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

Area of Science:

• Bioinformatics
• Genomics
• Clinical Genetics

Background:

• Public repositories for biological sequence variation data exist, but open-source tools for maintaining local variant collections are scarce.
• Clinics often curate local variant data, facing challenges with changing variant representations and clinical significance interpretations.

Purpose of the Study:

• To develop an open-source tool, LocalVar, to assist in the upkeep of local collections of genetic variant data.
• To address the burden of frequent changes in variant representation and interpretation for clinical curators.

Main Methods:

• Analyzed a dictionary of genetic variants from the Huntsman Cancer Institute over two years.
• Developed LocalVar using publicly available ClinVar files.
• Implemented features such as auto-complete search, duplicate detection, and asynchronous update suggestions.

Main Results:

• LocalVar provides functionality for efficient variant record entry and management.
• The tool automatically detects duplicate and synonymous variant records.
• It offers asynchronous suggestions for Human Genome Variation Society (HGVS) expression and interpretation updates.
• Extensive edit history tracking and flexible data export options are included.

Conclusions:

• LocalVar offers a robust solution for managing local variant data collections in clinical and research settings.
• The tool enhances data integrity and reduces the manual effort required for variant curation.
• It supports efficient workflows for handling evolving genetic variant information.