Cookies on this website
We use cookies to ensure that we give you the best experience on our website. If you click 'Continue' we'll assume that you are happy to receive all cookies and you won't see this message again. Click 'Find out more' for information on how to change your cookie settings.

The 10q26 locus in the second intron of FGFR2 is the locus most strongly associated with estrogen-receptor-positive breast cancer in genome-wide association studies. We conducted fine-scale mapping in case-control studies genotyped with a custom chip (iCOGS), comprising 41 studies (n = 89,050) of European ancestry, 9 Asian ancestry studies (n = 13,983), and 2 African ancestry studies (n = 2,028) from the Breast Cancer Association Consortium. We identified three statistically independent risk signals within the locus. Within risk signals 1 and 3, genetic analysis identified five and two variants, respectively, highly correlated with the most strongly associated SNPs. By using a combination of genetic fine mapping, data on DNase hypersensitivity, and electrophoretic mobility shift assays to study protein-DNA binding, we identified rs35054928, rs2981578, and rs45631563 as putative functional SNPs. Chromatin immunoprecipitation showed that FOXA1 preferentially bound to the risk-associated allele (C) of rs2981578 and was able to recruit ERα to this site in an allele-specific manner, whereas E2F1 preferentially bound the risk variant of rs35054928. The risk alleles were preferentially found in open chromatin and bound by Ser5 phosphorylated RNA polymerase II, suggesting that the risk alleles are associated with changes in transcription. Chromatin conformation capture demonstrated that the risk region was able to interact with the promoter of FGFR2, the likely target gene of this risk region. A role for FOXA1 in mediating breast cancer susceptibility at this locus is consistent with the finding that the FGFR2 risk locus primarily predisposes to estrogen-receptor-positive disease.

Original publication

DOI

10.1016/j.ajhg.2013.10.026

Type

Journal article

Journal

Am J Hum Genet

Publication Date

05/12/2013

Volume

93

Pages

1046 - 1060

Keywords

African Continental Ancestry Group, Alleles, Asian Continental Ancestry Group, Binding Sites, Breast Neoplasms, Case-Control Studies, Cell Line, Tumor, Chromatin Immunoprecipitation, Chromosome Mapping, E2F1 Transcription Factor, European Continental Ancestry Group, Female, Gene Expression Regulation, Neoplastic, Genetic Association Studies, Genetic Loci, Haplotypes, Hepatocyte Nuclear Factor 3-alpha, Humans, Position-Specific Scoring Matrices, Promoter Regions, Genetic, Protein Binding, RNA Interference, Receptor, Fibroblast Growth Factor, Type 2