From association to cause: fine mapping of the TNRC9gene region, a novel susceptibility locus identified in the first genome-wide association study for breast cancer

Abstract

We identified five novel breast cancer susceptibility loci in a recent Genome Wide Association Study [1] using 227,876 single nucleotide polymorphisms (SNPs) and up to 50,000 female breast cancer cases and controls from 22 studies. One of these loci, tagged by SNP rs3803662, lies in a large linkage disequilibrium (LD) block on chromosome 16q12. This region encompasses the largely uncharacterised TNRC9 gene (also known as TOX3/CAGF9) as well as a hypothetical gene LOC643714. This association is robust and has recently been independently verified [2]. The aim of the present study is to map the associated locus and ultimately identify the causal variant(s) responsible for the increased risk of breast cancer. There are 101 common variants in the 165 kb LD block covering the entire footprints of both genes catalogued by the International HapMap Project. These are efficiently tagged by 19 tagging SNPs (tagSNPs) that were genotyped in 2,270 breast cancer cases and 2,280 controls from the East Anglian region of the UK. Using these, we were able to exclude the coding region of TNRC9 and reduce the associated region to a 133 kb LD block including both the 5' end of the TNRC9 gene and the 3' end of LOC643714. This block was re-sequenced in 45 European subjects. Three hundred and forty-four SNPS were found, of which 170 were not previously recorded and 175 were common (minor allele frequency >0.05). Twenty-two of these SNPs are strongly correlated (r2 > 0.9) with the best tagSNP and have been genotyped, where possible, in an East Anglian case–control study set of increased size. Thus there are 23 potential causative variants, which are distributed across both genes. In an attempt to reduce this set of candidate causative SNPs and to further narrow the region of interest, they are being genotyped in breast cancer case–control sets from Asian and African-American populations. These populations exhibit greater haplotype diversity than the more closely related East Anglians, thus providing greater power to separate the causative variant(s) from the other candidates. To complement this work, a further study to determine the functional properties of the gene region in human breast cells has been initiated.