Fine mapping of 14q24.1 breast cancer susceptibility locus

Phoebe Lee, Yi Ping Fu, Jonine D. Figueroa, Ludmila Prokunina-Olsson, Jesus Gonzalez-Bosquet, Peter Kraft, Zhaoming Wang, Kevin B. Jacobs, Meredith Yeager, Marie Josèphe Horner, Susan E. Hankinson, Amy Hutchinson, Nilanjan Chatterjee, Montserrat Garcia-Closas, Regina G. Ziegler, Christine D. Berg, Saundra S. Buys, Catherine A. McCarty, Heather Spencer Feigelson, Michael J. ThunRyan Diver, Ross Prentice, Rebecca Jackson, Charles Kooperberg, Rowan Chlebowski, Jolanta Lissowska, Beata Peplonska, Louise A. Brinton, Margaret Tucker, Joseph F. Fraumeni, Robert N. Hoover, Gilles Thomas, David J. Hunter, Stephen J. Chanock

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


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. Singlemarker 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.

Original languageEnglish (US)
Pages (from-to)479-490
Number of pages12
JournalHuman Genetics
Issue number3
StatePublished - Mar 2012

Bibliographical note

Funding Information:
The WHI program is supported by contracts from the National Heart, Lung and Blood Institute, NIH. The authors thank the WHI investigators and staff for their dedication, and the study participants for making the program possible. A full listing of WHI investigators can be found at

Funding Information:
The PLCO study is supported by the Intramural Research Program of the Division of Cancer Epidemiology and Genetics and contracts from the Division of Cancer Prevention, National Cancer Institute, NIH, DHHS. The authors thank Dr Philip Prorok, Division of Cancer Prevention, National Cancer Institute; the Screening Center investigators and staff of the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Most importantly, we acknowledge the study participants for their contributions to making this study possible.

Funding Information:
Acknowledgments The Nurses’ Health Studies are supported by NIH grants CA 65725, CA87969, CA49449, CA67262, CA50385 and 5UO1CA098233. The authors thank Barbara Egan, Lori Egan, Helena Judge Ellis, Hardeep Ranu, and Pati Soule for assistance, and the participants in the Nurses’ Health Studies.


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