VarStack: a web tool for data retrieval to interpret somatic variants in cancer. (28th November 2020)

• Record Type: Journal Article
• Authors: Howard, Morgan; Kane, Bruce; Lepry, Mary; Stey, Paul; Ragavendran, Ashok; Gamsiz Uzun, Ece D
• Is Part Of: Database. Volume 2020(2020)
• Publication Date: 2020-11-28
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/baaa092
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: Advances in tumor genome sequencing created an urgent need for bioinformatics tools to support the interpretation of the clinical significance of the variants detected. VarStack is a web tool which is a base to retrieve somatic variant data relating to cancer from existing databases. VarStack incorporates data from several publicly available databases and presents them with an easy-to-navigate user interface. It currently supports data from the Catalogue of Somatic Mutations in Cancer, gnomAD, cBioPortal, ClinVar, OncoKB, CiViC and UCSC Genome Browser. It retrieves the data from these databases and returns them back to the user in a fraction of the time it would take to manually navigate each site independently. Users submit a variant with a gene symbol, peptide change and coding sequence change. They may select a variety of tumor-specific studies in cBioPortal to search through in addition to their original query. The results from the databases are presented in tabs. Users can export the results as an Excel file. VarStack also has the batch search feature in which the user can submit a list of variants and download an Excel file with the data from the databases. With the batch search and data download options, users can easily incorporate VarStack into their workflow or tools. VarStack saves time by providing somatic variant information to the user from multiple databases in an easy-to-export and interpretable format. VarStack is freely available under https://varstack.brown.edu .