Chapter 11: Genome-Wide Association Studies

被引:742
作者
Bush, William S. [1 ]
Moore, Jason H. [2 ,3 ]
机构
[1] Vanderbilt Univ, Sch Med, Dept Biomed Informat, Ctr Human Genet Res, Nashville, TN 37212 USA
[2] Dartmouth Med Sch, Inst Quantitat Biomed Sci, Dept Genet, Lebanon, NH USA
[3] Dartmouth Med Sch, Inst Quantitat Biomed Sci, Dept Community Family Med, Lebanon, NH USA
关键词
FACTOR-H POLYMORPHISM; MACULAR DEGENERATION; GENOTYPE IMPUTATION; MULTIPLE-SCLEROSIS; COMMON DISEASES; LOCI; RISK; METAANALYSIS; TRAITS; GENE;
D O I
10.1371/journal.pcbi.1002822
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Genome-wide association studies (GWAS) have evolved over the last ten years into a powerful tool for investigating the genetic architecture of human disease. In this work, we review the key concepts underlying GWAS, including the architecture of common diseases, the structure of common human genetic variation, technologies for capturing genetic information, study designs, and the statistical methods used for data analysis. We also look forward to the future beyond GWAS.
引用
收藏
页数:11
相关论文
共 55 条
[1]   A haplotype map of the human genome [J].
Altshuler, D ;
Brooks, LD ;
Chakravarti, A ;
Collins, FS ;
Daly, MJ ;
Donnelly, P ;
Gibbs, RA ;
Belmont, JW ;
Boudreau, A ;
Leal, SM ;
Hardenbol, P ;
Pasternak, S ;
Wheeler, DA ;
Willis, TD ;
Yu, FL ;
Yang, HM ;
Zeng, CQ ;
Gao, Y ;
Hu, HR ;
Hu, WT ;
Li, CH ;
Lin, W ;
Liu, SQ ;
Pan, H ;
Tang, XL ;
Wang, J ;
Wang, W ;
Yu, J ;
Zhang, B ;
Zhang, QR ;
Zhao, HB ;
Zhao, H ;
Zhou, J ;
Gabriel, SB ;
Barry, R ;
Blumenstiel, B ;
Camargo, A ;
Defelice, M ;
Faggart, M ;
Goyette, M ;
Gupta, S ;
Moore, J ;
Nguyen, H ;
Onofrio, RC ;
Parkin, M ;
Roy, J ;
Stahl, E ;
Winchester, E ;
Ziaugra, L ;
Shen, Y .
NATURE, 2005, 437 (7063) :1299-1320
[2]   The common PPARγ Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes [J].
Altshuler, D ;
Hirschhorn, JN ;
Klannemark, M ;
Lindgren, CM ;
Vohl, MC ;
Nemesh, J ;
Lane, CR ;
Schaffner, SF ;
Bolk, S ;
Brewer, C ;
Tuomi, T ;
Gaudet, D ;
Hudson, TJ ;
Daly, M ;
Groop, L ;
Lander, ES .
NATURE GENETICS, 2000, 26 (01) :76-80
[3]   A map of human genome variation from population-scale sequencing [J].
Altshuler, David ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Collins, Francis S. ;
De la Vega, Francisco M. ;
Donnelly, Peter ;
Egholm, Michael ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Knoppers, Bartha M. ;
Lander, Eric S. ;
Lehrach, Hans ;
Mardis, Elaine R. ;
McVean, Gil A. ;
Nickerson, DebbieA. ;
Peltonen, Leena ;
Schafer, Alan J. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Deiros, David ;
Metzker, Mike ;
Muzny, Donna ;
Reid, Jeff ;
Wheeler, David ;
Wang, Jun ;
Li, Jingxiang ;
Jian, Min ;
Li, Guoqing ;
Li, Ruiqiang ;
Liang, Huiqing ;
Tian, Geng ;
Wang, Bo ;
Wang, Jian ;
Wang, Wei ;
Yang, Huanming ;
Zhang, Xiuqing ;
Zheng, Huisong ;
Lander, Eric S. ;
Altshuler, David L. ;
Ambrogio, Lauren ;
Bloom, Toby ;
Cibulskis, Kristian ;
Fennell, Tim J. ;
Gabriel, Stacey B. .
NATURE, 2010, 467 (7319) :1061-1073
[4]   Integrating common and rare genetic variation in diverse human populations [J].
Altshuler, David M. ;
Gibbs, Richard A. ;
Peltonen, Leena ;
Dermitzakis, Emmanouil ;
Schaffner, Stephen F. ;
Yu, Fuli ;
Bonnen, Penelope E. ;
de Bakker, Paul I. W. ;
Deloukas, Panos ;
Gabriel, Stacey B. ;
Gwilliam, Rhian ;
Hunt, Sarah ;
Inouye, Michael ;
Jia, Xiaoming ;
Palotie, Aarno ;
Parkin, Melissa ;
Whittaker, Pamela ;
Chang, Kyle ;
Hawes, Alicia ;
Lewis, Lora R. ;
Ren, Yanru ;
Wheeler, David ;
Muzny, Donna Marie ;
Barnes, Chris ;
Darvishi, Katayoon ;
Hurles, Matthew ;
Korn, Joshua M. ;
Kristiansson, Kati ;
Lee, Charles ;
McCarroll, Steven A. ;
Nemesh, James ;
Keinan, Alon ;
Montgomery, Stephen B. ;
Pollack, Samuela ;
Price, Alkes L. ;
Soranzo, Nicole ;
Gonzaga-Jauregui, Claudia ;
Anttila, Verneri ;
Brodeur, Wendy ;
Daly, Mark J. ;
Leslie, Stephen ;
McVean, Gil ;
Moutsianas, Loukas ;
Nguyen, Huy ;
Zhang, Qingrun ;
Ghori, Mohammed J. R. ;
McGinnis, Ralph ;
McLaren, William ;
Takeuchi, Fumihiko ;
Grossman, Sharon R. .
NATURE, 2010, 467 (7311) :52-58
[5]  
Biernacka Joanna M, 2009, BMC Proc, V3 Suppl 7, pS5
[6]   A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals [J].
Browning, Brian L. ;
Browning, Sharon R. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 84 (02) :210-223
[7]   PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies [J].
Browning, Brian L. .
BMC BIOINFORMATICS, 2008, 9 (1)
[8]  
Bush WS, 2009, PACIFIC SYMPOSIUM ON BIOCOMPUTING 2009, P368
[9]   Replicating genotype-phenotype associations [J].
Chanock, Stephen J. ;
Manolio, Teri ;
Boehnke, Michael ;
Boerwinkle, Eric ;
Hunter, David J. ;
Thomas, Gilles ;
Hirschhorn, Joel N. ;
Abecasis, Goncalo ;
Altshuler, David ;
Bailey-Wilson, Joan E. ;
Brooks, Lisa D. ;
Cardon, Lon R. ;
Daly, Mark ;
Donnelly, Peter ;
Fraumeni, Joseph F., Jr. ;
Freimer, Nelson B. ;
Gerhard, Daniela S. ;
Gunter, Chris ;
Guttmacher, Alan E. ;
Guyer, Mark S. ;
Harris, Emily L. ;
Hoh, Josephine ;
Hoover, Robert ;
Kong, C. Augustine ;
Merikangas, Kathleen R. ;
Morton, Cynthia C. ;
Palmer, Lyle J. ;
Phimister, Elizabeth G. ;
Rice, John P. ;
Roberts, Jerry ;
Rotimi, Charles ;
Tucker, Margaret A. ;
Vogan, Kyle J. ;
Wacholder, Sholom ;
Wijsman, Ellen M. ;
Winn, Deborah M. ;
Collins, Francis S. .
NATURE, 2007, 447 (7145) :655-660
[10]   Evaluation of the Age-Related Eye Disease Study Clinical Lens Grading System AREDS Report No. 31 [J].
Chew, Emily Y. ;
Kim, Jonghyeon ;
Sperduto, Robert D. ;
Datiles, Manuel B., III ;
Coleman, Hanna R. ;
Thompson, Darby J. S. ;
Milton, Roy C. ;
Clayton, Janine A. ;
Hubbard, Larry D. ;
Danis, Ronald P. ;
Ferris, Frederick L., III .
OPHTHALMOLOGY, 2010, 117 (11) :2112-U299