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Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
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....
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844097/ https://www.ncbi.nlm.nih.gov/pubmed/30078747 http://dx.doi.org/10.1016/j.ccell.2018.07.001 |
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author | Kahles, André Lehmann, Kjong-Van Toussaint, Nora C. Hüser, Matthias Stark, Stefan G. Sachsenberg, Timo Stegle, Oliver Kohlbacher, Oliver Sander, Chris Rätsch, Gunnar |
author_facet | Kahles, André Lehmann, Kjong-Van Toussaint, Nora C. Hüser, Matthias Stark, Stefan G. Sachsenberg, Timo Stegle, Oliver Kohlbacher, Oliver Sander, Chris Rätsch, Gunnar |
author_sort | Kahles, André |
collection | PubMed |
description | 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”). |
format | Online Article Text |
id | pubmed-9844097 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
record_format | MEDLINE/PubMed |
spelling | pubmed-98440972023-01-17 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 Cell Article 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”). 2018-08-13 2018-08-02 /pmc/articles/PMC9844097/ /pubmed/30078747 http://dx.doi.org/10.1016/j.ccell.2018.07.001 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) ). |
spellingShingle | Article Kahles, André Lehmann, Kjong-Van Toussaint, Nora C. Hüser, Matthias Stark, Stefan G. Sachsenberg, Timo Stegle, Oliver Kohlbacher, Oliver Sander, Chris Rätsch, Gunnar Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title | Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title_full | Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title_fullStr | Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title_full_unstemmed | Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title_short | Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients |
title_sort | comprehensive analysis of alternative splicing across tumors from 8,705 patients |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9844097/ https://www.ncbi.nlm.nih.gov/pubmed/30078747 http://dx.doi.org/10.1016/j.ccell.2018.07.001 |
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