000256565 001__ 256565
000256565 005__ 20190317001024.0
000256565 0247_ $$2doi$$a10.7717/peerj.5362
000256565 02470 $$a10.7717/peerj.5362$$2DOI
000256565 037__ $$aARTICLE
000256565 245__ $$aDetection and benchmarking of somatic mutations in cancer genomes using RNA-seq data
000256565 260__ $$c2018-07-31
000256565 269__ $$a2018-07-31
000256565 336__ $$aJournal Articles
000256565 520__ $$aTo detect functional somatic mutations in tumor samples, whole-exome sequencing (WES) is often used for its reliability and relative low cost. RNA-seq, while generally used to measure gene expression, can potentially also be used for identification of somatic mutations. However there has been little systematic evaluation of the utility of RNA-seq for identifying somatic mutations. Here, we develop and evaluate a pipeline for processing RNA-seq data from glioblastoma multiforme (GBM) tumors in order to identify somatic mutations. The pipeline entails the use of the STAR aligner 2-pass procedure jointly with MuTect2 from genome analysis toolkit (GATK) to detect somatic variants. Variants identified from RNA-seq data were evaluated by comparison against the COSMIC and dbSNP databases, and also compared to somatic variants identified by exome sequencing. We also estimated the putative functional impact of coding variants in the most frequently mutated genes in GBM. Interestingly, variants identified by RNA-seq alone showed better representation of GBM-related mutations cataloged by COSMIC. RNA-seq-only data substantially outperformed the ability of WES to reveal potentially new somatic mutations in known GBM-related pathways, and allowed us to build a high-quality set of somatic mutations common to exome and RNA-seq calls. Using RNA-seq data in parallel with WES data to detect somatic mutations in cancer genomes can thus broaden the scope of discoveries and lend additional support to somatic variants identified by exome sequencing alone
000256565 700__ $$aCoudray, Alexandre$$0250942
000256565 700__ $$aBattenhouse, Anna M.
000256565 700__ $$aBucher, Philipp
000256565 700__ $$aIyer, Vishwanath R.
000256565 710__ $$aBucher Philipp
000256565 773__ $$tPeerJ$$j6$$qe5362
000256565 8560_ $$fpierre.devaud@epfl.ch
000256565 8564_ $$uhttps://infoscience.epfl.ch/record/256565/files/Coudray-PeerJ-2018.pdf$$zFinal$$s3370623
000256565 909C0 $$mrouayda.cavin@epfl.ch$$mgiovanna.ambrosini@epfl.ch$$mphilipp.bucher@epfl.ch$$0252244$$xU11780$$pGR-BUCHER
000256565 909CO $$qGLOBAL_SET$$pSV$$particle$$ooai:infoscience.epfl.ch:256565
000256565 960__ $$arouayda.cavin@epfl.ch
000256565 961__ $$amanon.velasco@epfl.ch
000256565 973__ $$aEPFL$$sPUBLISHED$$rREVIEWED
000256565 980__ $$aARTICLE
000256565 981__ $$aoverwrite