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      The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources

      research-article
      , PhD 1 , 2 , , BA 1 , , BS 2 , , MD 3 , , BA 4 , , PhD 5 , , PhD 6 , 7 , 2 , , MS 8 , , MD, PhD 9 , , PhD 10 , , MS 4 , , PhD 11 , 12 , , PhD 13 , , MS 14 , 15 , , PhD 16 , , Msc 17 , 18 , , MS 19 , , DM, FRCP, DCH 20 , , DM 21 , , PhD 17 , 22 , , PhD 9 , , MD, MPH 4 , , FMedSci, FRS 23 , , PhD 17 , , PhD 17 , , PhD 3 , , PhD 1 , , PhD, BSc 17 , 24 , , PhD 5 , , MSc 17 , , PhD 25 , , PhD 26 , , PhD 5 , , MS 27 , , PhD MBBS MRCP 28 , 29 , , MA 5 , , PhD 17 , , BM BCh DM 30 , , MS 31 , , PhD 11 , , PhD MRCP FESC 28 , 32 , 2 , , BS 27 , , PhD 17 , , PhD 33 , , MBChB 21 , , PhD 2 , 34 ,
      Genetics in medicine : official journal of the American College of Medical Genetics
      GenCC, The Gene Curation Coalition, database, gene curation, genetic diagnosis

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          Abstract

          Purpose

          Several groups and resources provide information that pertains to the validity of gene-disease relationships used in genomic medicine and research; however, universal standards and terminologies to define the evidence base for the role of a gene in disease, and a single harmonized resource were lacking. To tackle this issue, the Gene Curation Coalition (GenCC) was formed.

          Methods

          The GenCC drafted harmonized definitions for differing levels of gene-disease validity based on existing resources, and performed a modified Delphi survey with three rounds to narrow the list of terms. The GenCC also developed a unified database to display curated gene-disease validity assertions from its members.

          Results

          Based on 241 survey responses from the genetics community, a consensus term set was chosen for grading gene-disease validity and database submissions. As of December 2021, the database contains 15,241 gene-disease assertions on 4,569 unique genes from 12 submitters. When comparing submissions to the database from distinct sources, conflicts in assertions of gene-disease validity ranged from 5.3% to 13.4%.

          Conclusion

          Terminology standardization, sharing of gene-disease validity classifications, and resolution of curation conflicts will facilitate collaborations across international curation efforts and in turn, improve consistency in genetic testing and variant interpretation.

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          Most cited references21

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          Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

          The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1 In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next generation sequencing. By adopting and leveraging next generation sequencing, clinical laboratories are now performing an ever increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes and epigenetic assays for genetic disorders. By virtue of increased complexity, this paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP and CAP stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories including genotyping, single genes, panels, exomes and genomes. This report recommends the use of specific standard terminology: ‘pathogenic’, ‘likely pathogenic’, ‘uncertain significance’, ‘likely benign’, and ‘benign’ to describe variants identified in Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a CLIA-approved laboratory with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or equivalent.
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            The Human Genome Browser at UCSC

            As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
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              ClinVar: improving access to variant interpretations and supporting evidence

              Abstract ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant (‘provider interpretation’) or from groups such as patient registries that primarily provide phenotypic information from patients (‘phenotyping only’). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.
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                Author and article information

                Journal
                9815831
                Genet Med
                Genet Med
                Genetics in medicine : official journal of the American College of Medical Genetics
                1098-3600
                1530-0366
                04 May 2022
                August 2022
                04 May 2022
                05 August 2022
                : 24
                : 8
                : 1732-1742
                Affiliations
                [1 ]Geisinger Health System, Danville, PA, USA
                [2 ]Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
                [3 ]Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
                [4 ]Department of Genetic Medicine, Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, Baltimore, MD, 21287-4922, USA
                [5 ]Inserm, US14 - Orphanet, France
                [6 ]Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
                [7 ]MGB Laboratory for Molecular Medicine, Cambridge, MA, USA
                [8 ]Myriad Women's Health, San Francisco, CA, USA
                [9 ]Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
                [10 ]European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
                [11 ]HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
                [12 ]Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0PT, UK
                [13 ]Illumina Clinical Services Laboratory, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
                [14 ]National Library of Medicine, Bethesda, MD, USA
                [15 ]ICF, 9300 Lee Highway, Fairfax, VA, 22031, USA
                [16 ]Genome Interpretation, Genome Assembly and Annotation (GAA), European Molecular Biology Laboratory, European Bioinformatics Institute,, Wellcome Genome Campus, Hinxton,, Cambridge, CB10 1SD, UK
                [17 ]Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
                [18 ]Healx Ltd., Charter House, 66-68 Hills Rd, Cambridge, CB2 1LA, UK
                [19 ]Franklin by Genoox, Palo Alto, CA, USA
                [20 ]Department of Genetics, Addenbrooke's Hospital, Cambridge, UK
                [21 ]MRC Human Genetics Unit, MRC IGMM, The University of Edinburgh, Edinburgh, UK
                [22 ]SciBite Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
                [23 ]Wellcome Sanger Institute, Hinxton, UK
                [24 ]Open Targets, EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1DR, UK
                [25 ]AmbryGenetics, Aliso Viejo, CA, USA
                [26 ]National Human Genome Research Institute, National Institutes of Health, USA
                [27 ]Autism & Developmental Medicine Institute, Geisinger Health System, Danville, PA, USA
                [28 ]National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
                [29 ]Great Ormond Street Hospital, London, UK
                [30 ]Australian Genomics, Melbourne, Australia
                [31 ]Invitae, San Francisco, CA, USA
                [32 ]Royal Brompton & Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
                [33 ]Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
                [34 ]Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
                Author notes
                Corresponding Author: Heidi L Rehm, HREHM@ 123456mgh.harvard.edu , (617) 643-3217
                Article
                EMS144755
                10.1016/j.gim.2022.04.017
                7613247
                35507016
                0f3224af-ba23-40b1-8c09-d2ff30f4706c

                This work is licensed under a CC BY 4.0 International license.

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                Genetics
                gencc,the gene curation coalition,database,gene curation,genetic diagnosis
                Genetics
                gencc, the gene curation coalition, database, gene curation, genetic diagnosis

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