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The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

View ORCID ProfileAlex H Wagner, View ORCID ProfileLawrence Babb, View ORCID ProfileGil Alterovitz, View ORCID ProfileMichael Baudis, View ORCID ProfileMatthew Brush, View ORCID ProfileDaniel L Cameron, View ORCID ProfileMelissa Cline, View ORCID ProfileMalachi Griffith, View ORCID ProfileObi L Griffith, View ORCID ProfileSarah Hunt, David Kreda, Jennifer Lee, Javier Lopez, View ORCID ProfileEric Moyer, Tristan Nelson, View ORCID ProfileRonak Y Patel, View ORCID ProfileKevin Riehle, Peter N Robinson, Shawn Rynearson, View ORCID ProfileHelen Schuilenburg, View ORCID ProfileKirill Tsukanov, View ORCID ProfileBrian Walsh, View ORCID ProfileMelissa Konopko, View ORCID ProfileHeidi Rehm, View ORCID ProfileAndrew D Yates, View ORCID ProfileRobert R Freimuth, View ORCID ProfileReece K Hart
doi: https://doi.org/10.1101/2021.01.15.426843
Alex H Wagner
1The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43215, USA
2Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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  • For correspondence: Alex.Wagner@nationwidechildrens.org lbabb@broadinstitute.org reecehart@gmail.com
Lawrence Babb
3Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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  • For correspondence: Alex.Wagner@nationwidechildrens.org lbabb@broadinstitute.org reecehart@gmail.com
Gil Alterovitz
4Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
5Harvard Medical School, Boston, MA 02115, USA
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Michael Baudis
6University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
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Matthew Brush
7Oregon Health & Science University, Portland, OR 97239, USA
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Daniel L Cameron
8Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
9Department of Medical Biology, University of Melbourne, Melbourne, Australia
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Melissa Cline
10UC Santa Cruz Genomics Institute, Santa Cruz, CA 95060, USA
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Malachi Griffith
11Washington University School of Medicine, St. Louis, MO 63108, USA
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Obi L Griffith
11Washington University School of Medicine, St. Louis, MO 63108, USA
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Sarah Hunt
12European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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David Kreda
13Department of Biomedical Informatics, Harvard Medical School, Boston MA 02115, USA
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Jennifer Lee
14Essex Management LLC and National Cancer Institute, Rockville, MD 20850, USA
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Javier Lopez
15Genomics England, London EC1M 6BQ, UK
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Eric Moyer
16National Center for Biotechnology Information, National Library of Medicine National Institutes of Health, Bethesda, MD 20894, USA
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Tristan Nelson
17Gesinger Health, Danville, PA 17822, USA
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Ronak Y Patel
18Baylor College of Medicine, Houston, TX 77030, USA
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Kevin Riehle
18Baylor College of Medicine, Houston, TX 77030, USA
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Peter N Robinson
19Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
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Shawn Rynearson
20Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
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Helen Schuilenburg
12European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Kirill Tsukanov
12European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Brian Walsh
7Oregon Health & Science University, Portland, OR 97239, USA
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Melissa Konopko
21The Global Alliance for Genomics and Health, Torongto, Ontario, Canada
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Heidi Rehm
3Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
22Center for Genomic Medicine, Massachusetts General Hospital, Cambridge, MA 02142, USA
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Andrew D Yates
12European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Robert R Freimuth
23Center for Individualized Medicine, Division of Digital Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
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Reece K Hart
3Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
24MyOme, Inc., San Carlos, CA 94070, USA
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  • ORCID record for Reece K Hart
  • For correspondence: Alex.Wagner@nationwidechildrens.org lbabb@broadinstitute.org reecehart@gmail.com
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Abstract

Maximizing the personal, public, research, and clinical value of genomic information will require that clinicians, researchers, and testing laboratories exchange genetic variation data reliably. Developed by a partnership among national information resource providers, public initiatives, and diagnostic testing laboratories under the auspices of the Global Alliance for Genomics and Health (GA4GH), the Variation Representation Specification (VRS, pronounced “verse”) is an extensible framework for the semantically precise and computable representation of variation that complements contemporary human-readable and flat file standards for variation representation. VRS objects are designed to be semantically precise representations of variation, and leverage this design to enable unique, federated identification of molecular variation. We describe the components of this framework, including the terminology and information model, schema, data sharing conventions, and a reference implementation, each of which is intended to be broadly useful and freely available for community use. The specification, documentation, examples, and community links are available at https://vrs.ga4gh.org/.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://vrs.ga4gh.org

  • https://github.com/ga4gh/vrs

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted January 17, 2021.
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The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation
Alex H Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L Cameron, Melissa Cline, Malachi Griffith, Obi L Griffith, Sarah Hunt, David Kreda, Jennifer Lee, Javier Lopez, Eric Moyer, Tristan Nelson, Ronak Y Patel, Kevin Riehle, Peter N Robinson, Shawn Rynearson, Helen Schuilenburg, Kirill Tsukanov, Brian Walsh, Melissa Konopko, Heidi Rehm, Andrew D Yates, Robert R Freimuth, Reece K Hart
bioRxiv 2021.01.15.426843; doi: https://doi.org/10.1101/2021.01.15.426843
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The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation
Alex H Wagner, Lawrence Babb, Gil Alterovitz, Michael Baudis, Matthew Brush, Daniel L Cameron, Melissa Cline, Malachi Griffith, Obi L Griffith, Sarah Hunt, David Kreda, Jennifer Lee, Javier Lopez, Eric Moyer, Tristan Nelson, Ronak Y Patel, Kevin Riehle, Peter N Robinson, Shawn Rynearson, Helen Schuilenburg, Kirill Tsukanov, Brian Walsh, Melissa Konopko, Heidi Rehm, Andrew D Yates, Robert R Freimuth, Reece K Hart
bioRxiv 2021.01.15.426843; doi: https://doi.org/10.1101/2021.01.15.426843

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