LocalVar

LocalVar manages local collections of genetic variant records and synchronizes them with ClinVar to support accurate variant interpretation in clinical and research settings.

Key Features:

• Variant record ingestion: supports single and bulk entry of variant records for local collections.
• Duplicate detection and merge suggestions: automatically detects duplicate variant records and provides suggested merges to maintain a non-redundant dataset.
• Synonym management (HGVS): identifies HGVS expressions marked as synonyms in ClinVar and offers merge suggestions for synonymous records.
• Asynchronous ClinVar-based updates: suggests updates to HGVS expressions and variant interpretations asynchronously based on changes in ClinVar files.
• History tracking: records additions, merges, updates, and manual edits for auditing of variant record evolution.
• Data export: exports variant collections as CSV and edit histories and HGVS synonym bins as JSON.

Scientific Applications:

• Clinical variant interpretation: maintain synchronized local variant records and interpretations informed by ClinVar to support diagnostic and reporting workflows.
• Research cohort variant management: curate and de-duplicate institutional variant collections for research analyses and cohort studies.
• Precision medicine data maintenance: keep local variant databases current with ClinVar updates and HGVS synonym resolution to support precision medicine and personalized healthcare.

Methodology:

Interfaces with publicly available ClinVar files; identifies HGVS expressions marked as synonyms in ClinVar; performs automatic duplicate detection and generates merge suggestions; uses asynchronous processing to propose updates to HGVS expressions and variant interpretations based on ClinVar changes.