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.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
van Leeuwen EM,Kanterakis A,Deelen P,Kattenberg MV,Genome of the Netherlands Consortium.,Slagboom PE,de Bakker PI,Wijmenga C,Swertz MA,Boomsma DI,van Duijn CM,Karssen LC,Hottenga JJdoi
10.1038/nprot.2015.077subject
Has Abstractpub_date
2015-09-01 00:00:00pages
1285-96issue
9eissn
1754-2189issn
1750-2799pii
nprot.2015.077journal_volume
10pub_type
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