 231 Children With Cancer and Their Parents. J Pediatr Hematol Oncol 2023; 45:e244-e248. [PMID: 35537032 DOI: 10.1097/mph.0000000000002475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/30/2022] [Indexed: 11/26/2022]
Abstract
Application of next-generation sequencing may lead to the detection of secondary findings (SF) not related to the initially analyzed disease but to other severe medically actionable diseases. However, the analysis of SFs is not yet routinely performed. We mined whole-exome sequencing data of 231 pediatric cancer patients and their parents who had been treated in our center for the presence of SFs. By this approach, we identified in 6 children (2.6%) pathogenic germline variants in 5 of the noncancer-related genes on the American College of Medical Genetics and Genomics (ACMG) SF v3.0 list, of which the majority were related to cardiovascular diseases ( RYR2 , MYBPC3 , KCNQ1 ). Interestingly, only the patient harboring the KCNQ1 variant showed at the time point of the analysis signs of the related Long QT syndrome. Moreover, we report 3 variants of unknown significance which, although not classified as pathogenic, have been reported in the literature to occur in individuals with the respective disease. While the frequency of patients with SFs is low, the impact of such findings on the patients' life is enormous, with regard to the potential prevention of life-threatening diseases. Hence, we are convinced that such actionable SF should be routinely analyzed.
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Affiliation(s)
- Rabea Wagener
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Carolin Walter
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Harald M Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf
| | - Danielle Brandes
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Stavrieta Soura
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Deya Alzoubi
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Layal Yasin
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Ute Fischer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
| | - Triantafyllia Brozou
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty
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39
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Jansen ME, Rigter T, Fleur TMC, Souverein PC, Verschuren WMM, Vijverberg SJ, Swen JJ, Rodenburg W, Cornel MC. Predictive Value of SLCO1B1 c.521T>C Polymorphism on Observed Changes in the Treatment of 1136 Statin-Users. Genes (Basel) 2023; 14:456. [PMID: 36833383 PMCID: PMC9957000 DOI: 10.3390/genes14020456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Pharmacogenomic testing is a method to prevent adverse drug reactions. Pharmacogenomics could be relevant to optimize statin treatment, by identifying patients at high risk for adverse drug reactions. We aim to investigate the clinical validity and utility of pre-emptive pharmacogenomics screening in primary care, with SLCO1B1 c.521T>C as a risk factor for statin-induced adverse drug reactions. The focus was on changes in therapy as a proxy for adverse drug reactions observed in statin-users in a population-based Dutch cohort. In total, 1136 statin users were retrospectively genotyped for the SLCO1B1 c.521T>C polymorphism (rs4149056) and information on their statin dispensing was evaluated as cross-sectional research. Approximately half of the included participants discontinued or switched their statin treatment within three years. In our analyses, we could not confirm an association between the SLCO1B1 c.521T>C genotype and any change in statin therapy or arriving at a stable dose sooner in primary care. To be able to evaluate the predictive values of SLCO1B1 c.521T>C genotype on adverse drug reactions from statins, prospective data collection of actual adverse drug reactions and reasons to change statin treatment should be facilitated.
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Affiliation(s)
- Marleen E. Jansen
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, Personalized Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Section Community Genetics, 1081 HV Amsterdam, The Netherlands
- Centre for Health Protection, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands
| | - Tessel Rigter
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, Personalized Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Section Community Genetics, 1081 HV Amsterdam, The Netherlands
- Centre for Health Protection, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands
| | - Thom M. C. Fleur
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, Personalized Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Section Community Genetics, 1081 HV Amsterdam, The Netherlands
- Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Patrick C. Souverein
- Division of Pharmacoepidemiology & Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - W. M. Monique Verschuren
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, 3508 GA Utrecht, The Netherlands
| | - Susanne J. Vijverberg
- Department of Pulmonary Medicine and Amsterdam Public Health Research Institute, Personalized Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Jesse J. Swen
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Wendy Rodenburg
- Centre for Health Protection, National Institute for Public Health and the Environment, 3721 MA Bilthoven, The Netherlands
| | - Martina C. Cornel
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, Personalized Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Section Community Genetics, 1081 HV Amsterdam, The Netherlands
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40
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Codina-Solà M, Trujillano L, Abulí A, Rovira-Moreno E, Muñoz-Cabello P, Campos B, Fernández-Álvarez P, Palau D, Carrasco E, Valenzuela I, Cueto-González AM, Lasa-Aranzasti A, Limeres J, Leno-Colorado J, Costa-Roger M, Moles-Fernández A, Balmaña J, Díez O, Cuscó I, Garcia-Arumí E, Tizzano EF. An spanish study of secondary findings in families affected with mendelian disorders: choices, prevalence and family history. Eur J Hum Genet 2023; 31:223-230. [PMID: 36446894 PMCID: PMC9905470 DOI: 10.1038/s41431-022-01240-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
Clinical exome sequencing has the potential to identify pathogenic variants unrelated to the purpose of the study (secondary findings, SFs). Data describing actual choices of SFs in participants in a clinical setting and factors influencing their decision are virtually non-existant in Europe. In this work, we report the acceptance rate of SFs, calculate their prevalence and study factors associated with the decision in a cohort of patients affected with a rare genetic disorder in a Spanish Hospital. Finally, we re-examine the presence of previously non reported family history in positive cases. We retrospectively reviewed informed consent choices and SF results from 824 unrelated probands affected with rare genetic disorders who underwent whole-genome or exome sequencing. Ninety percent of families (740/824) affected with rare disorders wished to be informed of SFs. Declining SFs was associated with a prenatal setting (30% vs. 8.7%, p = 0.025), consanguinity (19% vs. 8.7%, p = 0.013), male gender (10.6% vs. 1.5%, p = 0.00865) and the proband being a minor (10.6% vs. 1.5%, p = 0.014). Overall, 27 pathogenic or likely pathogenic variants were identified in 27 individuals, with an SF prevalence of 3.6%. Disclosure of SFs increased the percentage of positive family histories and resulted in early diagnosis or changes in the management of 10 individuals from five families. We show that the acceptance of SFs in Spain is high and the disclosure of SFs leads to a clinically meaningful change in the medical management of individuals.
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Affiliation(s)
- Marta Codina-Solà
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain.
| | - Laura Trujillano
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Anna Abulí
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Patricia Muñoz-Cabello
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Paula Fernández-Álvarez
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Dolors Palau
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Estela Carrasco
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Anna Maria Cueto-González
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Javier Limeres
- European Reference Networks for rare, low prevalence and complex diseases of the heart (ERN GUARD-Heart), Barcelona, Spain
- Unidad de Cardiopatías Familiares, Servicio de Cardiología, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | - Jordi Leno-Colorado
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Mar Costa-Roger
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Alejandro Moles-Fernández
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Orland Díez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ivon Cuscó
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Department of Genetics, Hospital Sant Pau, Barcelona, Spain
| | - Elena Garcia-Arumí
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Eduardo Fidel Tizzano
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
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Blout Zawatsky CL, Bick D, Bier L, Funke B, Lebo M, Lewis KL, Orlova E, Qian E, Ryan L, Schwartz MLB, Soper ER. Elective genomic testing: Practice resource of the National Society of Genetic Counselors. J Genet Couns 2023; 32:281-299. [PMID: 36597794 DOI: 10.1002/jgc4.1654] [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: 03/31/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 01/05/2023]
Abstract
Genetic counseling for patients who are pursuing genetic testing in the absence of a medical indication, referred to as elective genomic testing (EGT), is becoming more common. This type of testing has the potential to detect genetic conditions before there is a significant health impact permitting earlier management and/or treatment. Pre- and post-test counseling for EGT is similar to indication-based genetic testing. Both require a complete family and medical history when ordering a test or interpreting a result. However, EGT counseling has some special considerations including greater uncertainties around penetrance and clinical utility and a lack of published guidelines. While certain considerations in the selection of a high-quality genetic testing laboratory are universal, there are some considerations that are unique to the selection of a laboratory performing EGT. This practice resource intends to provide guidance for genetic counselors and other healthcare providers caring for adults seeking pre- or post-test counseling for EGT. Genetic counselors and other genetics trained healthcare providers are the ideal medical professionals to supply accurate information to individuals seeking counseling about EGT enabling them to make informed decisions about testing and follow-up.
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Affiliation(s)
- Carrie L Blout Zawatsky
- Genomes2People, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Ariadne Labs, Boston, Massachusetts, USA.,The MGH Institute of Health Professions, Boston, Massachusetts, USA
| | | | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Matthew Lebo
- Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Cambridge, Massachusetts, USA.,Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Boston, Massachusetts, USA
| | - Katie L Lewis
- Center for Precision Health Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ekaterina Orlova
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Qian
- Department of Genetics, Yale University, New Haven, Connecticut, USA
| | | | - Marci L B Schwartz
- Cardiac Genome Clinic, Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Emily R Soper
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Lin S, Nateqi J, Weingartner-Ortner R, Gruarin S, Marling H, Pilgram V, Lagler FB, Aigner E, Martin AG. An artificial intelligence-based approach for identifying rare disease patients using retrospective electronic health records applied for Pompe disease. Front Neurol 2023; 14:1108222. [PMID: 37153672 PMCID: PMC10160659 DOI: 10.3389/fneur.2023.1108222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/03/2023] [Indexed: 05/10/2023] Open
Abstract
Objective We retrospectively screened 350,116 electronic health records (EHRs) to identify suspected patients for Pompe disease. Using these suspected patients, we then describe their phenotypical characteristics and estimate the prevalence in the respective population covered by the EHRs. Methods We applied Symptoma's Artificial Intelligence-based approach for identifying rare disease patients to retrospective anonymized EHRs provided by the "University Hospital Salzburg" clinic group. Within 1 month, the AI screened 350,116 EHRs reaching back 15 years from five hospitals, and 104 patients were flagged as probable for Pompe disease. Flagged patients were manually reviewed and assessed by generalist and specialist physicians for their likelihood for Pompe disease, from which the performance of the algorithms was evaluated. Results Of the 104 patients flagged by the algorithms, generalist physicians found five "diagnosed," 10 "suspected," and seven patients with "reduced suspicion." After feedback from Pompe disease specialist physicians, 19 patients remained clinically plausible for Pompe disease, resulting in a specificity of 18.27% for the AI. Estimating from the remaining plausible patients, the prevalence of Pompe disease for the greater Salzburg region [incl. Bavaria (Germany), Styria (Austria), and Upper Austria (Austria)] was one in every 18,427 people. Phenotypes for patient cohorts with an approximated onset of symptoms above or below 1 year of age were established, which correspond to infantile-onset Pompe disease (IOPD) and late-onset Pompe disease (LOPD), respectively. Conclusion Our study shows the feasibility of Symptoma's AI-based approach for identifying rare disease patients using retrospective EHRs. Via the algorithm's screening of an entire EHR population, a physician had only to manually review 5.47 patients on average to find one suspected candidate. This efficiency is crucial as Pompe disease, while rare, is a progressively debilitating but treatable neuromuscular disease. As such, we demonstrated both the efficiency of the approach and the potential of a scalable solution to the systematic identification of rare disease patients. Thus, similar implementation of this methodology should be encouraged to improve care for all rare disease patients.
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Affiliation(s)
- Simon Lin
- Science Department, Symptoma GmbH, Vienna, Austria
- Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Jama Nateqi
- Science Department, Symptoma GmbH, Vienna, Austria
- Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | | | | | | | - Vinzenz Pilgram
- Medical and Information Technology - MIT, University Hospital Salzburg (SALK), Salzburg, Austria
| | - Florian B. Lagler
- Medical and Information Technology - MIT, University Hospital Salzburg (SALK), Salzburg, Austria
- Department of Pediatrics and Institute for Inherited Metabolic Diseases, Paracelsus Medical University, Salzburg, Austria
| | - Elmar Aigner
- Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
- Medical and Information Technology - MIT, University Hospital Salzburg (SALK), Salzburg, Austria
| | - Alistair G. Martin
- Science Department, Symptoma GmbH, Vienna, Austria
- *Correspondence: Alistair G. Martin
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Genome screening, reporting, and genetic counseling for healthy populations. Hum Genet 2023; 142:181-192. [PMID: 36331656 PMCID: PMC9638226 DOI: 10.1007/s00439-022-02480-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/16/2022] [Indexed: 11/06/2022]
Abstract
Rapid advancements of genome sequencing (GS) technologies have enhanced our understanding of the relationship between genes and human disease. To incorporate genomic information into the practice of medicine, new processes for the analysis, reporting, and communication of GS data are needed. Blood samples were collected from adults with a PCR-confirmed SARS-CoV-2 (COVID-19) diagnosis (target N = 1500). GS was performed. Data were filtered and analyzed using custom pipelines and gene panels. We developed unique patient-facing materials, including an online intake survey, group counseling presentation, and consultation letters in addition to a comprehensive GS report. The final report includes results generated from GS data: (1) monogenic disease risks; (2) carrier status; (3) pharmacogenomic variants; (4) polygenic risk scores for common conditions; (5) HLA genotype; (6) genetic ancestry; (7) blood group; and, (8) COVID-19 viral lineage. Participants complete pre-test genetic counseling and confirm preferences for secondary findings before receiving results. Counseling and referrals are initiated for clinically significant findings. We developed a genetic counseling, reporting, and return of results framework that integrates GS information across multiple areas of human health, presenting possibilities for the clinical application of comprehensive GS data in healthy individuals.
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Majeed S, Mighton C, Malkin D, Bombard Y. Heath policy guiding the identification, analysis and management of secondary findings for individuals undergoing genomic sequencing: a systematic review protocol. BMJ Open 2022; 12:e065496. [PMID: 36549730 PMCID: PMC9791410 DOI: 10.1136/bmjopen-2022-065496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Genomic sequencing is increasingly enabling precision care across medical specialties; however, the discovery of genomic 'secondary findings' (SFs) unrelated to the patient's primary indication remains a profuse, unintended consequence. Existing practices within the continuum of SF identification, analysis and management are numerous, inconsistent and sometimes contradictory across health conditions and regions. Final decisions are often at the discretion of the genomic sequencing laboratory, bioinformatician or treating physician. This difference in healthcare delivery causes inconsistent information, disclosure and downstream impacts required to manage SFs and patient outcomes. Improving our understanding of the SF health policy landscape can determine components of the SF policy continuum spanning generation through to management that are in conflict, limitations of current guidance and existing needs across clinical settings. METHODS AND ANALYSIS We will carry out a systematic review to catalogue and appraise current guidance directing the identification, analysis and management of SFs for participants receiving genomic sequencing globally. We will conduct a comprehensive search of Medline (Medline R, Medline Epub Ahead of Print and Medline-In-Process & In-Data-Review Citations), Embase and Cochrane databases (n=5, inception to Feb 2022) and a grey literature search of international genomics websites (n=64; inception to May 2022). Key inclusion criteria include: guidance produced by health organisations, bioethics committees and professional associations, outlining recommendations for: (1) SF identification, (2) SF analysis or (3) SF management. Non-English language articles and conference abstracts will be excluded. Guidance will be critically appraised with the Appraisal of Guidelines for Research & Evaluation Instrument (AGREE) II tool. We will interpret our findings by process and across populations using a qualitative descriptive approach. ETHICS AND DISSEMINATION Our systematic review evaluates published data and does not require ethics review. Our findings will be disseminated through peer-reviewed publications, conference presentations and workshops with precision medicine stakeholders. PROSPERO REGISTRATION NUMBER CRD42022316079.
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Affiliation(s)
- Safa Majeed
- Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
- Institute of Health Policy, Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada
- Institute of Health Policy, Management, and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:jpm12122040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Correspondence: (Y.A.B.); (A.S.G.)
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Carrasco E, López-Fernández A, Codina-Sola M, Valenzuela I, Cueto-González AM, Villacampa G, Navarro V, Torres-Esquius S, Palau D, Cruellas M, Torres M, Perez-Dueñas B, Abulí A, Diez O, Sábado-Álvarez C, García-Arumí E, Tizzano EF, Moreno L, Balmaña J. Clinical and psychological implications of secondary and incidental findings in cancer susceptibility genes after exome sequencing in patients with rare disorders. J Med Genet 2022:jmg-2022-108929. [DOI: 10.1136/jmg-2022-108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background/ObjectivesExome sequencing may identify pathogenic variants unrelated with the purpose of the analysis. We investigated the frequency of secondary and incidental findings (SF/IF) in cancer susceptibility genes (CSG), their clinical actionability and the psychological impact in individuals with an SF/IF (cases) compared with individuals tested due to their cancer history (controls).MethodsThis study analysed 533 exomes ordered for non-cancer conditions. Medical records were reviewed for clinical actionability of SF/IF. Psychological impact was analysed using the Multidimensional Impact of Cancer Risk Assessment (MICRA) scale and compared between cases and controls with a propensity score weighting method.ResultsThe frequency of SF/IF in CSG was 2.1% (95% CI 1.1% to 3.8%): threeBRCA2, threePMS2, twoSDHB, and one each inBRCA1,MLH1andRAD51C. Among the relatives, 18 were carriers. Twenty enrolled for surveillance, and a neoplasm was diagnosed in 20%: three paragangliomas and one breast cancer. Cases presented higher MICRA mean scores than controls (21.3 vs 16.2 in MICRA total score, 6.3 vs 4.2 in the distress subscale, and 8.3 vs 6.6 in the uncertainty subscale; all p<0.001).ConclusionSF/IF in CSG were identified in 2.1% of patients. Despite a numerically higher psychological impact, the identification of SF/IF allowed early detection and cancer prevention in families without cancer history.
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McCormick CZ, Yu KD, Johns A, Campbell-Salome G, Hallquist MLG, Sturm AC, Buchanan AH. Investigating Psychological Impact after Receiving Genetic Risk Results-A Survey of Participants in a Population Genomic Screening Program. J Pers Med 2022; 12:jpm12121943. [PMID: 36556164 PMCID: PMC9781266 DOI: 10.3390/jpm12121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Genomic screening programs have potential to benefit individuals who may not be clinically ascertained, but little is known about the psychological impact of receiving genetic results in this setting. The current study sought to further the understanding of individuals’ psychological response to receiving an actionable genetic test result from genomic screening. Telephone surveys were conducted with patient-participants at 6 weeks and 6 months post genetic result disclosure between September 2019 and May 2021 and assessed emotional response to receiving results via the FACToR, PANAS, and decision regret scales. Overall, 354 (29.4%) study participants completed both surveys. Participants reported moderate positive emotions and low levels of negative emotions, uncertainty, privacy concern, and decision regret over time. There were significant decreases in negative emotions (p = 0.0004) and uncertainty (p = 0.0126) between time points on the FACToR scale. “Interested” was the highest scoring discrete emotion (T1 3.6, T2 3.3, scale 0−5) but was significantly lower at 6 months (<0.0001). Coupled with other benefits of genomic screening, these results of modest psychological impact waning over time adds support to clinical utility of population genomic screening programs. However, questions remain regarding how to elicit an emotional response that motivates behavior change without causing psychological harm.
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Affiliation(s)
| | | | - Alicia Johns
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | - Gemme Campbell-Salome
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- Department of Population Health Sciences, Geisinger, Danville, PA 17822, USA
| | | | - Amy C. Sturm
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
- 23andMe, Sunnyvale, CA 94086, USA
| | - Adam H. Buchanan
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
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Martone S, Buonagura AT, Marra R, Rosato BE, Del Giudice F, Bonfiglio F, Capasso M, Iolascon A, Andolfo I, Russo R. Clinical exome-based panel testing for medically actionable secondary findings in a cohort of 383 Italian participants. Front Genet 2022; 13:956723. [DOI: 10.3389/fgene.2022.956723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background: Next-generation sequencing-based genetic testing represents a great opportunity to identify hereditary predispositions to specific pathological conditions and to promptly implement health surveillance or therapeutic protocols in case of disease. The term secondary finding refers to the active search for causative variants in genes associated with medically actionable conditions.Methods: We evaluated 59 medically actionable ACMG genes using a targeted in silico analysis of clinical exome sequencing performed in 383 consecutive individuals referred to our Medical Genetics Unit. A three-tier classification system of SFs for assessing their clinical impact and supporting a decision-making process for reporting was established.Results: We identified SFs with high/moderate evidence of pathogenicity in 7.0% (27/383) of analyzed subjects. Among these, 12/27 (44.4%) were carriers of a high-risk recessive disease allele. The most represented disease domains were cancer predisposition (33.3%), cardiac disorders (16.7%), and familial hypercholesterolemia (12.5%).Conclusion: Although still debated, ensuring during NGS-based genetic testing an opportunistic screening might be valuable for personal and familial early management and surveillance of medically actionable disorders, the individual’s reproductive choices, and the prevalence assessment of underestimated hereditary genetic diseases.
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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [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: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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Elander J, Ullmark T, Ehrencrona H, Jonson T, Piccinelli P, Samuelsson S, Löwgren K, Falkenius-Schmidt K, Ehinger J, Stenfeldt K, Värendh M. Extended genetic diagnostics for children with profound sensorineural hearing loss by implementing massive parallel sequencing. Diagnostic outcome, family experience and clinical implementation. Int J Pediatr Otorhinolaryngol 2022; 159:111218. [PMID: 35779349 DOI: 10.1016/j.ijporl.2022.111218] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/12/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
OBJECTIVES The aim of this study was to investigate genetic outcomes, analyze the family experience, and describe the process of implementing genetic sequencing for children with profound sensorineural hearing loss (SNHL) at a tertial audiological center in southern Sweden. DESIGN This is a prospective pilot study including eleven children with profound bilateral SNHL who underwent cochlear implant surgery. Genetic diagnostic investigation was performed with whole exome sequencing (WES) complemented with XON-array to identify copy number variants, using a manually curated gene panel incorporating 179 genes associated with non-syndromic and syndromic SNHL. Mitochondrial DNA (mtDNA) from blood was examined separately. A patient reported experience measures (PREM) questionnaire was used to evaluate parental experience. We also describe here the process of implementing WES in an audiology department. RESULTS Six female and five male children (mean 3.4 years, SD 3.5 years), with profound bilateral SNHL were included. Genetic variants of interest were found in six subjects (55%), where three (27%) could be classified as pathogenic or likely pathogenic. Among the six cases, one child was found to have a homozygous pathogenic variant in MYO7A and two children had homozygous likely pathogenic variants in SLC26A4 and PCDH15, respectively. One was carrying a compound heterozygote frameshift variant of uncertain significance (VUS) on one allele and in trans, a likely pathogenic deletion on the other allele in PCDH15. Two subjects had homozygous VUS in PCDH15 and ADGRV1, respectively. In five of the cases the variants were in genes associated with Usher syndrome. For one of the likely pathogenic variants, the finding was related to Pendred syndrome. No mtDNA variants related to SNHL were found. The PREM questionnaire revealed that the families had difficulty in fully understanding the results of the genetic analysis. However, the parents of all eleven (100%) subjects still recommended that other families with children with SNHL should undergo genetic testing. Specifically addressed referrals for prompt complementary clinical examination and more individualized care were possible, based on the genetic results. Close clinical collaboration between different specialists, including physicians of audiology, audiologists, clinical geneticists, ophthalmologists, pediatricians, otoneurologists, physiotherapists and hearing habilitation teams was initiated during the implementation of the new regime. For all professionals involved, a better knowledge of the diversity of the genetic background of hearing loss was achieved. CONCLUSIONS Whole exome sequencing and XON-array using a panel of genes associated with SNHL had a high diagnostic yield, added value to the families, and provided guidance for further examinations and habilitation for the child. Great care should be taken to thoroughly inform parents about the genetic test result. Collaborations between departments were intensified and knowledge of hearing genomics was increased among the staff.
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Affiliation(s)
- Johanna Elander
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden.
| | - Tove Ullmark
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden; Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 85, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Paul Piccinelli
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Karolina Löwgren
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karolina Falkenius-Schmidt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Johannes Ehinger
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
| | - Karin Stenfeldt
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden; Lund University, Department of Clinical Sciences Lund, Logopedics, Phoniatrics and Audiology, 221 84, Lund, Sweden
| | - Maria Värendh
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Otorhinolaryngology, Head and Neck Surgery, 221 84, Lund, Sweden
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