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.
Overview publication
| Title | Population-specific genotype imputations using minimac or IMPUTE2. |
| Date | September 1st, 2015 |
| Issue name | Nature protocols |
| Issue number | v10.9:1285-96 |
| DOI | 10.1038/nprot.2015.077 |
| PubMed | 26226460 |
| Authors | |
| Info | Genome of the Netherlands Consortium, Swertz MA, Francioli LC, van Dijk F, Menelaou A, Neerincx PB, Pulit SL, Deelen P, Elbers CC, Palamara PF, Pe'er I, Abdellaoui A, Kloosterman WP, van Oven M, Vermaat M, Li M, Laros JF, Stoneking M, de Knijff P, Kayser M, Veldink JH, van den Berg LH, Byelas H, den Dunnen JT, Dijkstra M, Amin N, van der Velde KJ, Hottenga JJ, van Setten J, van Leeuwen EM, Kanterakis A, Kattenberg M, Karssen LC, van Schaik BD, Bot J, Nijman IJ, van Enckevort D, Mei H, Koval V, Ye K, Lameijer EW, Moed MH, Hehir-Kwa JY, Handsaker RE, Sunyaev SR, Sohail M, Hormozdiari F, Marschall T, Schönhuth A, Guryev V, de Bakker PI, Slagboom PE, Beekman MB, de Craen AJ, Suchiman HE, Hofman A, van Duijn C, Boomsma DI, Willemsen G, Wolffenbuttel BH, Platteel M, Pitts SJ, Potluri S, Cox DR, Li Q, Li Y, Du Y, Chen R, Cao H, Li N, Cao S, Wang J, Bovenberg JA, Wijmenga C, Swertz MA, van Duijn CM, Boomsma DI, Slagboom PE, van Ommen GB, de Bakker PI |
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