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Fine mapping at the 11q13 locus

Alison Dunning and colleagues report fine mapping of the 11q13 breast cancer susceptibility locus (Am. J. Hum. Genet. doi:10.1016/j.ajhg.2013.01.002, 27 March 2013). The original genome-wide association study (GWAS)-identified SNP tags a linkage disequilibrium block that spans 683 kb, and the authors selected 731 SNPs from this region to include on the iCOGS array. They genotyped 89,050 individuals of European ancestry and 12,893 individuals of Asian ancestry, all from studies included in BCAC. They identified 204 SNPs associated with overall breast cancer risk, finding that these were all associated with estrogen receptor (ER)-positive but not ER-negative breast cancer. Using stepwise logistic regression, they identified three independently associated SNPs. They selected five promising candidate SNPs for functional studies but did not detect any significant association of these SNPs with the expression of local genes in normal breast tissue or tumor samples. Using chromatin immunoprecipitation with sequencing (ChIP-seq) data from MCF7 cells, they found that these SNPs fell within two putative regulatory elements. Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and chromosome conformation capture (3C) analyses showed long-range interactions between these regulatory elements and the CCND1 promoter and/or terminator. Further functional studies identified a candidate causal variant in the putative CCND1 enhancer, which affected the binding of the ELK4 transcription factor. A second candidate causal variant, located within a silencer element that physically interacts with the CCND1 enhancer, affected binding of the GATA3 transcription factor.

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Bahcall, O. Fine mapping at the 11q13 locus. Nat Genet 45, 352 (2013). https://doi.org/10.1038/ng.2596

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