VarStack2-an interactive web tool for somatic variant interpretation in cancer.

Abstract

The rapid progress in tumour genome sequencing has created a need for bioinformatics tools to interpret the clinical significance of detected variants. VarStack² integrates information from several publicly available resources, including the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, cBioPortal, UCSC Genome Browser, and ClinicalTrials.gov, CIViC and presents it through a user-friendly interface. VarStack2 simplifies the process of retrieving data, saving users significant time compared to manually navigating each database individually. Users can input a variant by specifying a gene symbol, amino acid change, and coding sequence change, with the option to search tumour-specific studies in cBioPortal alongside their primary query. Results are organized into separate sections and can be exported in CSV format for further analysis. Additionally, VarStack2 offers a smart search feature that suggests variants for the gene of interest based on its database search results. These features make VarStack2 a useful tool for scientists and clinicians by enhancing the variant interpretation process and integrating somatic variant information into workflows. VarStack² is freely available at http://varstack.brown.edu/.