The 32 Stage 1 studies were genotyped using a variety of Affymetrix (6.0, GeneChip 500K, 250K, MIP50K and 10K) and Illumina (HumanHap 550K, 318K, HumanHap 300K, HumanHap 370K CNV, HumanHap610 quad, Human660W-Quad BeadChip, 6K and Human 1Mv1_C) genotyping arrays. Genotyping call rate cut-offs were at least 90% and SNPs were filtered for those with a minor allele frequency of greater than 1%. More details on the filtering criteria for genotypes in each individual study can be found in Supplementary Table 2.
