SNPs with the following criteria: SNP call rate >0.95, MAF >0.01, and HWE P-value >10−4. After QC, 517K SNPs remained on the Illumina and 350K SNPs remained on the Affy500 arrays. Of these, only 60K SNPs of Affy500 overlapped with Illumina660. To reuse the genotypes we used MACH for imputation of missing 457K SNPs in Affy500 based on HapMap CEU individuals. To guarantee the quality of imputation, we set the inclusion threshold to r2=0.3 as recommended. For 1670 (younger unrelated) controls from the Rotterdam Study, genotypes were generated with Illumina Infinium II HumanHap 550K and HumanHap550-Duo BeadChips (Illumina550).12, 13 Our data, therefore, differs from the usual simulation setting in the following way: the sib of each sibship genotyped with Affy500 was imputed to match the SNPs of other siblings and controls. The description of the study design and the different arrays used is given in Figure 1 and Table 1.
