OncoCis: annotation of cis-regulatory mutations in cancer

• Published in: Genome biology Vol. 15; no. 10; p. 485
• Main Authors: Perera, Dilmi, Chacon, Diego, Thoms, Julie A I, Poulos, Rebecca C, Shlien, Adam, Beck, Dominik, Campbell, Peter J, Pimanda, John E, Wong, Jason W H
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 01.01.2014; BioMed Central
• Subjects: Computational Biology; Databases, Genetic; DNA Mutational Analysis; Epigenomics; Gene Expression Regulation, Neoplastic; Humans; Method; Molecular Sequence Annotation; Mutation; Neoplasms - genetics; Promoter Regions, Genetic; Software; Telomerase - chemistry; Telomerase - genetics
• ISSN: 1474-760X; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/s13059-014-0485-0

Whole genome sequencing has enabled the identification of thousands of somatic mutations within non-coding genomic regions of individual cancer samples. However, identification of mutations that potentially alter gene regulation remains a major challenge. Here we present OncoCis, a new method that enables identification of potential cis-regulatory mutations using cell type-specific genome and epigenome-wide datasets along with matching gene expression data. We demonstrate that the use of cell type-specific information and gene expression can significantly reduce the number of candidate cis-regulatory mutations compared with existing tools designed for the annotation of cis-regulatory SNPs. The OncoCis webserver is freely accessible at https://powcs.med.unsw.edu.au/OncoCis/.