title: OncoCis: annotation of cis-regulatory mutations in  cancer.
abstract: 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/.
authors.affiliation: Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW, Australia, Sydney 2052, Australia.
authors.forename: Dilmi
authors.initials: D
authors.lastname: Perera
authors.forename: Diego
authors.initials: D
authors.lastname: Chacon
authors.forename: Julie A I
authors.initials: JA
authors.lastname: Thoms
authors.forename: Rebecca C
authors.initials: RC
authors.lastname: Poulos
authors.forename: Adam
authors.initials: A
authors.lastname: Shlien
authors.forename: Dominik
authors.initials: D
authors.lastname: Beck
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Campbell
authors.forename: John E
authors.initials: JE
authors.lastname: Pimanda
authors.forename: Jason W H
authors.initials: JW
authors.lastname: Wong
mesh_terms: D019295:Computational Biology; D004252:DNA Mutational Analysis; D030541:Databases, Genetic; D057890:Epigenomics; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D058977:Molecular Sequence Annotation; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012984:Software; D019098:Telomerase / Q000737:chemistry / Q000235:genetics
chemical_list: C509186:TERT protein, human; D019098:Telomerase