Kahles, AndréAndréKahlesLehmann, Kjong-VanKjong-VanLehmannToussaint, Nora CNora CToussaintHüser, MatthiasMatthiasHüserStark, Stefan GStefan GStarkSachsenberg, TimoTimoSachsenbergStegle, OliverOliverStegleKohlbacher, OliverOliverKohlbacherSander, ChrisChrisSanderRätsch, GunnarGunnarRätsch2024-10-082024-10-082018-08-13https://boris-portal.unibe.ch/handle/20.500.12422/64147Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects alternative splicing events and tumor variants by reanalyzing RNA and whole-exome sequencing data. Tumors have up to 30% more alternative splicing events than normal samples. Association analysis of somatic variants with alternative splicing events confirmed known trans associations with variants in SF3B1 and U2AF1 and identified additional trans-acting variants (e.g., TADA1, PPP2R1A). Many tumors have thousands of alternative splicing events not detectable in normal samples; on average, we identified ≈930 exon-exon junctions ("neojunctions") in tumors not typically found in GTEx normals. From Clinical Proteomic Tumor Analysis Consortium data available for breast and ovarian tumor samples, we confirmed ≈1.7 neojunction- and ≈0.6 single nucleotide variant-derived peptides per tumor sample that are also predicted major histocompatibility complex-I binders ("putative neoantigens").enCPTAC GTEx MS proteomics RNA-seq TCGA TCGA Pan-Cancer Atlas alternative splicing cancer exome immunoediting immunotherapy neoantigens splicing QTL tumor-specific splicing600 - Technology::610 - Medicine & healtharticle10.7892/boris.1263633007874710.1016/j.ccell.2018.07.001