Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

Hum Mol Genet. 2015 May 15;24(10):2966-84. doi: 10.1093/hmg/ddv035. Epub 2015 Feb 4.

Abstract

We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88-0.92]; P-value = 1.58 × 10(-25)). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08-1.17]; P-value = 7.89 × 10(-09)) and rs13294895 (OR = 1.09 [1.06-1.12]; P-value = 2.97 × 10(-11)). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06-1.18]; P-value = 2.77 × 10(-05)). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. In vitro analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the KLF4 gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.

Publication types

  • Multicenter Study
  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adult
  • Aged
  • Asian Continental Ancestry Group / genetics
  • Breast Neoplasms / genetics*
  • Chromosome Mapping
  • Chromosomes, Human, Pair 9*
  • Enhancer Elements, Genetic
  • Estrogen Receptor alpha / genetics
  • European Continental Ancestry Group / genetics
  • Female
  • GATA3 Transcription Factor / genetics
  • Genetic Association Studies
  • Genetic Loci*
  • Genetic Predisposition to Disease*
  • Hepatocyte Nuclear Factor 3-alpha / genetics
  • Humans
  • Kruppel-Like Transcription Factors / genetics
  • Middle Aged
  • Polymorphism, Single Nucleotide*
  • Risk

Substances

  • Estrogen Receptor alpha
  • FOXA1 protein, human
  • GATA3 Transcription Factor
  • GATA3 protein, human
  • GKLF protein
  • Hepatocyte Nuclear Factor 3-alpha
  • Kruppel-Like Transcription Factors
  • estrogen receptor alpha, human

Grant support