Genotype imputation for genome-wide association studies

被引：1105

作者：

Marchini, Jonathan ^{[1
]}

Howie, Bryan ^{[2
]}

机构：

[1] Univ Oxford, Dept Stat, Oxford OX1 3TG, England

[2] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

来源：

NATURE REVIEWS GENETICS | 2010年 / 11卷 / 07期

基金：

美国国家科学基金会; 英国医学研究理事会;

关键词：

HAPLOTYPE-PHASE INFERENCE; HIDDEN MARKOV-MODELS; SUSCEPTIBILITY LOCI; MULTIPLE-SCLEROSIS; STATISTICAL-METHOD; HLA ALLELES; METAANALYSIS; ACCURACY; REPLICATION; RISK;

D O I：

10.1038/nrg2796

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

In the past few years genome-wide association (GWA) studies have uncovered a large number of convincingly replicated associations for many complex human diseases. Genotype imputation has been used widely in the analysis of GWA studies to boost power, fine-map associations and facilitate the combination of results across studies using meta-analysis. This Review describes the details of several different statistical methods for imputing genotypes, illustrates and discusses the factors that influence imputation performance, and reviews methods that can be used to assess imputation performance and test association at imputed SNPs.

引用

页码：499 / 511

页数：13

共 55 条

[11] Efficiency and power in genetic association studies
de Bakker, PIW
Yelensky, R
Pe'er, I
Gabriel, SB
Daly, MJ
Altshuler, D
[J]. NATURE GENETICS, 2005, 37 (11) : 1217 - 1223
[12] Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
De Jager, Philip L.
Jia, Xiaoming
Wang, Joanne
de Bakker, Paul I. W.
Ottoboni, Linda
Aggarwal, Neelum T.
Piccio, Laura
Raychaudhuri, Soumya
Tran, Dong
Aubin, Cristin
Briskin, Rebeccah
Romano, Susan
Baranzini, Sergio E.
McCauley, Jacob L.
Pericak-Vance, Margaret A.
Haines, Jonathan L.
Gibson, Rachel A.
Naeglin, Yvonne
Uitdehaag, Bernard
Matthews, Paul M.
Kappos, Ludwig
Polman, Chris
McArdle, Wendy L.
Strachan, David P.
Evans, Denis
Cross, Anne H.
Daly, Mark J.
Compston, Alastair
Sawcer, Stephen J.
Weiner, Howard L.
Hauser, Stephen L.
Hafler, David A.
Oksenberg, Jorge R.
[J]. NATURE GENETICS, 2009, 41 (07) : 776 - U26
[13] GENERAL MODEL FOR GENETIC ANALYSIS OF PEDIGREE DATA
ELSTON, RC
STEWART, J
[J]. HUMAN HEREDITY, 1971, 21 (06) : 523 - &
[14] Genotype prediction using a dense map of SNPs
Evans, DM
Cardon, LR
Morris, AP
[J]. GENETIC EPIDEMIOLOGY, 2004, 27 (04) : 375 - 384
[15] EXCOFFIER L, 1995, MOL BIOL EVOL, V12, P921
[16] Fearnhead P, 2001, GENETICS, V159, P1299
[17] A second generation human haplotype map of over 3.1 million SNPs
Frazer, Kelly A.
Ballinger, Dennis G.
Cox, David R.
Hinds, David A.
Stuve, Laura L.
Gibbs, Richard A.
Belmont, John W.
Boudreau, Andrew
Hardenbol, Paul
Leal, Suzanne M.
Pasternak, Shiran
Wheeler, David A.
Willis, Thomas D.
Yu, Fuli
Yang, Huanming
Zeng, Changqing
Gao, Yang
Hu, Haoran
Hu, Weitao
Li, Chaohua
Lin, Wei
Liu, Siqi
Pan, Hao
Tang, Xiaoli
Wang, Jian
Wang, Wei
Yu, Jun
Zhang, Bo
Zhang, Qingrun
Zhao, Hongbin
Zhao, Hui
Zhou, Jun
Gabriel, Stacey B.
Barry, Rachel
Blumenstiel, Brendan
Camargo, Amy
Defelice, Matthew
Faggart, Maura
Goyette, Mary
Gupta, Supriya
Moore, Jamie
Nguyen, Huy
Onofrio, Robert C.
Parkin, Melissa
Roy, Jessica
Stahl, Erich
Winchester, Ellen
Ziaugra, Liuda
Altshuler, David
Shen, Yan
[J]. NATURE, 2007, 449 (7164) : 851 - U3
[18] Practical Issues in Imputation-Based Association Mapping
Guan, Yongtao
Stephens, Matthew
[J]. PLOS GENETICS, 2008, 4 (12):
[19] Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies
Hao, Ke
Chudin, Eugene
McElwee, Joshua
Schadt, Eric E.
[J]. BMC GENETICS, 2009, 10
[20] Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer
Houlston, Richard S.
Webb, Emily
Broderick, Peter
Pittman, Alan M.
Di Bernardo, Maria Chiara
Lubbe, Steven
Chandler, Ian
Vijayakrishnan, Jayaram
Sullivan, Kate
Penegar, Steven
Carvajal-Carmona, Luis
Howarth, Kimberley
Jaeger, Emma
Spain, Sarah L.
Walther, Axel
Barclay, Ella
Martin, Lynn
Gorman, Maggie
Domingo, Enric
Teixeira, Ana S.
Kerr, David
Cazier, Jean-Baptiste
Niittymaki, Iina
Tuupanen, Sari
Karhu, Auli
Aaltonen, Lauri A.
Tomlinson, Ian P. M.
Farrington, Susan M.
Tenesa, Albert
Prendergast, James G. D.
Barnetson, Rebecca A.
Cetnarskyj, Roseanne
Porteous, Mary E.
Pharoah, Paul D. P.
Koessler, Thibaud
Hampe, Jochen
Buch, Stephan
Schafmayer, Clemens
Tepel, Jurgen
Schreiber, Stefan
Voelzke, Henry
Chang-Claude, Jenny
Hoffmeister, Michael
Brenner, Hermann
Zanke, Brent W.
Montpetit, Alexandre
Hudson, Thomas J.
Gallinger, Steven
Campbell, Harry
Dunlop, Malcolm G.
[J]. NATURE GENETICS, 2008, 40 (12) : 1426 - 1435

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