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In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) 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 (SNPs) in their GWASs. 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 IMPUTE2. 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.

Original publication

DOI

10.1038/nprot.2015.077

Type

Journal article

Journal

Nature protocols

Publication Date

09/2015

Volume

10

Pages

1285 - 1296

Addresses

Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.

Keywords

Genome of the Netherlands Consortium, Haplotypes, Polymorphism, Single Nucleotide, Software, Meta-Analysis as Topic, Genome-Wide Association Study