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High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

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Item Type:Article
Title:High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
Creators Name:Zhang, Y. and Chen, F. and Fonseca, N.A. and He, Y. and Fujita, M. and Nakagawa, H. and Zhang, Z. and Brazma, A. and Creighton, C.J.
Abstract:The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.
Source:Nature Communications
ISSN:2041-1723
Publisher:Nature Publishing Group
Volume:11
Number:1
Page Range:736
Date:5 February 2020
Additional Information:Roland F. Schwarz is a member of the PCAWG Transcriptome Working Group.
Official Publication:https://doi.org/10.1038/s41467-019-13885-w
PubMed:View item in PubMed

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