Capture Hi-C identifies putative target genes at 33 breast cancer risk loci

Joseph S Baxter, Olivia C Leavy, Nicola H Dryden, Sarah Maguire, Nichola Johnson, Vita Fedele, Nikiana Simigdala, Lesley-Ann Martin, Simon Andrews, Steven W Wingett, Ioannis Assiotis, Kerry Fenwick, Ritika Chauhan, Alistair G Rust, Nick Orr, Frank Dudbridge, Syed Haider, Olivia Fletcher

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Abstract

Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes. 22 putative target genes are eQTLs, 32 are associated with DSS and 14 are somatically mutated in breast, or other, cancers. Identifying the target genes at GWAS risk loci will lead to a greater understanding of the mechanisms that influence breast cancer risk and prognosis.

Original languageEnglish
Article number1028
Number of pages13
JournalNature Communications
Volume9
DOIs
Publication statusPublished - 12 Mar 2018
Externally publishedYes

Keywords

  • Journal Article

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