Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
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Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. / Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan G; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Rätsch, Gunnar; Cancer Genome Atlas Research Network.
in: CANCER CELL, Jahrgang 34, Nr. 2, 13.08.2018, S. 211-224.e6.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
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TY - JOUR
T1 - Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
AU - Kahles, André
AU - Lehmann, Kjong-Van
AU - Toussaint, Nora C
AU - Hüser, Matthias
AU - Stark, Stefan G
AU - Sachsenberg, Timo
AU - Stegle, Oliver
AU - Kohlbacher, Oliver
AU - Sander, Chris
AU - Rätsch, Gunnar
AU - Cancer Genome Atlas Research Network
AU - Sauter, Guido
N1 - Copyright © 2018 Elsevier Inc. All rights reserved.
PY - 2018/8/13
Y1 - 2018/8/13
N2 - 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").
AB - 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").
KW - Journal Article
U2 - 10.1016/j.ccell.2018.07.001
DO - 10.1016/j.ccell.2018.07.001
M3 - SCORING: Journal article
C2 - 30078747
VL - 34
SP - 211-224.e6
JO - CANCER CELL
JF - CANCER CELL
SN - 1535-6108
IS - 2
ER -