Our 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").

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients / André, Kahles; Kjong-Van, Lehmann; Nora C, Toussaint; Matthias, Hüser; Stefan G, Stark; Timo, Sachsenberg; Oliver, Stegle; Oliver, Kohlbacher; Chris, Sander; Genome Atlas Research Network, Cancer; Cardinale, Vincenzo; Bragazzi, MARIA CONSIGLIA; Gaudio, Eugenio; Alvaro, Domenico; Gunnar, Rätsch. - In: CANCER CELL. - ISSN 1535-6108. - 34:2(2018), pp. 211-224.e6-224.e6. [10.1016/j.ccell.2018.07.001]

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

Vincenzo, Cardinale;Maria Consiglia, Bragazzi;Eugenio, Gaudio;Domenico, Alvaro;
2018

Abstract

Our 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").
2018
CPTAC; GTEx; MS proteomics; RNA-seq; TCGA; TCGA Pan-Cancer Atlas; alternative splicing; cancer; exome; immunoediting; immunotherapy; neoantigens; splicing QTL; tumor-specific splicing
01 Pubblicazione su rivista::01a Articolo in rivista
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients / André, Kahles; Kjong-Van, Lehmann; Nora C, Toussaint; Matthias, Hüser; Stefan G, Stark; Timo, Sachsenberg; Oliver, Stegle; Oliver, Kohlbacher; Chris, Sander; Genome Atlas Research Network, Cancer; Cardinale, Vincenzo; Bragazzi, MARIA CONSIGLIA; Gaudio, Eugenio; Alvaro, Domenico; Gunnar, Rätsch. - In: CANCER CELL. - ISSN 1535-6108. - 34:2(2018), pp. 211-224.e6-224.e6. [10.1016/j.ccell.2018.07.001]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/1135607
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