Population-specific Genotype Imputations Using Minimac or IMPUTE2

Overview

Journal Nat Protoc

Specialties Biology
Pathology
Science

Date 2015 Jul 31

PMID 26226460

Citations 57

Authors

Elisabeth M van Leeuwen

Alexandros Kanterakis

Patrick Deelen

Mathijs V Kattenberg

P Eline Slagboom

Paul I W de Bakker

Cisca Wijmenga

Morris A Swertz

Dorret I Boomsma

Cornelia M Van Duijn

Lennart C Karssen

Jouke Jan Hottenga

Affiliations

Soon will be listed here.

Abstract

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.

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