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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, Vol. 34, No. 2, 13.08.2018, p. 211-224.e6.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Kahles, A, Lehmann, K-V, Toussaint, NC, Hüser, M, Stark, SG, Sachsenberg, T, Stegle, O, Kohlbacher, O, Sander, C, Rätsch, G & Cancer Genome Atlas Research Network 2018, 'Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients', CANCER CELL, vol. 34, no. 2, pp. 211-224.e6. https://doi.org/10.1016/j.ccell.2018.07.001

APA

Kahles, A., Lehmann, K-V., Toussaint, N. C., Hüser, M., Stark, S. G., Sachsenberg, T., Stegle, O., Kohlbacher, O., Sander, C., Rätsch, G., & Cancer Genome Atlas Research Network (2018). Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. CANCER CELL, 34(2), 211-224.e6. https://doi.org/10.1016/j.ccell.2018.07.001

Vancouver

Kahles A, Lehmann K-V, Toussaint NC, Hüser M, Stark SG, Sachsenberg T et al. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. CANCER CELL. 2018 Aug 13;34(2):211-224.e6. https://doi.org/10.1016/j.ccell.2018.07.001

Bibtex

@article{2624162a489e428a87959d80ec9d7225,
title = "Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients",
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{"}).",
keywords = "Journal Article",
author = "Andr{\'e} Kahles and Kjong-Van Lehmann and Toussaint, {Nora C} and Matthias H{\"u}ser and Stark, {Stefan G} and Timo Sachsenberg and Oliver Stegle and Oliver Kohlbacher and Chris Sander and Gunnar R{\"a}tsch and {Cancer Genome Atlas Research Network} and Guido Sauter",
note = "Copyright {\textcopyright} 2018 Elsevier Inc. All rights reserved.",
year = "2018",
month = aug,
day = "13",
doi = "10.1016/j.ccell.2018.07.001",
language = "English",
volume = "34",
pages = "211--224.e6",
journal = "CANCER CELL",
issn = "1535-6108",
publisher = "Cell Press",
number = "2",

}

RIS

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 -