Population-specific genotype imputations using minimac or IMPUTE2

被引：81

作者：

van Leeuwen, Elisabeth M. ^{[1
]}

Kanterakis, Alexandros ^{[2
,3
]}

Deelen, Patrick ^{[2
,3
]}

Kattenberg, Mathijs V. ^{[4
]}

Slagboom, P. Eline ^{[5
,6
]}

de Bakker, Paul I. W. ^{[2
,7
,8
]}

Wijmenga, Cisca ^{[2
,3
]}

Swertz, Morris A. ^{[2
,3
]}

Boomsma, Dorret I. ^{[4
]}

van Duijn, Cornelia M. ^{[1
]}

Karssen, Lennart C. ^{[1
,9
]}

Hottenga, Jouke Jan ^{[4
]}

机构：

[1] Erasmus MC, Dept Epidemiol, Rotterdam, Netherlands

[2] Univ Groningen, Univ Med Ctr Groningen, Genom Coordinat Ctr, Groningen, Netherlands

[3] Univ Groningen, Univ Med Ctr Groningen, Dept Genet, Groningen, Netherlands

[4] Vrije Univ Amsterdam, Dept Biol Psychol, Amsterdam, Netherlands

[5] Leiden Univ, Dept Mol Epidemiol, Med Ctr, Leiden, Netherlands

[6] Leiden Univ, Netherlands Consortium Hlth Ageing, Med Ctr, Leiden, Netherlands

[7] Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands

[8] Univ Med Ctr Utrecht, Dept Epidemiol, Utrecht, Netherlands

[9] PolyOmica, Groningen, Netherlands

来源：

NATURE PROTOCOLS | 2015年 / 10卷 / 09期

关键词：

GENOME-WIDE ASSOCIATION; QUALITY-CONTROL; LOW-FREQUENCY; METAANALYSIS; CONVERSION; VARIANTS; FORMAT;

D O I：

10.1038/nprot.2015.077

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPSNPSNPs) in their GWASASs. To this end, genotypes that have not been measured in a given cohort can be imputed on the basis of a set of reference haplotypes. This protocol provides guidelines for performing imputations with two widely used tools: minimac and IMPUTEPUTEPUTEPUTE2. These guidelines were developed and used by the Genome of the Netherlands (GoNL) consortium, which has created a population-specific reference panel for genetic imputations and used this reference to impute various Dutch biobanks. We also describe several factors that might influence the final imputation quality. This protocol, which has been used by the largest Dutch biobanks, should take approximately several days, depending on the sample size of the biobank and the computer resources available.

引用

页码：1285 / 1296

页数：12

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