Year: 2013
Type: article
Study design: Observational Study
Abstract: Genome-wide association studies (GWAS) simultaneously investigating hundreds of thousands of single nucleotide polymorphisms (SNP) have become a powerful tool in the investigation of new disease susceptibility loci. Haplotypes are sometimes thought to be superior to SNPs and are promising in genetic association analyses. The application of genome-wide haplotype analysis, however, is hindered by the complexity of haplotypes themselves and sophistication in computation. We systematically analyzed the haplotype effects for breast cancer risk among 5,761 African American women (3,016 cases and 2,745 controls) using a sliding window approach on the genome-wide scale. Three regions on chromosomes 1, 4 and 18 exhibited moderate haplotype effects. Furthermore, among 21 breast cancer susceptibility loci previously established in European populations, 10p15 and 14q24 are likely to harbor novel haplotype effects. We also proposed a heuristic of determining the significance level and the effective number of independent tests by the permutation analysis on chromosome 22 data. It suggests that the effective number was approximately half of the total (7,794 out of 15,645), thus the half number could serve as a quick reference to evaluating genome-wide significance if a similar sliding window approach of haplotype analysis is adopted in similar populations using similar genotype density.
Source: PLoS ONE
Authors: Chi Song, Gary K. Chen, Robert C. Millikan, Christine B. Ambrosone, Esther M. John, Leslie Bernstein, Wei Zheng, Jennifer J. Hu, Regina G. Ziegler, Sarah Nyante, Elisa V. Bandera, Sue A. Ingles, Michael F. Press, Sandra L. Deming, Jorge L. Rodriguez-Gil, Stephen J. Chanock, Peggy Wan, Xin Sheng, Loreall C. Pooler, David J. Van Den Berg, Loic Le Marchand, Laurence N. Kolonel, Brian E. Henderson, Chris A. Haiman, Daniel O. Stram
Institutions: University of Southern California, USC Norris Comprehensive Cancer Center, University of North Carolina at Chapel Hill, UNC Lineberger Comprehensive Cancer Center, Roswell Park Comprehensive Cancer Center, Cancer Prevention Institute of California, Stanford Cancer Institute, Stanford University, City Of Hope National Medical Center, City of Hope, Beckman Research Institute, Vanderbilt University, Vanderbilt-Ingram Cancer Center, University of Miami, Sylvester Comprehensive Cancer Center, National Cancer Institute, Division of Cancer Epidemiology and Genetics, Rutgers Cancer Institute, University of Hawaii Cancer Center
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,382
Funders: U.S. Department of Defense, U.S. Department of Health and Human Services, Breast Cancer Research Foundation, Kenneth T. and Eileen L. Norris Foundation, California Breast Cancer Research Program, University of Southern California, University of Pittsburgh, Ministerio de Economía y Competitividad, National Institutes of Health, U.S. Army, National Heart, Lung, and Blood Institute, National Cancer Institute, National Institute of Environmental Health Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Medical Research and Materiel Command
Awards: G1017297203, G109231058, G1107292973, Women's Health Initiative, G1138412625, Women's Health Initiative, G1152199635, G121068745, G1253072103, Women's Health Initiative, Women's Health Initiative, G153510172, G156924709, G1569999668, Women's Health Initiative, G1593340546, G1617453120, G1623571357, G164076637, G1646017446, G1702743405, G1722492350, Women's Health Initiative, G1767941747, SPORE in Breast Cancer, G1798569254, G181468914, G206718646, G2108445782, G211028185, Women's Health Initiative, G2182082016, G2253702613, G2295046671, G2313542652, VITAMIN D RECEPTOR GENE POLYMORPHISM AND BREAST CANCER, G2407663899, G2417273319, G2547046739, G2548880556, G257474614, G2646530656, G2852769941, G2880260212, G299563851, G3053443584, G306350359, G3157549237, G3290335435, Women's Health Initiative, G3337978133, Women's Health Initiative Memory Study (WHIMS), G3404453056, G3544793024, Women's Health Initiative, G3642616392, G3696348274, G3907652395, G4002295999, Women's Health Initiative, G4039713129, Women's Health Initiative, G413560588, G4214622172, G4216744017, G422195599, G4281851297, COORDINATING CENTER FOR WOMEN'S HEALTH INITIATIVE, G429396632, G4321061599, G4407166175, G443607800, G445374210, G4454202622, Women's Health Initiative, G4560602636, G4562239163, G4816767106, G484043965, Women's Health Initiative, G4907478063, G4940723635, G5111245462, G5183277930, FOR ALL FIELD CENTER FOR WHI EXTENSION, G530368906, G532295152, The Nashville Breast Health Study, G5415877130, Women's Health Initiative, G5528430224, G555506801, G5654214539, G5959015892, G603760282, G6272687058, G6289736641, G6424558485, G6464247198, G6522987136, G6554032491, G6670851527, Women's Health Initiative, Women's Health Initiative, G7066869570, G7071300326, G7223985928, G7272550893, Women's Health Initiative, G7323080267, Women's Health Initiative, G7582705761, G7646998162, G7651777114, G77261304, CLINICAL CENTER FOR THE CLINICAL TRIAL & OBSERVATIONAL STUDY OF WHI, BREAST CANCER AND THE BIRTH CONTROL PILL, G8332978792, G8606667874, G870117454, G8780700017, G8820111440, G8934942062, G9000008935, G9000032209, G9000061634, G9000072420, G9000073604, G9000123264, G9000131094, G9000151586, G9000179242, G9000182874, G9000216949, G9000286278, G9000355445, Cancer Center Support Grant, G908924418, G921773184, Women's Health Initiative, G985928507, G999174792
OpenAlex ID: W2010352552