We adopted an experimental design with 2,000 cases for each disease and 3,000 combined controls. All 17,000 samples were genotyped with the GeneChip 500K Mapping Array Set (Affymetrix chip), which comprises 500,568 SNPs, as described in Methods. The power of this study (estimated from simulations that mimic linkage disequilibrium patterns in the HapMap Caucasian sample (CEU), see Methods) averaged across SNPs with minor allele frequencies (MAFs) above 5% is estimated to be 43% for alleles with a relative risk of 1.3, increasing to 80% for a relative risk of 1.5, for a P-value threshold of 5×10-7 (Supplementary Table 2).
