Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer.

ABSTRACT: Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isofo

SUBMITTER: Cotto KC 

PROVIDER: S-EPMC10033906 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature