TY - JOUR
T1 - Population-specific genotype imputations using minimac or IMPUTE2
AU - van Leeuwen, Elisabeth M
AU - Kanterakis, Alexandros
AU - Deelen, Patrick
AU - Kattenberg, Mathijs V
AU - Slagboom, P Eline
AU - de Bakker, Paul I W
AU - Wijmenga, Cisca
AU - Swertz, Morris A
AU - Boomsma, Dorret I
AU - van Duijn, Cornelia M
AU - Karssen, Lennart C
AU - Hottenga, Jouke Jan
PY - 2015/9
Y1 - 2015/9
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84940521469&partnerID=8YFLogxK
U2 - 10.1038/nprot.2015.077
DO - 10.1038/nprot.2015.077
M3 - Article
C2 - 26226460
SN - 1754-2189
VL - 10
SP - 1285
EP - 1296
JO - Nature Protocols
JF - Nature Protocols
IS - 9
ER -