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

Joseph S Baxter ORCID logo; Olivia CLeavy; Nicola HDryden; SarahMaguire; NicholaJohnson; Vita Fedele ORCID logo; NikianaSimigdala; Lesley-AnnMartin; SimonAndrews; Steven WWingett; +8 more... IoannisAssiotis; KerryFenwick; RitikaChauhan; Alistair GRust; NickOrr; Frank Dudbridge ORCID logo; SyedHaider; Olivia Fletcher ORCID logo; (2018) Capture Hi-C identifies putative target genes at 33 breast cancer risk loci. Nature communications, 9 (1). 1028-. ISSN 2041-1723 DOI: 10.1038/s41467-018-03411-9
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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.



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