LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVar Article Swipe
Michael T. Watkins
,
Wendy Kohlmann
,
Therese Berry
,
Neetha Sama
,
Cathryn Koptiuch
,
Shawn Rynearson
,
Karen Eilbeck
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.22541/au.162261754.44560305/v1
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.22541/au.162261754.44560305/v1
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).
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- Type
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- Language
- en
- Landing Page
- https://doi.org/10.22541/au.162261754.44560305/v1
- https://www.authorea.com/doi/pdf/10.22541/au.162261754.44560305
- OA Status
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- Cited By
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- Related Works
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- OpenAlex ID
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https://doi.org/10.22541/au.162261754.44560305/v1Digital Object Identifier
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LocalVar: a local variant collection manager to asynchronously detect synonyms, HGVS expression changes, and variant interpretation changes from ClinVarWork title
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preprintOpenAlex work type
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enPrimary language
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2021Year of publication
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2021-06-02Full publication date if available
- Authors
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Michael T. Watkins, Wendy Kohlmann, Therese Berry, Neetha Sama, Cathryn Koptiuch, Shawn Rynearson, Karen EilbeckList of authors in order
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https://doi.org/10.22541/au.162261754.44560305/v1Publisher landing page
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https://www.authorea.com/doi/pdf/10.22541/au.162261754.44560305Direct link to full text PDF
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goldOpen access status per OpenAlex
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https://www.authorea.com/doi/pdf/10.22541/au.162261754.44560305Direct OA link when available
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