The genotyped SNPs in common between the remaining Illumina (N=269,840) and Affymetrix (N=646,601) SNPs were relatively few (N=137,768). Therefore, genome-wide association analyses of the combined data could only be conducted using imputed genotypes. After initial QC checks, both datasets were imputed separately by MACH (Abecasis, unpublished) using the data from the European HapMap 1+2, Release 22 Build 36. Only SNPs with an imputation quality score (R2) greater than 0.3 were retained, which resulted in a total number of 2,380,486 imputed Illumina and 2,369,130 imputed Affymetrix SNPs.
