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Rowlands CF, Garrett A, Allen S, Durkie M, Burghel GJ, Robinson R, Callaway A, Field J, Frugtniet B, Palmer-Smith S, Grant J, Pagan J, McDevitt T, McVeigh TP, Hanson H, Whiffin N, Jones M, Turnbull C. The PS4-likelihood ratio calculator: flexible allocation of evidence weighting for case-control data in variant classification. J Med Genet 2024; 61:983-991. [PMID: 39227160 DOI: 10.1136/jmg-2024-110034] [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: 04/05/2024] [Accepted: 08/05/2024] [Indexed: 09/05/2024]
Abstract
BACKGROUND The 2015 American College of Medical Genetics/Association of Molecular Pathology (ACMG/AMP) variant classification framework specifies that case-control observations can be scored as 'strong' evidence (PS4) towards pathogenicity. METHODS We developed the PS4-likelihood ratio calculator (PS4-LRCalc) for quantitative evidence assignment based on the observed variant frequencies in cases and controls. Binomial likelihoods are computed for two models, each defined by prespecified OR thresholds. Model 1 represents the hypothesis of association between variant and phenotype (eg, OR≥5) and model 2 represents the hypothesis of non-association (eg, OR≤1). RESULTS PS4-LRCalc enables continuous quantitation of evidence for variant classification expressed as a likelihood ratio (LR), which can be log-converted into log LR (evidence points). Using PS4-LRCalc, observed data can be used to quantify evidence towards either pathogenicity or benignity. Variants can also be evaluated against models of different penetrance. The approach is applicable to balanced data sets generated for more common phenotypes and smaller data sets more typical in very rare disease variant evaluation. CONCLUSION PS4-LRCalc enables flexible evidence quantitation on a continuous scale for observed case-control data. The converted LR is amenable to incorporation into the now widely used 2018 updated Bayesian ACMG/AMP framework.
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Affiliation(s)
- Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alice Garrett
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sophie Allen
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, NEY Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- The Leeds Genetics Laboratory, NEY Genomic Laboratory Hub, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alison Callaway
- Wessex Genetics Laboratory Service, University Hospital Southampton NHS Foundation Trust, Salisbury, UK
| | - Joanne Field
- Genomics and Molecular Medicine Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Bethan Frugtniet
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Sheila Palmer-Smith
- Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Jonathan Grant
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, G51 4TF, UK
| | - Judith Pagan
- South East Scotland Clinical Genetics, Western General Hospital, Edinburgh, UK
| | - Trudi McDevitt
- CHI Crumlin Department of Clinical Genetics, Dublin, Ireland
| | | | - Helen Hanson
- Peninsula Regional Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Exeter, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Eli and Edythe L Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- The Royal Marsden NHS Foundation Trust, London, UK
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2
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Gebetsberger J, Prüller F. Classic Light Transmission Platelet Aggregometry: Do We Still Need it? Hamostaseologie 2024; 44:304-315. [PMID: 38065556 DOI: 10.1055/a-2117-4614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2024] Open
Abstract
For more than 50 years, light transmission aggregometry has been accepted as the gold standard test for diagnosing inherited platelet disorders in platelet-rich plasma, although there are other functional approaches performed in whole blood. In this article, several advantages and disadvantages of this technique over other laboratory approaches are discussed in the view of recent guidelines, and the necessity of functional assays, such as light transmission aggregometry in the era of molecular genetic testing, is highlighted.
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Affiliation(s)
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
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3
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Spier I, Yin X, Richardson M, Pineda M, Laner A, Ritter D, Boyle J, Mur P, Hansen TVO, Shi X, Mahmood K, Plazzer JP, Ognedal E, Nordling M, Farrington SM, Yamamoto G, Baert-Desurmont S, Martins A, Borras E, Tops C, Webb E, Beshay V, Genuardi M, Pesaran T, Capellá G, Tavtigian SV, Latchford A, Frayling IM, Plon SE, Greenblatt M, Macrae FA, Aretz S. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genet Med 2024; 26:100992. [PMID: 37800450 PMCID: PMC10922469 DOI: 10.1016/j.gim.2023.100992] [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: 02/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023] Open
Abstract
PURPOSE The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. METHODS Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. RESULTS The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). CONCLUSION The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
| | - Xiaoyu Yin
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | | | - Marta Pineda
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | | | - Deborah Ritter
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Julie Boyle
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Thomas V O Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Parkville, Australia; Melbourne Bioinformatics, University of Melbourne, Parkville, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia
| | | | - Margareta Nordling
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | | | | | | | - Carli Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, and Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Gabriel Capellá
- European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547; Hereditary Cancer Program, Catalan Institute of Oncology - ONCOBELL, IDIBELL, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Salud Carlos III, Madrid, Spain
| | - Sean V Tavtigian
- Department of Oncological Sciences, School of Medicine, University of Utah, Salt Lake City, UT; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Andrew Latchford
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Department of Surgery and Cancer, Imperial College, London, United Kingdom
| | - Ian M Frayling
- Polyposis Registry, St. Mark's Hospital, London, United Kingdom; Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, Cardiff University, United Kingdom
| | - Sharon E Plon
- Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Marc Greenblatt
- Larner College of Medicine, University of Vermont, Burlington, VT
| | - Finlay A Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia; Department of Medicine, University of Melbourne, Parkville, Australia
| | - Stefan Aretz
- Institute of Human Genetics, Medical Faculty, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No 739547
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Derrick CJ, Szenker-Ravi E, Santos-Ledo A, Alqahtani A, Yusof A, Eley L, Coleman AHL, Tohari S, Ng AYJ, Venkatesh B, Alharby E, Mansard L, Bonnet-Dupeyron MN, Roux AF, Vaché C, Roume J, Bouvagnet P, Almontashiri NAM, Henderson DJ, Reversade B, Chaudhry B. Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish. Hum Mol Genet 2024; 33:150-169. [PMID: 37815931 PMCID: PMC10772043 DOI: 10.1093/hmg/ddad171] [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: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Developmental studies have shown that the evolutionarily conserved Wnt Planar Cell Polarity (PCP) pathway is essential for the development of a diverse range of tissues and organs including the brain, spinal cord, heart and sensory organs, as well as establishment of the left-right body axis. Germline mutations in the highly conserved PCP gene VANGL2 in humans have only been associated with central nervous system malformations, and functional testing to understand variant impact has not been performed. Here we report three new families with missense variants in VANGL2 associated with heterotaxy and congenital heart disease p.(Arg169His), non-syndromic hearing loss p.(Glu465Ala) and congenital heart disease with brain defects p.(Arg135Trp). To test the in vivo impact of these and previously described variants, we have established clinically-relevant assays using mRNA rescue of the vangl2 mutant zebrafish. We show that all variants disrupt Vangl2 function, although to different extents and depending on the developmental process. We also begin to identify that different VANGL2 missense variants may be haploinsufficient and discuss evidence in support of pathogenicity. Together, this study demonstrates that zebrafish present a suitable pipeline to investigate variants of unknown significance and suggests new avenues for investigation of the different developmental contexts of VANGL2 function that are clinically meaningful.
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Affiliation(s)
- Christopher J Derrick
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | | | - Adrian Santos-Ledo
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Ahlam Alqahtani
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Amirah Yusof
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
| | - Lorraine Eley
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Alistair H L Coleman
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Alvin Yu-Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- MGI Tech Singapore Pte Ltd, 21 Biopolis Rd, 138567, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Luke Mansard
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | | | - Anne-Francoise Roux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Christel Vaché
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Joëlle Roume
- Département de Génétique, CHI Poissy, St Germain-en-Laye, 10 Rue du Champ Gaillard, 78300 Poissy, France
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU de Martinique, Fort de France, Fort-de-France 97261, Martinique, France
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Deborah J Henderson
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Bruno Reversade
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- Smart-Health Initiative, BESE, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Medical Genetics Department, Koç Hospital Davutpaşa Caddesi 34010 Topkapı Istanbul, Istanbul, Turkey
| | - Bill Chaudhry
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
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Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
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Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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6
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Liu S, Zhong M, Huang Y, Zhang Q, Chen T, Xu X, Peng W, Wang X, Feng X, Kang L, Lu Y, Cheng J, Bu F, Yuan H. Quantitative thresholds for variant enrichment in 13,845 cases: improving pathogenicity classification in genetic hearing loss. Genome Med 2023; 15:116. [PMID: 38111038 PMCID: PMC10726519 DOI: 10.1186/s13073-023-01271-7] [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: 07/21/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines recommend using variant enrichment among cases as "strong" evidence for pathogenicity per the PS4 criterion. However, quantitative support for PS4 thresholds from real-world Mendelian case-control cohorts is lacking. METHODS To address this gap, we evaluated and established PS4 thresholds using data from the Chinese Deafness Genetics Consortium. A total of 9,050 variants from 13,845 patients with hearing loss (HL) and 6,570 ancestry-matched controls were analyzed. Positive likelihood ratio and local positive likelihood ratio values were calculated to determine the thresholds corresponding to each strength of evidence across three variant subsets. RESULTS In subset 1, consisting of variants present in both cases and controls with an allele frequency (AF) in cases ≥ 0.0005, an odds ratio (OR) ≥ 6 achieved strong evidence, while OR ≥ 3 represented moderate evidence. For subset 2, which encompassed variants present in both cases and controls with a case AF < 0.0005, and subset 3, comprising variants found only in cases and absent from controls, we defined the PS4_Supporting threshold (OR > 2.27 or allele count ≥ 3) and the PS4_Moderate threshold (allele count ≥ 6), respectively. Reanalysis applying the adjusted PS4 criteria changed the classification of 15 variants and enabled diagnosis of an additional four patients. CONCLUSIONS Our study quantified evidence strength thresholds for variant enrichment in genetic HL cases, highlighting the importance of defining disease/gene-specific thresholds to improve the precision and accuracy of clinical genetic testing.
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Affiliation(s)
- Sihan Liu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Mingjun Zhong
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Huang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Qian Zhang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Ting Chen
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Wan Peng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaolu Wang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Lu Kang
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Yu Lu
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Jing Cheng
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Fengxiao Bu
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
| | - Huijun Yuan
- Department of Oto-Rhino-Laryngology, West China Hospital, Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital, Sichuan University, Chengdu, 610000, China.
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Goetsch Weisman A, Weiss McQuaid S, Radtke HB, Stoll J, Brown B, Gomes A. Neurofibromatosis- and schwannomatosis-associated tumors: Approaches to genetic testing and counseling considerations. Am J Med Genet A 2023; 191:2467-2481. [PMID: 37485904 DOI: 10.1002/ajmg.a.63346] [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: 03/25/2023] [Revised: 05/26/2023] [Accepted: 06/24/2023] [Indexed: 07/25/2023]
Abstract
Neurofibromatosis (NF) and schwannomatosis (SWN) are genetic conditions characterized by the risk of developing nervous system tumors. Recently revised diagnostic criteria include the addition of genetic testing to confirm a pathogenic variant, as well as to detect the presence of mosaicism. Therefore, the use and interpretation of both germline and tumor-based testing have increasing importance in the diagnostic approach, treatment decisions, and risk stratification of these conditions. This focused review discusses approaches to genetic testing of NF- and SWN-related tumor types, which are somewhat rare and perhaps lesser known to non-specialized clinicians. These include gastrointestinal stromal tumors, breast cancer, plexiform neurofibromas with or without transformation to malignant peripheral nerve sheath tumors, gliomas, and schwannomas, and emphasizes the need for inclusion of genetic providers in patient care and appropriate pre- and post-test education, genetic counseling, and focused evaluation by a medical geneticist or other healthcare provider familiar with clinical manifestations of these disorders.
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Affiliation(s)
- Allison Goetsch Weisman
- Division of Genetics, Genomics and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shelly Weiss McQuaid
- Division of Genetics, Genomics and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Oncology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Heather B Radtke
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Children's Tumor Foundation, New York, New York, USA
| | | | - Bryce Brown
- Medical Genomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alicia Gomes
- Medical Genomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
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8
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Aiyer S, Kalutskaya E, Agdamag AC, Tang WHW. Genetic Evaluation and Screening in Cardiomyopathies: Opportunities and Challenges for Personalized Medicine. J Pers Med 2023; 13:887. [PMID: 37373876 PMCID: PMC10302702 DOI: 10.3390/jpm13060887] [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: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Cardiomyopathy is a major cause of heart failure caused by abnormalities of the heart muscles that make it harder for it to fill or eject blood. With technological advances, it is important for patients and families to understand that there are potential monogenic etiologies of cardiomyopathy. A multidisciplinary approach to clinical genetic screening for cardiomyopathies involving genetic counseling and clinical genetic testing is beneficial for patients and families. With early identification of inherited cardiomyopathy, patients can initiate guideline-directed medical therapies earlier, resulting in a greater likelihood of improving prognoses and health outcomes. Identifying impactful genetic variants will also allow for cascade testing to determine at-risk family members through clinical (phenotype) screening and risk stratification. Addressing genetic variants of uncertain significance and causative variants that may change in pathogenicity is also important to consider. This review will dive into the clinical genetic testing approaches for the various cardiomyopathies, the significance of early detection and treatment, the value of family screening, the personalized treatment process associated with genetic evaluation, and current strategies for clinical genetic testing outreach.
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Affiliation(s)
- Sahana Aiyer
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Emilia Kalutskaya
- Boonshoft School of Medicine, Wright State University, Fairborn, OH 45435, USA
| | - Arianne C. Agdamag
- Department of Cardiovascular Medicine, Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - W. H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Cardiovascular Medicine, Heart Vascular and Thoracic Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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9
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Hernandez CC, Shen Y, Hu N, Shen W, Narayanan V, Ramsey K, He W, Zou L, Macdonald RL. GABRG2 Variants Associated with Febrile Seizures. Biomolecules 2023; 13:414. [PMID: 36979350 PMCID: PMC10046037 DOI: 10.3390/biom13030414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Febrile seizures (FS) are the most common form of epilepsy in children between six months and five years of age. FS is a self-limited type of fever-related seizure. However, complicated prolonged FS can lead to complex partial epilepsy. We found that among the GABAA receptor subunit (GABR) genes, most variants associated with FS are harbored in the γ2 subunit (GABRG2). Here, we characterized the effects of eight variants in the GABAA receptor γ2 subunit on receptor biogenesis and channel function. Two-thirds of the GABRG2 variants followed the expected autosomal dominant inheritance in FS and occurred as missense and nonsense variants. The remaining one-third appeared as de novo in the affected probands and occurred only as missense variants. The loss of GABAA receptor function and dominant negative effect on GABAA receptor biogenesis likely caused the FS phenotype. In general, variants in the GABRG2 result in a broad spectrum of phenotypic severity, ranging from asymptomatic, FS, genetic epilepsy with febrile seizures plus (GEFS+), and Dravet syndrome individuals. The data presented here support the link between FS, epilepsy, and GABRG2 variants, shedding light on the relationship between the variant topological occurrence and disease severity.
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Affiliation(s)
- Ciria C. Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanwen Shen
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Wen He
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Liping Zou
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Robert L. Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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10
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Adam F, Fluri M, Scherz A, Rabaglio M. Occurrence of variants of unknown clinical significance in genetic testing for hereditary breast and ovarian cancer syndrome and Lynch syndrome: a literature review and analytical observational retrospective cohort study. BMC Med Genomics 2023; 16:7. [PMID: 36647026 PMCID: PMC9843935 DOI: 10.1186/s12920-023-01437-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND PURPOSE Over the last decade, the implementation of multigene panels for hereditary tumor syndrome has increased at our institution (Inselspital, University Hospital Berne, Switzerland). The aim of this study was to determine the prevalence of variants of unknown significance (VUS) in patients with suspected Lynch syndrome and suspected hereditary breast and ovarian cancer syndrome, the latter in connection with the trend toward ordering larger gene panels. RESULTS Retrospectively collected data from 1057 patients at our institution showed at least one VUS in 126 different cases (11.9%). In patients undergoing genetic testing for BRCA1/2, the prevalence of VUS was 6%. When < 10 additional genes were tested in addition to BRCA1/2, the prevalence increased to 13.8%, and 31.8% for > 10 additional genes, respectively. The gene most frequently affected with a VUS was ATM. 6% of our patients who were tested for Lynch syndrome had a VUS result in either MLH1, MSH2 or MSH6. CONCLUSIONS Our data demonstrate that panel testing statistically significantly increases VUS rates due to variants in non-BRCA genes. Good genetic counseling before and after obtaining results is therefore particularly important when conducting multigene panels to minimize patient uncertainty due to VUS results.
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Affiliation(s)
- Felicia Adam
- Medical Faculty of the University of Bern, Bern, Switzerland
| | - Muriel Fluri
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Amina Scherz
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Manuela Rabaglio
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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11
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Salehipour D, Farncombe KM, Andric V, Ansar S, Delong S, Li E, Macpherson S, Ridd S, Ritter DI, Thaxton C, Kim RH. Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is. Database (Oxford) 2023; 2023:6972759. [PMID: 36617168 PMCID: PMC9825735 DOI: 10.1093/database/baac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/23/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023]
Abstract
Von Hippel-Lindau (VHL) disease is a rare, autosomal dominant disorder that predisposes individuals to developing tumors in many organs. There is significant phenotypic variability and genetic variants encountered within this syndrome, posing a considerable challenge to patient care. The lack of VHL variant data sharing paired with the absence of aggregated genotype-phenotype information results in an arduous process, when characterizing genetic variants and predicting patient prognosis. To address these gaps in knowledge, the Clinical Genome Resource (ClinGen) VHL Variant Curation Expert Panel (VCEP) has been resolving a list of variants of uncertain significance within the VHL gene. Through community curation, we crowdsourced the laborious task of variant annotation by modifying the ClinGen Community Curation (C3)-developed Baseline Annotation protocol and annotating all published VHL cases with the reported genotype-phenotype information in Hypothes.is, an open-access web annotation tool. This process, incorporated into the ClinGen VCEP's workflow, will aid in their curation efforts. To facilitate the curation at all levels of genetics expertise, our team developed a 4-day biocuration training protocol and resource guide. To date, 91.3% of annotations have been completed by undergraduate and high-school students without formal academic genetics specialization. Here, we present our VHL-specific annotation protocol utilizing Hypothes.is, which offers a standardized method to present case-resolution data, and our biocuration training protocol, which can be adapted for other rare disease platforms. By facilitating training for community curation of VHL disease, we increased student engagement with clinical genetics while enhancing knowledge translation in the field of hereditary cancer. Database URL: https://hypothes.is/groups/dKymJJpZ/vhl-hypothesis-annotation.
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Affiliation(s)
- Dena Salehipour
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, 200 Elizabeth St, Toronto, ON M5G 2C4, Canada
| | - Veronica Andric
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Safa Ansar
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Sean Delong
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Eric Li
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Samantha Macpherson
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Sarah Ridd
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 1102 Bates Ave, Houston, TX 77030, USA
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina, 120 Mason Farm Rd, Chapel Hill, Chapel Hill, NC 27514, USA
| | - Raymond H Kim
- *Corresponding author: Tel: +416-946-2270; Fax: +416-946-6528;
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12
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Boettcher S, Simons M. Model organisms for functional validation in genetic renal disease. MED GENET-BERLIN 2022; 34:287-296. [PMID: 38836086 PMCID: PMC11006349 DOI: 10.1515/medgen-2022-2162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Functional validation is key for establishing new disease genes in human genetics. Over the years, model organisms have been utilized in a very effective manner to prove causality of genes or genetic variants for a wide variety of diseases. Also in hereditary renal disease, model organisms are very helpful for functional validation of candidate genes and variants identified by next-generation sequencing strategies and for obtaining insights into the pathophysiology. Due to high genetic conservation as well as high anatomical and physiological similarities with the human kidney, almost all genetic kidney diseases can be studied in the mouse. However, mouse work is time consuming and expensive, so there is a need for alternative models. In this review, we will provide an overview of model organisms used in renal research, focusing on mouse, zebrafish, frog, and fruit flies.
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Affiliation(s)
- Susanne Boettcher
- Sektion Nephrogenetik, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Matias Simons
- Sektion Nephrogenetik, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
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13
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Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annu Rev Genet 2022; 56:441-465. [PMID: 36055970 DOI: 10.1146/annurev-genet-072920-032107] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Scalable sequence-function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies. In this review, we explore current applications and prospects for the field and outline the principles underlying scalable functional assay design, with a focus on the study of single-nucleotide coding and noncoding variants.
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Affiliation(s)
- Daniel Tabet
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Victoria Parikh
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine and Endocrine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA;
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14
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Zidoune H, Ladjouze A, Chellat-Rezgoune D, Boukri A, Dib SA, Nouri N, Tebibel M, Sifi K, Abadi N, Satta D, Benelmadani Y, Bignon-Topalovic J, El-Zaiat-Munsch M, Bashamboo A, McElreavey K. Novel Genomic Variants, Atypical Phenotypes and Evidence of a Digenic/Oligogenic Contribution to Disorders/Differences of Sex Development in a Large North African Cohort. Front Genet 2022; 13:900574. [PMID: 36110220 PMCID: PMC9468775 DOI: 10.3389/fgene.2022.900574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In a majority of individuals with disorders/differences of sex development (DSD) a genetic etiology is often elusive. However, new genes causing DSD are routinely reported and using the unbiased genomic approaches, such as whole exome sequencing (WES) should result in an increased diagnostic yield. Here, we performed WES on a large cohort of 125 individuals all of Algerian origin, who presented with a wide range of DSD phenotypes. The study excluded individuals with congenital adrenal hypoplasia (CAH) or chromosomal DSD. Parental consanguinity was reported in 36% of individuals. The genetic etiology was established in 49.6% (62/125) individuals of the total cohort, which includes 42.2% (35/83) of 46, XY non-syndromic DSD and 69.2% (27/39) of 46, XY syndromic DSD. No pathogenic variants were identified in the 46, XX DSD cases (0/3). Variants in the AR, HSD17B3, NR5A1 and SRD5A2 genes were the most common causes of DSD. Other variants were identified in genes associated with congenital hypogonadotropic hypogonadism (CHH), including the CHD7 and PROKR2. Previously unreported pathogenic/likely pathogenic variants (n = 30) involving 25 different genes were identified in 22.4% of the cohort. Remarkably 11.5% of the 46, XY DSD group carried variants classified as pathogenic/likely pathogenic variant in more than one gene known to cause DSD. The data indicates that variants in PLXNA3, a candidate CHH gene, is unlikely to be involved in CHH. The data also suggest that NR2F2 variants may cause 46, XY DSD.
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Affiliation(s)
- Housna Zidoune
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | | | - Djalila Chellat-Rezgoune
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Asma Boukri
- Department of Endocrinology and Diabetology, CHU Ibn Badis Constantine, Constantine, Algeria
| | | | - Nassim Nouri
- Department of Endocrinology and Diabetology, CHU Ibn Badis Constantine, Constantine, Algeria
| | - Meryem Tebibel
- Department of Pediatric Surgery, CHU Beni Messous, Algiers, Algeria
| | - Karima Sifi
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Noureddine Abadi
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Dalila Satta
- Laboratory of Molecular and Cellular Biology, Department of Animal Biology, University Frères Mentouri Constantine 1, Constantine, Algeria
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | - Yasmina Benelmadani
- Department of Medicine, Laboratory of Biology and Molecular Genetics, University Salah Boubnider Constantine 3, Constantine, Algeria
| | | | | | - Anu Bashamboo
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
| | - Ken McElreavey
- Human Developmental Genetics Unit, Institut Pasteur, CNRS, Paris, France
- *Correspondence: Ken McElreavey,
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15
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Anderson CL, Munawar S, Reilly L, Kamp TJ, January CT, Delisle BP, Eckhardt LL. How Functional Genomics Can Keep Pace With VUS Identification. Front Cardiovasc Med 2022; 9:900431. [PMID: 35859585 PMCID: PMC9291992 DOI: 10.3389/fcvm.2022.900431] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/09/2022] [Indexed: 01/03/2023] Open
Abstract
Over the last two decades, an exponentially expanding number of genetic variants have been identified associated with inherited cardiac conditions. These tremendous gains also present challenges in deciphering the clinical relevance of unclassified variants or variants of uncertain significance (VUS). This review provides an overview of the advancements (and challenges) in functional and computational approaches to characterize variants and help keep pace with VUS identification related to inherited heart diseases.
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Affiliation(s)
- Corey L. Anderson
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Saba Munawar
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Louise Reilly
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Timothy J. Kamp
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Craig T. January
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian P. Delisle
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, United States
| | - Lee L. Eckhardt
- Cellular and Molecular Arrythmias Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
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16
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Iversen ES, Lipton G, Hart SN, Lee KY, Hu C, Polley EC, Pesaran T, Yussuf A, LaDuca H, Chao E, Karam R, Goldgar DE, Couch FJ, Monteiro ANA. An integrative model for the comprehensive classification of BRCA1 and BRCA2 variants of uncertain clinical significance. NPJ Genom Med 2022; 7:35. [PMID: 35665744 PMCID: PMC9166814 DOI: 10.1038/s41525-022-00302-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2022] [Indexed: 12/14/2022] Open
Abstract
Loss-of-function variants in the BRCA1 and BRCA2 susceptibility genes predispose carriers to breast and/or ovarian cancer. The use of germline testing panels containing these genes has grown dramatically, but the interpretation of the results has been complicated by the identification of many sequence variants of undefined cancer relevance, termed "Variants of Uncertain Significance (VUS)." We have developed functional assays and a statistical model called VarCall for classifying BRCA1 and BRCA2 VUS. Here we describe a multifactorial extension of VarCall, called VarCall XT, that allows for co-analysis of multiple forms of genetic evidence. We evaluated the accuracy of models defined by the combinations of functional, in silico protein predictors, and family data for VUS classification. VarCall XT classified variants of known pathogenicity status with high sensitivity and specificity, with the functional assays contributing the greatest predictive power. This approach could be used to identify more patients that would benefit from personalized cancer risk assessment and management.
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Affiliation(s)
- Edwin S. Iversen
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Gary Lipton
- grid.26009.3d0000 0004 1936 7961Department of Statistical Science, Duke University, Durham, NC 27708 USA
| | - Steven N. Hart
- grid.66875.3a0000 0004 0459 167XDepartment of Health Sciences Research, Mayo Clinic, Rochester, MN 55901 USA
| | - Kun Y. Lee
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Chunling Hu
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Eric C. Polley
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Tina Pesaran
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Amal Yussuf
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Holly LaDuca
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Elizabeth Chao
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - Rachid Karam
- grid.465138.d0000 0004 0455 211XAmbry Genetics Corporation, Aliso Viejo, CA 92656 USA
| | - David E. Goldgar
- grid.223827.e0000 0001 2193 0096Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - Fergus J. Couch
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
| | - Alvaro N. A. Monteiro
- grid.468198.a0000 0000 9891 5233Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612 USA
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17
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Lyon E, Temple-Smolkin RL, Hegde M, Gastier-Foster JM, Palomaki GE, Richards CS. An Educational Assessment of Evidence Used for Variant Classification: A Report of the Association for Molecular Pathology. J Mol Diagn 2022; 24:555-565. [PMID: 35429647 DOI: 10.1016/j.jmoldx.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
The Association for Molecular Pathology Variant Interpretation Testing Among Laboratories (VITAL) Working Group convened to evaluate the Standards and Guidelines for the Interpretation of Sequence Variants implementation into clinical practice, identify problematic classification rules, and define implementation challenges. Variants and associated clinical information were provided to volunteer respondents. Participant variant classifications were compared with intended consensus-derived classifications of the Working Group. The 24 variant challenges received 1379 responses; 1119 agreed with the intended response (81%; 95% CI, 79% to 83%). Agreement ranged from 44% to 100%, with 16 challenges (67%; 47% to 82%) reaching consensus (≥80% agreement). Participant classifications were also compared to a calculated interpretation of the ACMG Guidelines using the participant-reported criteria as input. The 24 variant challenges had 1368 responses with specific evidence provided and 1121 (82%; 80% to 84%) agreed with the calculated interpretation. Agreement for challenges ranged from 63% to 98%; 15 (63%; 43% to 79%) reaching consensus. Among 81 individual participants, 32 (40%; 30% to 50%) reached agreement with at least 80% of the intended classifications and 42 (52%; 41% to 62%) with the calculated classifications. This study demonstrated that although variant classification remains challenging, published guidelines are being utilized and adapted to improve variant calling consensus. This study identified situations where clarifications are warranted and provides a model for competency assessment.
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Affiliation(s)
- Elaine Lyon
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Madhuri Hegde
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Global Genetics Laboratory, PerkinElmer Genomics, Pittsburgh, Pennsylvania
| | - Julie M Gastier-Foster
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Departments of Pediatrics and Pathology/Immunology, Baylor College of Medicine, Houston, Texas; Pathology Department, Texas Children's Hospital, Houston, Texas; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Glenn E Palomaki
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, Rhode Island
| | - C Sue Richards
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Molecular and Medical Genetics and Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon.
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18
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Bellè F, Mercatanti A, Lodovichi S, Congregati C, Guglielmi C, Tancredi M, Caligo MA, Cervelli T, Galli A. Validation and Data-Integration of Yeast-Based Assays for Functional Classification of BRCA1 Missense Variants. Int J Mol Sci 2022; 23:ijms23074049. [PMID: 35409408 PMCID: PMC8999655 DOI: 10.3390/ijms23074049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022] Open
Abstract
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their functional impact and pathogenicity. As the expression of pathogenic BRCA1 variants in Saccharomyces cerevisiae increases the frequency of intra- and inter-chromosomal homologous recombination (HR), and gene reversion (GR), we validated the two HR and the GR assays by testing 23 benign and 23 pathogenic variants and compared the results with those that were obtained in the small colony phenotype (SCP) assay, an additional yeast-based assay, that was validated previously. We demonstrated that they scored high accuracy, sensitivity, and sensibility. By using a classifier that was based on majority of voting, we have integrated data from HR, GR, and SCP assays and developed a reliable method, named yBRCA1, with high sensitivity to obtain an accurate VUS functional classification (benign or pathogenic). The classification of BRCA1 variants, important for assessing the risk of developing BOC, is often difficult to establish with genetic methods because they occur rarely in the population. This study provides a new tool to get insights on the functional impact of the BRCA1 variants.
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Affiliation(s)
- Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alberto Mercatanti
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56125 Pisa, Italy;
| | - Chiara Guglielmi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, 56125 Pisa, Italy; (C.G.); (M.T.)
- Correspondence: (M.A.C.); (A.G.)
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
| | - Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR via Moruzzi 1, 56125 Pisa, Italy; (F.B.); (A.M.); (S.L.); (T.C.)
- Correspondence: (M.A.C.); (A.G.)
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19
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Liang F, Fu X, Ding S, Li L. Use of a Network-Based Method to Identify Latent Genes Associated with Hearing Loss in Children. Front Cell Dev Biol 2021; 9:783500. [PMID: 34912812 PMCID: PMC8667072 DOI: 10.3389/fcell.2021.783500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Hearing loss is a total or partial inability to hear. Approximately 5% of people worldwide experience this condition. Hearing capacity is closely related to language, social, and basic emotional development; hearing loss is particularly serious in children. The pathogenesis of childhood hearing loss remains poorly understood. Here, we sought to identify new genes potentially associated with two types of hearing loss in children: congenital deafness and otitis media. We used a network-based method incorporating a random walk with restart algorithm, as well as a protein-protein interaction framework, to identify genes potentially associated with either pathogenesis. A following screening procedure was performed and 18 and 87 genes were identified, which potentially involved in the development of congenital deafness or otitis media, respectively. These findings provide novel biomarkers for clinical screening of childhood deafness; they contribute to a genetic understanding of the pathogenetic mechanisms involved.
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Affiliation(s)
- Feng Liang
- Anaesthesia Department, China-Japan Union Hospital, JiLin University, Changchun, China
| | - Xin Fu
- Anaesthesia Department, China-Japan Union Hospital, JiLin University, Changchun, China
| | - ShiJian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Lin Li
- Department of Otorhinolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
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20
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Peng J, Xiang J, Jin X, Meng J, Song N, Chen L, Abou Tayoun A, Peng Z. VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss. Hum Mutat 2021; 42:1567-1575. [PMID: 34428318 DOI: 10.1002/humu.24277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/13/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022]
Abstract
The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named Variant Interpretation Platform for genetic Hearing Loss (VIP-HL), aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants in which 82 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 93% (76/82) rules, significantly higher than that of by InterVar (48%; 39/82). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.
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Affiliation(s)
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xiangqian Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nana Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lisha Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.,Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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21
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Pathogenic Intronic Splice-Affecting Variants in MYBPC3 in Three Patients with Hypertrophic Cardiomyopathy. CARDIOGENETICS 2021. [DOI: 10.3390/cardiogenetics11020009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Genetic variants in MYBPC3 are one of the most common causes of hypertrophic cardiomyopathy (HCM). While variants in MYBPC3 affecting canonical splice site dinucleotides are a well-characterised cause of HCM, only recently has work begun to investigate the pathogenicity of more deeply intronic variants. Here, we present three patients with HCM and intronic splice-affecting MYBPC3 variants and analyse the impact of variants on splicing using in vitro minigene assays. We show that the three variants, a novel c.927-8G>A variant and the previously reported c.1624+4A>T and c.3815-10T>G variants, result in MYBPC3 splicing errors. Analysis of blood-derived patient RNA for the c.3815-10T>G variant revealed only wild type spliced product, indicating that mis-spliced transcripts from the mutant allele are degraded. These data indicate that the c.927-8G>A variant of uncertain significance and likely benign c.3815-10T>G should be reclassified as likely pathogenic. Furthermore, we find shortcomings in commonly applied bioinformatics strategies to prioritise variants impacting MYBPC3 splicing and re-emphasise the need for functional assessment of variants of uncertain significance in diagnostic testing.
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22
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Houge G, Laner A, Cirak S, de Leeuw N, Scheffer H, den Dunnen JT. Stepwise ABC system for classification of any type of genetic variant. Eur J Hum Genet 2021; 30:150-159. [PMID: 33981013 PMCID: PMC8821602 DOI: 10.1038/s41431-021-00903-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/13/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022] Open
Abstract
The American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) system for variant classification is score based with five classes: benign, likely benign, variant of unknown significance (VUS), likely pathogenic, and pathogenic. Here, we present a variant classification model that can be an add-on or alternative to ACMG classification: A stepwise system that can classify any type of genetic variant (e.g., hypomorphic alleles, imprinted alleles, copy number variants, runs of homozygosity, enhancer variants, and variants related to traits). We call it the ABC system because classification is first functional (A), then clinical (B), and optionally a standard comment that fits the clinical question is selected (C). Both steps A and B have 1–5 grading when knowledge is sufficient, if not, class “zero” is assigned. Functional grading (A) only concerns biological consequences with the stages normal function (1), likely normal function (2), hypothetical functional effect (3), likely functional effect (4), and proven functional effect (5). Clinical grading (B) is genotype–phenotype focused with the stages “right type of gene” (1), risk factor (2), and pathogenic (3–5, depending on penetrance). Both grades are listed for each variant and combined to generate a joint class ranging from A to F. Importantly, the A–F classes are linked to standard comments, reflecting laboratory or national policy. In step A, the VUS class is split into class 0 (true unknown) and class 3 (hypothetical functional effect based on molecular predictions or de novo occurrence), providing a rationale for variant-of-interest reporting when the clinical picture could fit the finding. The system gives clinicians a better guide to variant significance.
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Affiliation(s)
- Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | | | - Sebahattin Cirak
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics and Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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23
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Chao JT, Roskelley CD, Loewen CJR. MAPS: machine-assisted phenotype scoring enables rapid functional assessment of genetic variants by high-content microscopy. BMC Bioinformatics 2021; 22:202. [PMID: 33879063 PMCID: PMC8056608 DOI: 10.1186/s12859-021-04117-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/02/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic testing is widely used in evaluating a patient's predisposition to hereditary diseases. In the case of cancer, when a functionally impactful mutation (i.e. genetic variant) is identified in a disease-relevant gene, the patient is at elevated risk of developing a lesion in their lifetime. Unfortunately, as the rate and coverage of genetic testing has accelerated, our ability to assess the functional status of new variants has fallen behind. Therefore, there is an urgent need for more practical, streamlined and cost-effective methods for classifying variants. RESULTS To directly address this issue, we designed a new approach that uses alterations in protein subcellular localization as a key indicator of loss of function. Thus, new variants can be rapidly functionalized using high-content microscopy (HCM). To facilitate the analysis of the large amounts of imaging data, we developed a new software toolkit, named MAPS for machine-assisted phenotype scoring, that utilizes deep learning to extract and classify cell-level features. MAPS helps users leverage cloud-based deep learning services that are easy to train and deploy to fit their specific experimental conditions. Model training is code-free and can be done with limited training images. Thus, MAPS allows cell biologists to easily incorporate deep learning into their image analysis pipeline. We demonstrated an effective variant functionalization workflow that integrates HCM and MAPS to assess missense variants of PTEN, a tumor suppressor that is frequently mutated in hereditary and somatic cancers. CONCLUSIONS This paper presents a new way to rapidly assess variant function using cloud deep learning. Since most tumor suppressors have well-defined subcellular localizations, our approach could be widely applied to functionalize variants of uncertain significance and help improve the utility of genetic testing.
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Affiliation(s)
- Jesse T Chao
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada.
| | - Calvin D Roskelley
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada
| | - Christopher J R Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, V6T1Z3, Canada
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24
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Truty R, Ouyang K, Rojahn S, Garcia S, Colavin A, Hamlington B, Freivogel M, Nussbaum RL, Nykamp K, Aradhya S. Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. Am J Hum Genet 2021; 108:696-708. [PMID: 33743207 PMCID: PMC8059334 DOI: 10.1016/j.ajhg.2021.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.
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Affiliation(s)
| | - Karen Ouyang
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Sarah Garcia
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | | | | | | | | | - Keith Nykamp
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
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25
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Plumereau Q, Theriault O, Pouliot V, Moreau A, Morel E, Fressart V, Denjoy I, Delinière A, Bessière F, Chevalier P, Gamal El-Din TM, Chahine M. Novel G1481V and Q1491H SCN5A Mutations Linked to Long QT Syndrome Destabilize the Nav1.5 Inactivation State. CJC Open 2021; 3:256-266. [PMID: 33778442 PMCID: PMC7984979 DOI: 10.1016/j.cjco.2020.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/02/2022] Open
Abstract
Background Nav1.5, which is encoded by the SCN5A gene, is the predominant voltage-gated Na+ channel in the heart. Several mutations of this gene have been identified and reported to be involved in several cardiac rhythm disorders, including type 3 long QT interval syndrome, that can cause sudden cardiac death. We analyzed the biophysical properties of 2 novel variants of the Nav1.5 channel (Q1491H and G1481V) detected in 5- and 12-week-old infants diagnosed with a prolonged QT interval. Methods The Nav1.5 wild-type and the Q1491H and G1481V mutant channels were reproduced in vitro. Wild-type or mutant channels were cotransfected in human embryonic kidney (HEK) 293 cells with the beta 1 regulatory subunit. Na+ currents were recorded using the whole-cell configuration of the patch-clamp technique. Results The Q1491H mutant channel exhibited a lower current density, a persistent Na+ current, an enhanced window current due to a +20-mV shift of steady-state inactivation, a +10-mV shift of steady-state activation, a faster onset of slow inactivation, and a recovery from fast inactivation with fast and slow time constants of recovery. The G1481V mutant channel exhibited an increase in current density and a +7-mV shift of steady-state inactivation. The observed defects are characteristic of gain-of-function mutations typical of type 3 long QT interval syndrome. Conclusions The 5- and 12-week-old infants displayed prolonged QT intervals. Our analyses of the Q1491H and G1481V mutations correlated with the clinical diagnosis. The observed biophysical dysfunctions associated with both mutations were most likely responsible for the sudden deaths of the 2 infants.
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Affiliation(s)
| | | | | | - Adrien Moreau
- Inserm U1046, CNRS UMR 9214, Université de Montpellier, Montpellier, France
| | - Elodie Morel
- Lyon Reference Center for Inherited Arrhythmias, Louis Pradel Cardiovascular Hospital, Bron, France
| | - Véronique Fressart
- Centre de Génétique Moléculaire et Chromosomique, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - Antoine Delinière
- Lyon Reference Center for Inherited Arrhythmias, Louis Pradel Cardiovascular Hospital, Bron, France
| | - Francis Bessière
- Lyon Reference Center for Inherited Arrhythmias, Louis Pradel Cardiovascular Hospital, Bron, France
| | - Philippe Chevalier
- Lyon Reference Center for Inherited Arrhythmias, Louis Pradel Cardiovascular Hospital, Bron, France.,Department of Rhythmology, Louis Pradel Cardiovascular Hospital, Lyon, France.,Université de Lyon, Lyon, France
| | | | - Mohamed Chahine
- CERVO Brain Research Center, Quebec City, Quebec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
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26
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Yogasundaram H, Alhumaid W, Dzwiniel T, Christian S, Oudit GY. Cardiomyopathies and Genetic Testing in Heart Failure: Role in Defining Phenotype-Targeted Approaches and Management. Can J Cardiol 2021; 37:547-559. [PMID: 33493662 DOI: 10.1016/j.cjca.2021.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/29/2022] Open
Abstract
Cardiomyopathies represent an important cause of heart failure, often affecting young individuals, and have important implications for relatives. Genetic testing for cardiomyopathies is an established care pathway in contemporary cardiology practice. The primary cardiomyopathies where genetic testing is indicated are hypertrophic, dilated, arrhythmogenic, and restrictive cardiomyopathies, with left ventricular noncompaction as a variant phenotype. Early identification and initiation of therapies in patients with inherited cardiomyopathies allow for targeting asymptomatic and presymptomatic patients in stages A and B of the American College of Cardiology/American Heart Association classification of heart failure. The current approach for genetic testing uses gene panel-based testing with the ability to extend to whole-exome and whole-genome sequencing in rare instances. The central components of genetic testing include defining the genetic basis of the diagnosis, providing prognostic information, and the ability to screen and risk-stratify relatives. Genetic testing for cardiomyopathies should be coordinated by a multidisciplinary team including adult and pediatric cardiologists, genetic counsellors, and geneticists, with access to expertise in cardiac imaging and electrophysiology. A pragmatic approach for addressing genetic variants of uncertain significance is important. In this review, we highlight the indications for genetic testing in the various cardiomyopathies, the value of early diagnosis and treatment, family screening, and the care process involved in genetic counselling and testing.
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Affiliation(s)
- Haran Yogasundaram
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Waleed Alhumaid
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Tara Dzwiniel
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Susan Christian
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Gavin Y Oudit
- Department of Medicine, Division of Cardiology, University of Alberta, Edmonton, Alberta, Canada; Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, Alberta, Canada.
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27
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Garrett A, Durkie M, Callaway A, Burghel GJ, Robinson R, Drummond J, Torr B, Cubuk C, Berry IR, Wallace AJ, Ellard S, Eccles DM, Tischkowitz M, Hanson H, Turnbull C. Combining evidence for and against pathogenicity for variants in cancer susceptibility genes: CanVIG-UK consensus recommendations. J Med Genet 2020; 58:297-304. [PMID: 33208383 PMCID: PMC8086256 DOI: 10.1136/jmedgenet-2020-107248] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
Accurate classification of variants in cancer susceptibility genes (CSGs) is key for correct estimation of cancer risk and management of patients. Consistency in the weighting assigned to individual elements of evidence has been much improved by the American College of Medical Genetics (ACMG) 2015 framework for variant classification, UK Association for Clinical Genomic Science (UK-ACGS) Best Practice Guidelines and subsequent Cancer Variant Interpretation Group UK (CanVIG-UK) consensus specification for CSGs. However, considerable inconsistency persists regarding practice in the combination of evidence elements. CanVIG-UK is a national subspecialist multidisciplinary network for cancer susceptibility genomic variant interpretation, comprising clinical scientist and clinical geneticist representation from each of the 25 diagnostic laboratories/clinical genetic units across the UK and Republic of Ireland. Here, we summarise the aggregated evidence elements and combinations possible within different variant classification schemata currently employed for CSGs (ACMG, UK-ACGS, CanVIG-UK and ClinGen gene-specific guidance for PTEN, TP53 and CDH1). We present consensus recommendations from CanVIG-UK regarding (1) consistent scoring for combinations of evidence elements using a validated numerical 'exponent score' (2) new combinations of evidence elements constituting likely pathogenic' and 'pathogenic' classification categories, (3) which evidence elements can and cannot be used in combination for specific variant types and (4) classification of variants for which there are evidence elements for both pathogenicity and benignity.
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Affiliation(s)
- Alice Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury Hospital NHS Foundation Trust, Salisbury, Wiltshire, UK.,Human Genetics and Genomic Medicine, University of Southampton Faculty of Medicine, Southampton, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Rachel Robinson
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - James Drummond
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, Cambridgeshire, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Cankut Cubuk
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK
| | - Ian R Berry
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine and NW Laboratory Genetics Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sian Ellard
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Diana M Eccles
- Cancer Sciences Research Group, University of Southampton Faculty of Medicine, Southampton, UK
| | - Marc Tischkowitz
- Department of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Helen Hanson
- Department of Clinical Genetics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, London, UK .,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
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28
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A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies. Hum Genet 2020; 140:593-607. [PMID: 33095315 PMCID: PMC7981318 DOI: 10.1007/s00439-020-02228-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/14/2020] [Indexed: 11/04/2022]
Abstract
Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can provide an accurate diagnosis, 24–60% of ciliopathy patients who undergo genetic testing do not receive a genetic diagnosis. This is partly because following current guidelines from the American College of Medical Genetics and the Association for Molecular Pathology, it is difficult to provide a confident clinical diagnosis of disease caused by missense or non-coding variants, which account for more than one-third of cases of disease. Mutations in PRPF31 are the second most common cause of the degenerative retinal ciliopathy autosomal dominant retinitis pigmentosa. Here, we present a high-throughput high-content imaging assay providing quantitative measure of effect of missense variants in PRPF31 which meets the recently published criteria for a baseline standard in vitro test for clinical variant interpretation. This assay utilizes a new PRPF31+/– human retinal cell line generated using CRISPR gene editing to provide a stable cell line with significantly fewer cilia in which novel missense variants are expressed and characterised. We show that high-content imaging of cells expressing missense variants in a ciliopathy gene on a null background can allow characterisation of variants according to the cilia phenotype. We hope that this will be a useful tool for clinical characterisation of PRPF31 variants of uncertain significance, and can be extended to variant classification in other ciliopathies.
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29
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Zhang J, Yao Y, He H, Shen J. Clinical Interpretation of Sequence Variants. CURRENT PROTOCOLS IN HUMAN GENETICS 2020; 106:e98. [PMID: 32176464 PMCID: PMC7431429 DOI: 10.1002/cphg.98] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.
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Affiliation(s)
- Junyu Zhang
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yanyi Yao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Haixian He
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
- NHC Key Laboratory of Otorhinolaryngology, Shandong University, Jinan, China
| | - Jun Shen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
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30
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Brnich SE, Abou Tayoun AN, Couch FJ, Cutting GR, Greenblatt MS, Heinen CD, Kanavy DM, Luo X, McNulty SM, Starita LM, Tavtigian SV, Wright MW, Harrison SM, Biesecker LG, Berg JS. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med 2019; 12:3. [PMID: 31892348 PMCID: PMC6938631 DOI: 10.1186/s13073-019-0690-2] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria for different types of evidence. This includes the strong evidence codes PS3 and BS3 for "well-established" functional assays demonstrating a variant has abnormal or normal gene/protein function, respectively. However, they did not provide detailed guidance on how functional evidence should be evaluated, and differences in the application of the PS3/BS3 codes are a contributor to variant interpretation discordance between laboratories. This recommendation seeks to provide a more structured approach to the assessment of functional assays for variant interpretation and guidance on the use of various levels of strength based on assay validation. METHODS The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated functional evidence from ClinGen Variant Curation Expert Panel-developed rule specifications and expert opinions to refine the PS3/BS3 criteria over multiple in-person and virtual meetings. We estimated the odds of pathogenicity for assays using various numbers of variant controls to determine the minimum controls required to reach moderate level evidence. Feedback from the ClinGen Steering Committee and outside experts were incorporated into the recommendations at multiple stages of development. RESULTS The SVI Working Group developed recommendations for evaluators regarding the assessment of the clinical validity of functional data and a four-step provisional framework to determine the appropriate strength of evidence that can be applied in clinical variant interpretation. These steps are as follows: (1) define the disease mechanism, (2) evaluate the applicability of general classes of assays used in the field, (3) evaluate the validity of specific instances of assays, and (4) apply evidence to individual variant interpretation. We found that a minimum of 11 total pathogenic and benign variant controls are required to reach moderate-level evidence in the absence of rigorous statistical analysis. CONCLUSIONS The recommendations and approach to functional evidence evaluation described here should help clarify the clinical variant interpretation process for functional assays. Further, we hope that these recommendations will help develop productive partnerships with basic scientists who have developed functional assays that are useful for interrogating the function of a variety of genes.
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Affiliation(s)
- Sarah E Brnich
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Ahmad N Abou Tayoun
- Genomics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Garry R Cutting
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Dona M Kanavy
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Xi Luo
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Shannon M McNulty
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Matt W Wright
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, 120 Mason Farm Rd., Chapel Hill, NC, 27599-7264, USA.
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