Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,294 bioRxiv papers from 263,837 authors.
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group,
Natalie R Davidson,
Nuno A Fonseca,
Cameron M Soulette,
Marc D Perry,
Katherine A Hoadley,
Jan O Korbel,
Maximillian G Marin,
Chandra Sekhar Pedamallu,
Stefan G Stark,
Sebastian M Waszak,
PCAWG Transcriptome Working Group,
Chad J Creighton,
B.F. Francis Ouellette,
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network,
Angela N Brooks,
Roland F Schwarz,
Posted 03 Sep 2017
bioRxiv DOI: 10.1101/183889
Posted 03 Sep 2017
We present the most comprehensive catalogue of cancer-associated gene alterations through characterization of tumor transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes project. Using matched whole-genome sequencing data, we attributed RNA alterations to germline and somatic DNA alterations, revealing likely genetic mechanisms. We identified 444 associations of gene expression with somatic non-coding single-nucleotide variants. We found 1,872 splicing alterations associated with somatic mutation in intronic regions, including novel exonization events associated with Alu elements. Somatic copy number alterations were the major driver of total gene and allele-specific expression (ASE) variation. Additionally, 82% of gene fusions had structural variant support, including 75 of a novel class called "bridged" fusions, in which a third genomic location bridged two different genes. Globally, we observe transcriptomic alteration signatures that differ between cancer types and have associations with DNA mutational signatures. Given this unique dataset of RNA alterations, we also identified 1,012 genes significantly altered through both DNA and RNA mechanisms. Our study represents an extensive catalog of RNA alterations and reveals new insights into the heterogeneous molecular mechanisms of cancer gene alterations.
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