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Fine scale mapping of the breast cancer 16q12 locus.


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.

SUBMITTER: Udler MS 

PROVIDER: S-EPMC2876886 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature

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Fine scale mapping of the breast cancer 16q12 locus.

Udler Miriam S MS   Ahmed Shahana S   Healey Catherine S CS   Meyer Kerstin K   Struewing Jeffrey J   Maranian Melanie M   Kwon Erika M EM   Zhang Jinghui J   Tyrer Jonathan J   Karlins Eric E   Platte Radka R   Kalmyrzaev Bolot B   Dicks Ed E   Field Helen H   Maia Ana-Teresa AT   Prathalingam Radhika R   Teschendorff Andrew A   McArthur Stewart S   Doody David R DR   Luben Robert R   Caldas Carlos C   Bernstein Leslie L   Kolonel Laurence K LK   Henderson Brian E BE   Wu Anna H AH   Le Marchand Loic L   Ursin Giske G   Press Michael F MF   Lindblom Annika A   Margolin Sara S   Shen Chen-Yang CY   Yang Show-Lin SL   Hsiung Chia-Ni CN   Kang Daehee D   Yoo Keun-Young KY   Noh Dong-Young DY   Ahn Sei-Hyun SH   Malone Kathleen E KE   Haiman Christopher A CA   Pharoah Paul D PD   Ponder Bruce A J BA   Ostrander Elaine A EA   Easton Douglas F DF   Dunning Alison M AM  

Human molecular genetics 20100323 12


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, includin  ...[more]

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