We used meta-analysis to combine the T2D association results for the stage 1 WTCCC, DGI and FUSION samples. The combined stage 1 data are comprised of 10,128 samples: 4,549 T2D cases and 5,579 controls. We used association results from directly genotyped SNPs, where available, and imputed genotype association results at all other positions. 2,168,847 genotyped and imputed autosomal SNPs passed QC and had MAF>0.01 in each of the three samples (44,750 were genotyped in all three samples, 308,628 were genotyped in two samples, 245,158 were genotyped in one sample, 1,570,311 were imputed in all samples). All association results were expressed relative to the forward strand of the reference genome based on dbSNP125. For our initial analysis, which was used to select signals for stage 2 genotyping, for each SNP we combined the ORs for a given reference allele weighted by the confidence intervals using a fixed effects model. We investigated evidence for heterogeneity of ORs using two commonly used statistics: Cochrans's Q statistic and I2 (25).
