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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.

Original publication

DOI

10.1093/hmg/ddv035

Type

Journal article

Journal

Human molecular genetics

Publication Date

05/2015

Volume

24

Pages

2966 - 2984

Addresses

The Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research and nicholas.orr@icr.ac.uk.

Keywords

GENICA Network, kConFab Investigators, Australian Ovarian Cancer Study Group, Chromosomes, Human, Pair 9, Humans, Breast Neoplasms, Genetic Predisposition to Disease, Estrogen Receptor alpha, Risk, Chromosome Mapping, Polymorphism, Single Nucleotide, Adult, Aged, Middle Aged, Asian Continental Ancestry Group, European Continental Ancestry Group, Female, GATA3 Transcription Factor, Hepatocyte Nuclear Factor 3-alpha, Kruppel-Like Transcription Factors, Enhancer Elements, Genetic, Genetic Loci, Genetic Association Studies