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 () and Olivia Fletcher ()
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Joseph S. Baxter: The Institute of Cancer Research
Olivia C. Leavy: The London School of Hygiene and Tropical Medicine
Nicola H. Dryden: The Institute of Cancer Research
Sarah Maguire: The Institute of Cancer Research
Nichola Johnson: The Institute of Cancer Research
Vita Fedele: The Institute of Cancer Research
Nikiana Simigdala: The Institute of Cancer Research
Lesley-Ann Martin: The Institute of Cancer Research
Simon Andrews: The Babraham Institute
Steven W. Wingett: The Babraham Institute
Ioannis Assiotis: The Institute of Cancer Research
Kerry Fenwick: The Institute of Cancer Research
Ritika Chauhan: The Institute of Cancer Research
Alistair G. Rust: The Institute of Cancer Research
Nick Orr: The Institute of Cancer Research
Frank Dudbridge: The London School of Hygiene and Tropical Medicine
Syed Haider: The Institute of Cancer Research
Olivia Fletcher: The Institute of Cancer Research

Nature Communications, 2018, vol. 9, issue 1, 1-13

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-03411-9

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