FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation

Abstract

Genome-wide association studies have identified FGFR2 as a breast cancer (BC) susceptibility gene in populations of European and Asian descent, but a causative variant has not yet been conclusively identified. We hypothesized that the weaker linkage disequilibrium across this associated region in populations of African ancestry might help refine the set of candidate-causal single nucleotide polymorphisms (SNPs) previously identified by our group. Eight candidate-causal SNPs were evaluated in 1253 African American invasive BC cases and 1245 controls. A significant association with BC risk was found with SNP rs2981578 (unadjusted per-allele odds ratio = 1.20, 95% confidence interval 1.03-1.41, P(trend) = 0.02), with the odds ratio estimate similar to that reported in European and Asian subjects. To extend the fine-mapping, genotype data from the African American studies were analyzed jointly with data from European (n = 7196 cases, 7275 controls) and Asian (n = 3901 cases, 3205 controls) studies. In the combined analysis, SNP rs2981578 was the most strongly associated. Five other SNPs were too strongly correlated to be excluded at a likelihood ratio of < 1/100 relative to rs2981578. Analysis of DNase I hypersensitive sites indicated that only two of these map to highly accessible chromatin, one of which, SNP rs2981578, has previously been implicated in up-regulating FGFR2 expression. Our results demonstrate that the association of SNPs in FGFR2 with BC risk extends to women of African American ethnicity, and illustrate the utility of combining association analysis in datasets of diverse ethnic groups with functional experiments to identify disease susceptibility variants.

Figure 1.

Diagram of FGFR2 and linkage disequilibrium blocks containing candidate SNPs. (A) The upper diagram is a map of the whole FGFR2 gene viewed relative to common (MAF >5%) SNPs in HapMap CEU. The lower diagram is a map of the 25 kb region of linkage derived from the resequence data. The most strongly associated tagSNP is rs2981582. The positions of remaining candidate SNPs are labeled with filled circles on the map with relative chromosomal positions indicated on the bar. The two variants that could not be genotyped are labeled with open circles. (B) 25 kb LD blocks in HapMap CEU, JPT+CHB and YRI populations. (C) LD block of the seven candidate-SNPs in study populations SEARCH, Seoul Breast Cancer Project and MEC-African Americans (MEC-AA).

Figure 2.

DNase I hypersensitivity profiles of the genomic region of FGFR2 covering exons 1–3. Profiles for the two breast (PMC42 and MCF-7) and one prostate (RWPE-1) cell line were generated using two different concentrations of DNase I. The ACME (45) algorithm was used to generate the plots with a 95% cut-off and a sliding window of 500 bp. Grey diamonds indicate SNPs that were excluded on the basis of the likelihood ratio test. Two SNPs that could not be genotyped are indicated by the thick dotted line. Mammalian conservation of 17 species was taken from the UCSC genome browser (28).