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.
Highlights
Advances in sequencing technologies and bioinformatics have improved precision medicineapproaches by identifying tumor-specific variants
Catalogue of Somatic Mutations in Cancer (COSMIC) (1, 2), gnomAD (3), cBioPortal (4, 5), ClinVar (6), OncoKB (7), CiViC (8) and UCSC Genome Browser (9) are among the existing databases used by physicians and scientists for variant interpretation
We developed VarStack 1.0 in order to provide somatic variant information from the multiple databases on a fast and easy-to-interpret platform with UCSC Genome Browser visualization
Summary
Advances in sequencing technologies and bioinformatics have improved precision medicineapproaches by identifying tumor-specific variants. Catalogue of Somatic Mutations in Cancer (COSMIC) (1, 2), gnomAD (3), cBioPortal (4, 5), ClinVar (6), OncoKB (7), CiViC (8) and UCSC Genome Browser (9) are among the existing databases used by physicians and scientists for variant interpretation. VarStack is a web tool which retrieves up-to-date variant information from COSMIC, gnomAD, cBioPortal, ClinVar, OncoKB as well as UCSC Genome Browser and displays the output in separate tabs. It takes the gene name, amino acid and nucleotide change of a variant as an input. The user enters the list of variants in a search box, and the web tool returns an Excel file with the data in separate tabs for ClinVar, COSMIC, gnomAD and OncoKB. R package cgdsr was used to retrieve data from cBioPortal studies (4) (Figure 1). cgdsr is an application programming interface (API) that accesses the Cancer Genomics Data Server
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