DNA samples (41) were genotyped in different projects and genotyping was performed on Affymetrix 6.0 (N=298), Affymetrix Perlegen 5.0 (N=3697), Illumina 370 (N=290), Illumina 660 (N=1439), Illumina Omni Express 1M (N=455) platforms. Calls were made with platform specific software (Genotyper, Beadstudio). The quality control thresholds for SNPs were MAF > 1%, HWE > 0.00001, call rate >95% and 0.30 <Heterozygosity <0.35. Samples were excluded from the data if their expected sex and IBD status did not match, or if the genotype missing rate was >10%. SNPs were aligned to the positive strand of the Hapmap-2-Build 36-release-24 CEU reference set. Alignment was checked using individuals and family members tested on multiple platforms. SNPs were excluded if allele frequencies differed more than 15% with the reference set and/or the other platforms. The data of the platforms were merged into a single dataset (N=5856). This merged set was imputed against the reference set using IMPUTE v2. After imputation, genotype dosage was calculated if the highest genotype probability was above 90%. Badly imputed SNPs were removed based on HWE < 0.00001, proper info < 0.40, MAF < 1%, allele frequency difference >.15 against reference.
