VarStack

VarStack retrieves and compiles somatic variant data from multiple cancer genomics databases to support interpretation of somatic mutations in cancer research.

Key Features:

• Data Integration: Aggregates information from COSMIC, gnomAD, cBioPortal, ClinVar, OncoKB, and the UCSC Genome Browser.
• Query Parameters: Accepts queries specified by gene symbol, peptide change, and coding sequence change.
• Tumor-Specific Studies: Allows selection of tumor-specific studies available in cBioPortal to restrict searches.
• Batch Search Capability: Supports batch submission of variant lists and returns consolidated data for multiple queries.
• CSV Export: Exports query and batch results as CSV files for downstream analysis.
• Automated Data Compilation: Retrieves and compiles data from the integrated databases based on submitted queries.

Scientific Applications:

• Clinical interpretation: Aids interpretation of the clinical significance of somatic mutations for oncologists, geneticists, and bioinformaticians.
• Personalized medicine: Provides aggregated variant annotations to support personalized medicine approaches.
• Cancer genomics research: Facilitates analysis of tumor genome sequencing data and cross-study variant comparisons.

Methodology:

Retrieves and compiles data from COSMIC, gnomAD, cBioPortal, ClinVar, OncoKB, and the UCSC Genome Browser based on queries specified by gene symbol, peptide change, or coding sequence change; supports selection of tumor-specific cBioPortal studies, batch submission of variant lists, and exporting consolidated results as CSV.