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Razuvayevskaya O, Lopez I, Dunham I, Ochoa D. Genetic factors associated with reasons for clinical trial stoppage. Nat Genet 2024; 56:1862-1867. [PMID: 39075208 PMCID: PMC11387188 DOI: 10.1038/s41588-024-01854-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/02/2024] [Indexed: 07/31/2024]
Abstract
Many drug discovery projects are started but few progress fully through clinical trials to approval. Previous work has shown that human genetics support for the therapeutic hypothesis increases the chance of trial progression. Here, we applied natural language processing to classify the free-text reasons for 28,561 clinical trials that stopped before their endpoints were met. We then evaluated these classes in light of the underlying evidence for the therapeutic hypothesis and target properties. We found that trials are more likely to stop because of a lack of efficacy in the absence of strong genetic evidence from human populations or genetically modified animal models. Furthermore, certain trials are more likely to stop for safety reasons if the drug target gene is highly constrained in human populations and if the gene is broadly expressed across tissues. These results support the growing use of human genetics to evaluate targets for drug discovery programs.
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Affiliation(s)
- Olesya Razuvayevskaya
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Irene Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - David Ochoa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
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2
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Ross JE, Mohan S, Zhang J, Sullivan MJ, Bury L, Lee K, Futchi I, Frantz A, McDougal D, Perez Botero J, Cattaneo M, Cooper N, Downes K, Gresele P, Keenan C, Lee AI, Megy K, Morange PE, Morgan NV, Schulze H, Zimowski K, Freson K, Lambert MP. Evaluating the clinical validity of genes related to hemostasis and thrombosis using the Clinical Genome Resource gene curation framework. J Thromb Haemost 2024; 22:645-665. [PMID: 38016518 PMCID: PMC10922649 DOI: 10.1016/j.jtha.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Inherited bleeding, thrombotic, and platelet disorders (BTPDs) are a heterogeneous set of diseases, many of which are very rare globally. Over the past 5 decades, the genetic basis of some of these disorders has been identified, and recently, high-throughput sequencing has become the primary means of identifying disease-causing genetic variants. OBJECTIVES Knowledge of the clinical validity of a gene-disease relationship is essential to provide an accurate diagnosis based on results of diagnostic gene panel tests and inform the construction of such panels. The Scientific and Standardization Committee for Genetics in Thrombosis and Hemostasis undertook a curation process for selecting 96 TIER1 genes for BTPDs. The purpose of the process was to evaluate the evidence supporting each gene-disease relationship and provide an expert-reviewed classification for the clinical validity of genes associated with BTPDs. METHODS The Clinical Genome Resource (ClinGen) Hemostasis/Thrombosis Gene Curation Expert Panel assessed the strength of evidence for TIER1 genes using the semiquantitative ClinGen gene-disease clinical validity framework. ClinGen Lumping and Splitting guidelines were used to determine the appropriate disease entity or entities for each gene, and 101 gene-disease relationships were identified for curation. RESULTS The final outcome included 68 Definitive (67%), 26 Moderate (26%), and 7 Limited (7%) classifications. The summary of each curation is available on the ClinGen website. CONCLUSION Expert-reviewed assignment of gene-disease relationships by the ClinGen Hemostasis/Thrombosis Gene Curation Expert Panel facilitates accurate molecular diagnoses of BTPDs by clinicians and diagnostic laboratories. These curation efforts can allow genetic testing to focus on genes with a validated role in disease.
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Affiliation(s)
- Justyne E Ross
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shruthi Mohan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Zhang
- KingMed Diagnostics, Guangzhou, Guangdong, China
| | - Mia J Sullivan
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA
| | - Loredana Bury
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isabella Futchi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annabelle Frantz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dara McDougal
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Juliana Perez Botero
- Versiti Blood Center of Wisconsin, Milwaukee, Wisconsin, USA; Division of Hematology/Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marco Cattaneo
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Nichola Cooper
- Centre for Haematology, Imperial College London, London, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Catriona Keenan
- Haemostasis Molecular Diagnostic Laboratory, National Coagulation Centre, St James's Hospital, Dublin, Ireland
| | - Alfred I Lee
- Section of Hematology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Pierre-Emmanuel Morange
- INSERM, INRAE, C2VN, Aix Marseille University, Marseille, France; Hematology Laboratory, La Timone Hospital, APHM, Marseille, France
| | - Neil V Morgan
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Harald Schulze
- Institute of Experimental Biomedicine, Julius-Maximilians-University Wuerzburg, Wuerzburg, Germany
| | - Karen Zimowski
- Aflac Cancer and Blood Disorders Center, Emory University/Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
| | - Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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3
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Rizzuti M, Sali L, Melzi V, Scarcella S, Costamagna G, Ottoboni L, Quetti L, Brambilla L, Papadimitriou D, Verde F, Ratti A, Ticozzi N, Comi GP, Corti S, Gagliardi D. Genomic and transcriptomic advances in amyotrophic lateral sclerosis. Ageing Res Rev 2023; 92:102126. [PMID: 37972860 DOI: 10.1016/j.arr.2023.102126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder and the most common motor neuron disease. ALS shows substantial clinical and molecular heterogeneity. In vitro and in vivo models coupled with multiomic techniques have provided important contributions to unraveling the pathomechanisms underlying ALS. To date, despite promising results and accumulating knowledge, an effective treatment is still lacking. Here, we provide an overview of the literature on the use of genomics, epigenomics, transcriptomics and microRNAs to deeply investigate the molecular mechanisms developing and sustaining ALS. We report the most relevant genes implicated in ALS pathogenesis, discussing the use of different high-throughput sequencing techniques and the role of epigenomic modifications. Furthermore, we present transcriptomic studies discussing the most recent advances, from microarrays to bulk and single-cell RNA sequencing. Finally, we discuss the use of microRNAs as potential biomarkers and promising tools for molecular intervention. The integration of data from multiple omic approaches may provide new insights into pathogenic pathways in ALS by shedding light on diagnostic and prognostic biomarkers, helping to stratify patients into clinically relevant subgroups, revealing novel therapeutic targets and supporting the development of new effective therapies.
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Affiliation(s)
- Mafalda Rizzuti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Sali
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Melzi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Simone Scarcella
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Costamagna
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Quetti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Brambilla
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Federico Verde
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Nicola Ticozzi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giacomo Pietro Comi
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania Corti
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Delia Gagliardi
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
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De Sousa SMC, Shen A, Yates CJ, Clifton-Bligh R, Santoreneos S, King J, Toubia J, Trivellin G, Lania AG, Stratakis CA, Torpy DJ, Scott HS. PAM variants in patients with thyrotrophinomas, cyclical Cushing's disease and prolactinomas. Front Endocrinol (Lausanne) 2023; 14:1305606. [PMID: 38075079 PMCID: PMC10710132 DOI: 10.3389/fendo.2023.1305606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Germline loss-of-function variants in PAM, encoding peptidylglycine α-amidating monooxygenase (PAM), were recently discovered to be enriched in conditions of pathological pituitary hypersecretion, specifically: somatotrophinoma, corticotrophinoma, and prolactinoma. PAM is the sole enzyme responsible for C-terminal amidation of peptides, and plays a role in the biosynthesis and regulation of multiple hormones, including proopiomelanocortin (POMC). Methods We performed exome sequencing of germline and tumour DNA from 29 individuals with functioning pituitary adenomas (12 prolactinomas, 10 thyrotrophinomas, 7 cyclical Cushing's disease). An unfiltered analysis was undertaken of all PAM variants with population prevalence <5%. Results We identified five coding, non-synonymous PAM variants of interest amongst seven individuals (six germline, one somatic). The five variants comprised four missense variants and one truncating variant, all heterozygous. Each variant had some evidence of pathogenicity based on population prevalence, conservation scores, in silico predictions and/or prior functional studies. The yield of predicted deleterious PAM variants was thus 7/29 (24%). The variants predominated in individuals with thyrotrophinomas (4/10, 40%) and cyclical Cushing's disease (2/7, 29%), compared to prolactinomas (1/12, 8%). Conclusion This is the second study to demonstrate a high yield of suspected loss-of-function, predominantly germline, PAM variants in individuals with pathological pituitary hypersecretion. We have extended the association with corticotrophinoma to include the specific clinical entity of cyclical Cushing's disease and demonstrated a novel association between PAM variants and thyrotrophinoma. PAM variants might act as risk alleles for pituitary adenoma formation, with a possible genotype-phenotype relationship between truncating variants and altered temporal secretion of cortisol.
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Affiliation(s)
- Sunita M. C. De Sousa
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- South Australian Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Angeline Shen
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Christopher J. Yates
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Roderick Clifton-Bligh
- Cancer Genetics Laboratory, Kolling Institute, Royal North Shore Hospital, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- Department of Endocrinology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Stephen Santoreneos
- Department of Neurosurgery, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - James King
- Department of Surgery, University of Melbourne, Melbourne, VIC, Australia
| | - John Toubia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Giampaolo Trivellin
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Andrea G. Lania
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
| | - Constantine A. Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, United States
- Human Genetics and Precision Medicine, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology Hellas, Heraklion, Greece
- Research Institute, ELPEN, Athens, Greece
| | - David J. Torpy
- Endocrine & Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Hamish S. Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An SA Pathology and University of South Australia Alliance, Adelaide, SA, Australia
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5
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Wang Q, Lin X, Lai K, Liu Y, Qin T, Tan H, Li J, Lin Z, Zhang X, Li X, Lin H, Chen W. Novel compound heterozygous variants of the SEC23A gene in a Chinese family with cranio-lenticulo-sutural dysplasia based on data from a large cohort of congenital cataract patients. BMC Med Genomics 2023; 16:241. [PMID: 37828500 PMCID: PMC10568747 DOI: 10.1186/s12920-023-01667-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Cranio-lenticulo-sutural dysplasia (CLSD) is a rare dysmorphic syndrome characterized by skeletal dysmorphism, late-closing fontanels, and cataracts. CLSD is caused by mutations in the SEC23A gene (OMIM# 607812) and can be inherited in either an autosomal dominant or autosomal recessive pattern. To date, only four mutations have been reported to cause CLSD. This study aims to identify the disease-causing variants in a large cohort of congenital cataract patients, to expand the genotypic and phenotypic spectrum of CLSD, and to confirm the association between SEC23A and autosomal recessive CLSD (ARCLSD). METHODS We collected detailed medical records and performed comprehensive ocular examinations and whole-exome sequencing (WES) on 115 patients with congenital cataracts. After suspecting that a patient may have CLSD based on the sequencing results, we proceeded to conduct transmission electron microscopy (TEM) on the cultured skin fibroblasts. The clinical validity of the reported gene-disease relationships for the gene and the disease was evaluated using the ClinGen gene curation framework. RESULTS Two novel compound heterozygous variants (c.710A > C p.Asp237Ala, c.1946T > C p.Leu649Pro) of the SEC23A gene, classified as variant of uncertain significance, were identified in the proband with skeletal, cardiac, ocular, and hearing defects. The observation of typical distended endoplasmic reticulum cisternae further supported the diagnosis of CLSD. Application of the ClinGen gene curation framework confirmed the association between SEC23A and ARCLSD. CONCLUSION This study expands the genotypic and phenotypic spectrum of CLSD, proposes TEM as a supplemental diagnostic method, and indicates that congenital cataracts are a typical sign of ARCLSD.
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Affiliation(s)
- Qiwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xiaoshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Kunbei Lai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Yinghui Liu
- Department of Dermatology, Dermatology Hospital, Southern Medical University, 510091, Guangzhou, Guangdong Province, China
| | - Tingfeng Qin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Haowen Tan
- Aegicare Biotech, 518000, Shenzhen, Guangdong Province, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Zhuoling Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xulin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Xiaoyan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China.
| | - Weirong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Sun Yat-sen University, 510060, Guangzhou, Guangdong Province, China.
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6
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Wang Q, Qin T, Tan H, Ding X, Lin X, Li J, Lin Z, Sun L, Lin H, Chen W. Broadening the genotypic and phenotypic spectrum of MAF in three Chinese Han congenital cataracts families. Am J Med Genet A 2022; 188:2888-2898. [PMID: 36097645 DOI: 10.1002/ajmg.a.62947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 01/31/2023]
Abstract
Pathogenic variants in the v-maf avian musculoaponeurotic fibrosarcoma oncogene homologue (MAF) encoding a transcription factor (from a unique subclass of basic leucine zipper transcription factors) are associated with isolated congenital cataracts (CCs) and Aymé-Gripp syndrome (AYGRPS). We collected detailed disease histories from, and performed comprehensive ophthalmic and systemic examinations in 269 patients with CCs; we then performed whole-exome sequencing. Pathogenicity assessments were evaluated using multiple predictive tools. The clinical validities of the reported gene-disease relationships for MAF genes (MAF-CCs and MAF-AYGRPS) were assessed using the ClinGen gene curation framework. We identified two novel (c.173C>A, p.Thr58Asn and c.947T>C, p. Leu316Pro) variants and one known (c.173C>T, p.Thr58Ile) MAF missense variant in three patients. We described novel phenotypes including cleft palate, macular hypoplasia, and retinal neovascularization in the peripheral avascular area and analyzed the genotype-phenotype correlations. We demonstrated associations of variants in the MAF C-terminal DNA-binding domain with CCs and associations of variants in the N-terminal transactivation domain of MAF with AYGRPS. We thus expand the genotypic and phenotypic spectrum of the MAF gene. The ClinGen gene curation framework results suggested that variants in different domains of MAF are associated with different diseases.
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Affiliation(s)
- Qiwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Tingfeng Qin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | | | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Xiaoshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Zhuolin Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Limei Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Weirong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
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7
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Li MM, Tayoun AA, DiStefano M, Pandya A, Rehm HL, Robin NH, Schaefer AM, Yoshinaga-Itano C. Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1392-1406. [PMID: 35802133 DOI: 10.1016/j.gim.2022.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.
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Affiliation(s)
- Marilyn M Li
- Department of Pathology and Laboratory Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Mohammed Bin Rashid University, Dubai, United Arab Emirates
| | | | - Arti Pandya
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Nathaniel H Robin
- Departments of Genetics and Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Amanda M Schaefer
- Department of Otolaryngology-Head & Neck Surgery, Molecular Otolaryngology and Renal Research Laboratories, University of Iowa, Iowa City, IA
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Thaxton C, Good ME, DiStefano MT, Luo X, Andersen EF, Thorland E, Berg J, Martin CL, Rehm HL, Riggs ER. Utilizing ClinGen gene-disease validity and dosage sensitivity curations to inform variant classification. Hum Mutat 2021; 43:1031-1040. [PMID: 34694049 PMCID: PMC9035475 DOI: 10.1002/humu.24291] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/12/2021] [Accepted: 10/19/2021] [Indexed: 11/05/2022]
Abstract
Understanding whether there is enough evidence to implicate a gene's role in a given disease, as well as the mechanisms by which variants in this gene might cause this disease, is essential to determine clinical relevance. The National Institutes of Health-funded Clinical Genome Resource (ClinGen) has developed evaluation frameworks to assess both the strength of evidence supporting a relationship between a gene and disease (gene-disease validity), and whether loss (haploinsufficiency) or gain (triplosensitivity) of individual genes or genomic regions is a mechanism for disease (dosage sensitivity). ClinGen actively applies these frameworks across multiple disease domains, and makes this information publicly available via its website (https://www.clinicalgenome.org/) for use in multiple applications, including clinical variant classification. Here, we describe how the results of these curation processes can be utilized to inform the appropriate application of pathogenicity criteria for both sequence and copy number variants, as well as to guide test development and inform genomic filtering pipelines.
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Affiliation(s)
- Courtney Thaxton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Molly E Good
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | | | - Xi Luo
- Department of Pediatric/Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - Erica F Andersen
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,ARUP Laboratories, Salt Lake City, Utah, USA
| | - Erik Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jonathan Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Heidi L Rehm
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Erin R Riggs
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
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9
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Jordan E, Peterson L, Ai T, Asatryan B, Bronicki L, Brown E, Celeghin R, Edwards M, Fan J, Ingles J, James CA, Jarinova O, Johnson R, Judge DP, Lahrouchi N, Lekanne Deprez RH, Lumbers RT, Mazzarotto F, Medeiros Domingo A, Miller RL, Morales A, Murray B, Peters S, Pilichou K, Protonotarios A, Semsarian C, Shah P, Syrris P, Thaxton C, van Tintelen JP, Walsh R, Wang J, Ware J, Hershberger RE. Evidence-Based Assessment of Genes in Dilated Cardiomyopathy. Circulation 2021; 144:7-19. [PMID: 33947203 PMCID: PMC8247549 DOI: 10.1161/circulationaha.120.053033] [Citation(s) in RCA: 230] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/13/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Each of the cardiomyopathies, classically categorized as hypertrophic cardiomyopathy, dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy, has a signature genetic theme. Hypertrophic cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy are largely understood as genetic diseases of sarcomere or desmosome proteins, respectively. In contrast, >250 genes spanning >10 gene ontologies have been implicated in DCM, representing a complex and diverse genetic architecture. To clarify this, a systematic curation of evidence to establish the relationship of genes with DCM was conducted. METHODS An international panel with clinical and scientific expertise in DCM genetics evaluated evidence supporting monogenic relationships of genes with idiopathic DCM. The panel used the Clinical Genome Resource semiquantitative gene-disease clinical validity classification framework with modifications for DCM genetics to classify genes into categories on the basis of the strength of currently available evidence. Representation of DCM genes on clinically available genetic testing panels was evaluated. RESULTS Fifty-one genes with human genetic evidence were curated. Twelve genes (23%) from 8 gene ontologies were classified as having definitive (BAG3, DES, FLNC, LMNA, MYH7, PLN, RBM20, SCN5A, TNNC1, TNNT2, TTN) or strong (DSP) evidence. Seven genes (14%; ACTC1, ACTN2, JPH2, NEXN, TNNI3, TPM1, VCL) including 2 additional ontologies were classified as moderate evidence; these genes are likely to emerge as strong or definitive with additional evidence. Of these 19 genes, 6 were similarly classified for hypertrophic cardiomyopathy and 3 for arrhythmogenic right ventricular cardiomyopathy. Of the remaining 32 genes (63%), 25 (49%) had limited evidence, 4 (8%) were disputed, 2 (4%) had no disease relationship, and 1 (2%) was supported by animal model data only. Of the 16 evaluated clinical genetic testing panels, most definitive genes were included, but panels also included numerous genes with minimal human evidence. CONCLUSIONS In the curation of 51 genes, 19 had high evidence (12 definitive/strong, 7 moderate). It is notable that these 19 genes explain only a minority of cases, leaving the remainder of DCM genetic architecture incompletely addressed. Clinical genetic testing panels include most high-evidence genes; however, genes lacking robust evidence are also commonly included. We recommend that high-evidence DCM genes be used for clinical practice and that caution be exercised in the interpretation of variants in variable-evidence DCM genes.
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Affiliation(s)
- Elizabeth Jordan
- Division of Human Genetics (E.J., L.P., T.A., R.E.H.), Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus
| | - Laiken Peterson
- Division of Human Genetics (E.J., L.P., T.A., R.E.H.), Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus
| | - Tomohiko Ai
- Division of Human Genetics (E.J., L.P., T.A., R.E.H.), Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus
| | - Babken Asatryan
- Department for Cardiology, Inselspital, Bern University Hospital, University of Bern, Switzerland (B.A.)
| | - Lucas Bronicki
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Canada (L.B., O.J.)
- Department of Laboratory and Pathology Medicine, University of Ottawa, Ontario, Canada (L.B., O.J.)
| | - Emily Brown
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD (E.B., C.A.J., B.M.)
| | - Rudy Celeghin
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Italy (R.C., K.P.)
| | - Matthew Edwards
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom (M.E.)
| | - Judy Fan
- Department of Medicine, University of California, Los Angeles (J.F., J. Wang)
| | - Jodie Ingles
- Cardio Genomics Program at Centenary Institute, University of Sydney, Australia (J.I.)
| | - Cynthia A. James
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD (E.B., C.A.J., B.M.)
| | - Olga Jarinova
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, Canada (L.B., O.J.)
- Department of Laboratory and Pathology Medicine, University of Ottawa, Ontario, Canada (L.B., O.J.)
| | - Renee Johnson
- Victor Chang Cardiac Research Institute, Sydney, Australia (R.J.)
- Department of Medicine, University of New South Wales, Sydney, Australia (R.J.)
| | - Daniel P. Judge
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston (D.P.J.)
| | - Najim Lahrouchi
- Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam Cardiovascular Sciences, Amsterdam Universitair Medische Centra, University of Amsterdam, the Netherlands (N.L., R.W.)
| | - Ronald H. Lekanne Deprez
- Department of Clinical Genetics, Amsterdam University Medical Center location Academic Medical Center, the Netherlands (R.H.L.D.)
| | - R. Thomas Lumbers
- Institute of Health Informatics, University College London, London, UK (R.T.L.)
- Health Data Research UK London, University College London, UK (R.T.L.)
- University College London British Heart Foundation Research Accelerator, London, United Kingdom (R.T.L.)
| | - Francesco Mazzarotto
- Cardiovascular Research Center, Royal Brompton and Harefield Hospitals, National Health Service Foundation Trust, London, United Kingdom (F.M., J. Ware)
- National Heart and Lung Institute, Imperial College London, United Kingdom (F.M., J. Ware)
- Department of Clinical and Experimental Medicine, University of Florence, Italy (F.M.)
- Cardiomyopathy Unit, Careggi University Hospital, Florence, Italy (F.M.)
| | | | - Rebecca L. Miller
- Cardiovascular Genomics Center, Inova Heart and Vascular Institute, Falls Church, VA (R.L.M., P. Shah)
| | | | - Brittney Murray
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD (E.B., C.A.J., B.M.)
| | - Stacey Peters
- Department of Cardiology and Genomic Medicine, Royal Melbourne Hospital, Australia (S.P.)
| | - Kalliopi Pilichou
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Italy (R.C., K.P.)
| | - Alexandros Protonotarios
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, London, United Kingdom (A.P., P. Syrris)
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Australia (C.S.)
| | - Palak Shah
- Cardiovascular Genomics Center, Inova Heart and Vascular Institute, Falls Church, VA (R.L.M., P. Shah)
| | - Petros Syrris
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, London, United Kingdom (A.P., P. Syrris)
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina, Chapel Hill (C.T.)
| | - J. Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, The Netherlands (J.P.v.T.)
| | - Roddy Walsh
- Department of Clinical and Experimental Cardiology, Heart Centre, Amsterdam Cardiovascular Sciences, Amsterdam Universitair Medische Centra, University of Amsterdam, the Netherlands (N.L., R.W.)
| | - Jessica Wang
- Department of Medicine, University of California, Los Angeles (J.F., J. Wang)
| | - James Ware
- Cardiovascular Research Center, Royal Brompton and Harefield Hospitals, National Health Service Foundation Trust, London, United Kingdom (F.M., J. Ware)
- National Heart and Lung Institute, Imperial College London, United Kingdom (F.M., J. Ware)
- Medical Research Council London Institute for Medical Sciences, Imperial College London, United Kingdom (J. Ware)
| | - Ray E. Hershberger
- Division of Human Genetics (E.J., L.P., T.A., R.E.H.), Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus
- Division of Cardiovascular Medicine (R.E.H.), Department of Internal Medicine, Wexner Medical Center, The Ohio State University, Columbus
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10
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Balzotti M, Meng L, Muzzey D, Johansen Taber K, Beauchamp K, Curation Team MG, Curation Team BG, Mar-Heyming R, Buckley B, Moyer K. Clinical validity of expanded carrier screening: Evaluating the gene-disease relationship in more than 200 conditions. Hum Mutat 2020; 41:1365-1371. [PMID: 32383249 PMCID: PMC7496796 DOI: 10.1002/humu.24033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 01/31/2023]
Abstract
Clinical guidelines consider expanded carrier screening (ECS) to be an acceptable method of carrier screening. However, broader guideline support and payer adoption require evidence for associations between the genes on ECS panels and the conditions for which they aim to identify carriers. We applied a standardized framework for evaluation of gene‐disease association to assess the clinical validity of conditions screened by ECS panels. The Clinical Genome Resource (ClinGen) gene curation framework was used to assess genetic and experimental evidence of associations between 208 genes and conditions screened on two commercial ECS panels. Twenty‐one conditions were previously classified by ClinGen, and the remaining 187 were evaluated by curation teams at two laboratories. To ensure consistent application of the framework across the laboratories, concordance was evaluated on a subset of conditions. All 208 evaluated conditions met the evidence threshold for supporting a gene‐disease association. Furthermore, 203 of 208 (98%) achieved the strongest (“Definitive”) level of gene‐disease association. All conditions evaluated by both commercial laboratories were similarly classified. Assessment using the ClinGen standardized framework revealed strong evidence of gene‐disease association for conditions on two ECS panels. This result establishes the disease‐level clinical validity of the panels considered herein.
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Affiliation(s)
- Marie Balzotti
- Myriad Women's Health, Myriad Genetics, South San Francisco, California
| | - Linyan Meng
- Division of Clinical Genomic Interpretation, Baylor Genetics, Houston, Texas
| | - Dale Muzzey
- Myriad Women's Health, Myriad Genetics, South San Francisco, California
| | | | - Kyle Beauchamp
- Myriad Women's Health, Myriad Genetics, South San Francisco, California.,Tempus, Redwood City, California
| | | | | | - Rebecca Mar-Heyming
- Myriad Women's Health, Myriad Genetics, South San Francisco, California.,Ambry Genetics, Aliso Viejo, California
| | - Bethany Buckley
- Myriad Women's Health, Myriad Genetics, South San Francisco, California.,Invitae, San Francisco, California
| | - Krista Moyer
- Myriad Women's Health, Myriad Genetics, South San Francisco, California
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11
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McGlaughon JL, Pasquali M, Wallace K, Ross J, Senol-Cosar O, Shen W, Weaver MA, Feigenbaum A, Lyon E, Enns GM, Mao R, Baudet HG. Assessing the strength of evidence for genes implicated in fatty acid oxidation disorders using the ClinGen clinical validity framework. Mol Genet Metab 2019; 128:122-128. [PMID: 31399326 DOI: 10.1016/j.ymgme.2019.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 07/16/2019] [Indexed: 12/30/2022]
Abstract
Newborn screening is an incredibly useful tool for the early identification of many metabolic disorders, including fatty acid oxidation (FAO) disorders. In many cases, molecular tests are necessary to reach a final diagnosis, highlighting the need for a thorough evaluation of genes implicated in FAO disorders. Using the ClinGen (Clinical Genome Resource) clinical validity framework, thirty genes were analyzed for the strength of evidence supporting their association with FAO disorders. Evidence was gathered from the literature by biocurators and presented to disease experts for review in order to assign a clinical validity classification of Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Reported Evidence. Of the gene-disease relationships evaluated, 22/30 were classified as Definitive, three as Moderate, one as Limited, three as No Reported Evidence and one as Disputed. Gene-disease relationships with a Limited, Disputed, and No Reported Evidence were found on two, six, and up to four panels out of 30 FAO disorder-specific panels, respectively, in the National Institute of Health Genetic Testing Registry, while over 70% of the genes on panels are definitively associated with an FAO disorder. These results highlight the need to systematically assess the clinical relevance of genes implicated in fatty acid oxidation disorders in order to improve the interpretation of genetic testing results and diagnosis of patients with these disorders.
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Affiliation(s)
- Jennifer L McGlaughon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Marzia Pasquali
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Kathleen Wallace
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Justyne Ross
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA
| | - Ozlem Senol-Cosar
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA; Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, MA, USA
| | - Wei Shen
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, MD, USA
| | - Annette Feigenbaum
- Department of Pediatrics, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Elaine Lyon
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University, Stanford, CA, USA
| | - Rong Mao
- University of Utah and ARUP Laboratories, Salt Lake City, UT, USA
| | - Heather G Baudet
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, NC, USA.
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12
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ClinGen expert clinical validity curation of 164 hearing loss gene-disease pairs. Genet Med 2019; 21:2239-2247. [PMID: 30894701 PMCID: PMC7280024 DOI: 10.1038/s41436-019-0487-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/01/2019] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Proper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semiquantitative framework to assign clinical validity to gene-disease relationships. METHODS The ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss. RESULTS The final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website ( https://search.clinicalgenome.org/kb/gene-validity ). CONCLUSION This gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.
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13
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Rehm HL, Berg JS, Plon SE. ClinGen and ClinVar – Enabling Genomics in Precision Medicine. Hum Mutat 2018. [DOI: 10.1002/humu.23654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Heidi L. Rehm
- Medical and Population Genetics ProgramThe Broad Institute of MIT and Harvard Cambridge Massachusetts
- Center for Genomic MedicineMassachusetts General Hospital Boston Massachusetts
| | - Jonathan S. Berg
- Department of GeneticsUniversity of North Carolina at Chapel Hill Chapel Hill North Carolina
| | - Sharon E. Plon
- Departments of Molecular and Human Genetics and PediatricsBaylor College of Medicine Houston Texas
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