Fine mapping of 14q24.1 breast cancer susceptibility locus.

Author(s): Lee P,  Fu YP,  Figueroa JD,  Prokunina-Olsson L,  Gonzalez-Bosquet J,  Kraft P,  Wang Z,  Jacobs KB,  Yeager M,  Horner MJ,  Hankinson SE,  Hutchinson A,  Chatterjee N,  Garcia-Closas M,  Ziegler RG,  Berg CD,  Buys SS,  McCarty CA,  Feigelson HS,  Thun MJ,  Diver R,  Prentice R,  Jackson R,  Kooperberg C,  Chlebowski R,  Lissowska J,  Peplonska B,  Brinton LA,  Tucker M,  Fraumeni JF Jr,  Hoover RN,  Thomas G,  Hunter DJ,  Chanock SJ

Journal: Hum Genet

Date: 2012 Mar

Major Program(s) or Research Group(s): EDRG, PLCO

PubMed ID: 21959381

PMC ID: PMC4159746

Abstract: In the National Cancer Institute Cancer Genetic Markers of Susceptibility (CGEMS) genome-wide association study of breast cancer, a single nucleotide polymorphism (SNP) marker, rs999737, in the 14q24.1 interval, was associated with breast cancer risk. In order to fine map this region, we imputed a 3.93 MB region flanking rs999737 for Stages 1 and 2 of the CGEMS study (5,692 cases, 5,576 controls) using the combined reference panels of the HapMap 3 and the 1000 Genomes Project. Single-marker association testing and variable-sized sliding-window haplotype analysis were performed, and for both analyses the initial tagging SNP rs999737 retained the strongest association with breast cancer risk. Investigation of contiguous regions did not reveal evidence for an additional independent signal. Therefore, we conclude that rs999737 is an optimal tag SNP for common variants in the 14q24.1 region and thus narrow the candidate variants that should be investigated in follow-up laboratory evaluation.