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Hum Mol Genet. 2010 Jun 15;19(12):2507-15. doi: 10.1093/hmg/ddq122. Epub 2010 Mar 23.

Fine scale mapping of the breast cancer 16q12 locus.

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1
Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

Abstract

Recent genome-wide association studies have identified a breast cancer susceptibility locus on 16q12 with an unknown biological basis. We used a set of single nucleotide polymorphism (SNP) markers to generate a fine-scale map and narrowed the region of association to a 133 kb DNA segment containing the largely uncharacterized hypothetical gene LOC643714, a short intergenic region and the 5' end of TOX3. Re-sequencing this segment in European subjects identified 293 common polymorphisms, including a set of 26 highly correlated candidate causal variants. By evaluation of these SNPs in five breast cancer case-control studies involving more than 23 000 subjects from populations of European and Southeast Asian ancestry, all but 14 variants could be excluded at odds of <1:100. Most of the remaining variants lie in the intergenic region, which exhibits evolutionary conservation and open chromatin conformation, consistent with a regulatory function. African-American case-control studies exhibit a different pattern of association suggestive of an additional causative variant.

PMID:
20332101
PMCID:
PMC2876886
DOI:
10.1093/hmg/ddq122
[Indexed for MEDLINE]
Free PMC Article
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