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Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms.
Roberts, Angharad M; DiStefano, Marina T; Riggs, Erin Rooney; Josephs, Katherine S; Alkuraya, Fowzan S; Amberger, Joanna; Amin, Mutaz; Berg, Jonathan S; Cunningham, Fiona; Eilbeck, Karen; Firth, Helen V; Foreman, Julia; Hamosh, Ada; Hay, Eleanor; Leigh, Sarah; Martin, Christa L; McDonagh, Ellen M; Perrett, Daniel; Ramos, Erin M; Robinson, Peter N; Rath, Ana; van Sant, David; Stark, Zornitza; Whiffin, Nicola; Rehm, Heidi L; Ware, James S.
Afiliación
  • Roberts AM; National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK.
  • DiStefano MT; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK.
  • Riggs ER; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  • Josephs KS; Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA.
  • Alkuraya FS; National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK.
  • Amberger J; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
  • Amin M; Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia.
  • Berg JS; Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA.
  • Cunningham F; INSERM, US14-Orphanet, Paris, France.
  • Eilbeck K; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599.
  • Firth HV; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom.
  • Foreman J; Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah.
  • Hamosh A; Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK.
  • Hay E; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
  • Leigh S; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
  • Martin CL; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom.
  • McDonagh EM; Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA.
  • Perrett D; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK.
  • Ramos EM; Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK.
  • Robinson PN; Clinical Genome Resource (ClinGen), USA.
  • Rath A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom.
  • van Sant D; Open Targets, Cambridge, UK.
  • Stark Z; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom.
  • Whiffin N; National Human Genome Research Institute, National Institutes of Health, USA.
  • Rehm HL; The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA.
  • Ware JS; INSERM, US14-Orphanet, Paris, France.
medRxiv ; 2023 Apr 03.
Article en En | MEDLINE | ID: mdl-37066232
PURPOSE: The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS: Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS: We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION: The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2023 Tipo del documento: Article Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2023 Tipo del documento: Article Pais de publicación: Estados Unidos