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

Author

Listed:
  • Joseph S. Baxter

    (The Institute of Cancer Research)

  • Olivia C. Leavy

    (The London School of Hygiene and Tropical Medicine
    University of Leicester)

  • 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
    University of Leicester)

  • Syed Haider

    (The Institute of Cancer Research)

  • Olivia Fletcher

    (The Institute of Cancer Research)

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.

Suggested Citation

  • 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 & K, 2018. "Capture Hi-C identifies putative target genes at 33 breast cancer risk loci," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03411-9
    DOI: 10.1038/s41467-018-03411-9
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