LocalVar: a local variant collection manager to asynchronously detect
synonyms, HGVS expression changes, and variant interpretation changes
from ClinVar
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).