Skip to main content
Journal cover image

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

Publication ,  Journal Article
Kahles, A; Lehmann, K-V; Toussaint, NC; Hüser, M; Stark, SG; Sachsenberg, T; Stegle, O; Kohlbacher, O; Sander, C; Rätsch, G ...
Published in: Cancer Cell
August 13, 2018

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").

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Cancer Cell

DOI

EISSN

1878-3686

Publication Date

August 13, 2018

Volume

34

Issue

2

Start / End Page

211 / 224.e6

Location

United States

Related Subject Headings

  • Sequence Analysis, RNA
  • Quantitative Trait Loci
  • Polymorphism, Single Nucleotide
  • Oncology & Carcinogenesis
  • Neoplasms
  • Humans
  • Exome Sequencing
  • Alternative Splicing
  • 3211 Oncology and carcinogenesis
  • 3101 Biochemistry and cell biology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Kahles, A., Lehmann, K.-V., Toussaint, N. C., Hüser, M., Stark, S. G., Sachsenberg, T., … Rätsch, G. (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
Kahles, André, Kjong-Van Lehmann, Nora C. Toussaint, Matthias Hüser, Stefan G. Stark, Timo Sachsenberg, Oliver Stegle, et al. “Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.Cancer Cell 34, no. 2 (August 13, 2018): 211-224.e6. https://doi.org/10.1016/j.ccell.2018.07.001.
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.
Kahles, André, et al. “Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.Cancer Cell, vol. 34, no. 2, Aug. 2018, pp. 211-224.e6. Pubmed, doi:10.1016/j.ccell.2018.07.001.
Kahles A, Lehmann K-V, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Cancer Genome Atlas Research Network, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell. 2018 Aug 13;34(2):211-224.e6.
Journal cover image

Published In

Cancer Cell

DOI

EISSN

1878-3686

Publication Date

August 13, 2018

Volume

34

Issue

2

Start / End Page

211 / 224.e6

Location

United States

Related Subject Headings

  • Sequence Analysis, RNA
  • Quantitative Trait Loci
  • Polymorphism, Single Nucleotide
  • Oncology & Carcinogenesis
  • Neoplasms
  • Humans
  • Exome Sequencing
  • Alternative Splicing
  • 3211 Oncology and carcinogenesis
  • 3101 Biochemistry and cell biology