Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

ABSTRACT: We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing patterns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- an

SUBMITTER: Lehmann KV 

PROVIDER: S-EPMC4333684 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature