Genotype imputation for genome-wide association studies

被引：1125
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：
英国医学研究理事会; 美国国家科学基金会;
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
收藏
页码：499 / 511
页数：13
相关论文
共 55 条
[1]   Efficient multilocus association testing for whole genome association studies using localized haplotype clustering [J].
Browning, Brian L. ;
Browning, Sharon R. .
GENETIC EPIDEMIOLOGY, 2007, 31 (05) :365-375
[2]   Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies [J].
Browning, Brian L. ;
Yu, Zhaoxia .
AMERICAN JOURNAL OF HUMAN GENETICS, 2009, 85 (06) :847-861
[3]   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
[4]   Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering [J].
Browning, Sharon R. ;
Browning, Brian L. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2007, 81 (05) :1084-1097
[5]   Multilocus association mapping using variable-length Markov chains [J].
Browning, Sharon R. .
AMERICAN JOURNAL OF HUMAN GENETICS, 2006, 78 (06) :903-913
[6]   Missing data imputation and haplotype phase inference for genome-wide association studies [J].
Browning, Sharon R. .
HUMAN GENETICS, 2008, 124 (05) :439-450
[7]   In silico method for inferring genotypes in pedigrees [J].
Burdick, Joshua T. ;
Chen, Wei-Min ;
Abecasis, Goncalo R. ;
Cheung, Vivian G. .
NATURE GENETICS, 2006, 38 (09) :1002-1004
[8]   Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium [J].
Carlson, CS ;
Eberle, MA ;
Rieder, MJ ;
Yi, Q ;
Kruglyak, L ;
Nickerson, DA .
AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 74 (01) :106-120
[9]   Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci [J].
Cooper, Jason D. ;
Smyth, Deborah J. ;
Smiles, Adam M. ;
Plagnol, Vincent ;
Walker, Neil M. ;
Allen, James E. ;
Downes, Kate ;
Barrett, Jeffrey C. ;
Healy, Barry C. ;
Mychaleckyj, Josyf C. ;
Warram, James H. ;
Todd, John A. .
NATURE GENETICS, 2008, 40 (12) :1399-1401
[10]   Practical aspects of imputation-driven meta-analysis of genome-wide association studies [J].
de Bakker, Paul I. W. ;
Ferreira, Manuel A. R. ;
Jia, Xiaoming ;
Neale, Benjamin M. ;
Raychaudhuri, Soumya ;
Voight, Benjamin F. .
HUMAN MOLECULAR GENETICS, 2008, 17 :R122-R128
123456