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Dolman L, Page A, Babb L, Freimuth RR, Arachchi H, Bizon C, Brush M, Fiume M, Haendel M, Hansen DP, Milosavljevic A, Patel RY, Pawliczek P, Yates AD, Rehm HL. ClinGen advancing genomic data-sharing standards as a GA4GH driver project. Hum Mutat 2019; 39:1686-1689. [PMID: 30311379 DOI: 10.1002/humu.23625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 11/11/2022]
Abstract
The Clinical Genome Resource (ClinGen)'s work to develop a knowledge base to support the understanding of genes and variants for use in precision medicine and research depends on robust, broadly applicable, and adaptable technical standards for sharing data and information. To forward this goal, ClinGen has joined with the Global Alliance for Genomics and Health (GA4GH) to support the development of open, freely-available technical standards and regulatory frameworks for secure and responsible sharing of genomic and health-related data. In its capacity as one of the 15 inaugural GA4GH "Driver Projects," ClinGen is providing input on the key standards needs of the global genomics community, and has committed to participate on GA4GH Work Streams to support the development of: (1) a standard model for computer-readable variant representation; (2) a data model for linking variant data to annotations; (3) a specification to enable sharing of genomic variant knowledge and associated clinical interpretations; and (4) a set of best practices for use of phenotype and disease ontologies. ClinGen's participation as a GA4GH Driver Project will provide a robust environment to test drive emerging genomic knowledge sharing standards and prove their utility among the community, while accelerating the construction of the ClinGen evidence base.
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Affiliation(s)
- Lena Dolman
- Global Alliance for Genomics and Health Headquarters, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Angela Page
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Robert R Freimuth
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Harindra Arachchi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, North Carolina
| | - Matthew Brush
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, Oregon
| | - Marc Fiume
- Global Alliance for Genomics and Health Headquarters, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,DNAstack, Toronto, Ontario, Canada
| | - Melissa Haendel
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, Oregon.,Linus Pauling Institute, Oregon State University, Corvallis, Oregon
| | - David P Hansen
- Australian e-Health Research Centre, CSIRO, UQ Health Sciences Building, Herston, Qld, Australia
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Piotr Pawliczek
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
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Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK. hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update. Hum Mutat 2018; 39:1803-1813. [PMID: 30129167 PMCID: PMC6282708 DOI: 10.1002/humu.23615] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/15/2018] [Accepted: 08/13/2018] [Indexed: 11/29/2022]
Abstract
The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in public variant databases and the scientific literature. Inconsistent application of the HGVS guidelines can lead to misinterpretation of variants in clinical settings. Reliable software tools are essential to ensure consistent application of the HGVS guidelines when reporting and interpreting variants. We present the hgvs Python package, a comprehensive tool for manipulating sequence variants according to the HGVS nomenclature guidelines. Distinguishing features of the hgvs package include: (1) parsing, formatting, validating, and normalizing variants on genome, transcript, and protein sequences; (2) projecting variants between aligned sequences, including those with gapped alignments; (3) flexible installation using remote or local data (fully local installations eliminate network dependencies); (4) extensive automated tests; and (5) open source development by a community from eight organizations worldwide. This report summarizes recent and significant updates to the hgvs package since its original release in 2014, and presents results of extensive validation using clinical relevant variants from ClinVar and HGMD.
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Affiliation(s)
- Meng Wang
- School of Life Sciences, Peking University, Beijing, China
| | | | - Raymond Dalgleish
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | - Peter J Freeman
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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