The WTCCC stage 1 sample consists of 1,924 T2D cases and 2,938 population controls from the UK3,4. These samples were genotyped on the Affymetrix GeneChip Human Mapping 500k Array Set. The call frequency of included samples was >0.97. 393,143 autosomal SNPs passed quality control (QC) criteria: Hardy-Weinberg equilibrium [HWE] p>10−4 in T2D cases and controls, call frequency >0.95, minor allele frequency (MAF)>0.01, and good clustering, as defined in3,4.
