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LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar
  • +4
  • Michael Watkins,
  • Wendy Kohlmann,
  • Therese Berry,
  • Neetha Sama,
  • Cathryn Koptiuch,
  • Shawn Rynearson,
  • Karen Eilbeck
Michael Watkins
University of Utah Health
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Wendy Kohlmann
Huntsman Cancer Institute Cancer Hospital
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Therese Berry
Huntsman Cancer Institute Cancer Hospital
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Neetha Sama
Huntsman Cancer Institute Cancer Hospital
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Cathryn Koptiuch
Huntsman Cancer Institute Cancer Hospital
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Shawn Rynearson
University of Utah Health
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Karen Eilbeck
University of Utah Health
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Abstract

While there are several public repositories of biological sequence variation data and associated annotations, there is little open-source tooling designed specifically for the upkeep of local collections of variant data. Many clinics curate and maintain such local collections and are burdened by frequent changes in the representation of those variants and evolving interpretations of clinical significance. A dictionary of genetic variants from the Huntsman Cancer Institute was analyzed over a period of two years and used to inform the development of LocalVar. This tool is institution-agnostic and uses publicly available ClinVar files to provide the following functionality: auto-complete search bar to pre-empt duplicate entries; single or bulk new variant record entry; auto-detection and merge suggestions for duplicate variant records; auto-detection and merge suggestions for variant records with HGVS expressions that are marked as synonyms in ClinVar; asynchronous suggestion of HGVS expression or variant interpretation updates; history tracking of additions, merges, updates, or other manual edits made to variant records; and the easy export of the collection (.csv), edit history (.json), or HGVS synonym bins (.json).

Peer review status:UNDER REVIEW

27 May 2021Submitted to Human Mutation
30 May 2021Assigned to Editor
30 May 2021Submission Checks Completed
02 Jun 2021Reviewer(s) Assigned