We genotyped the prioritized SNPs in cases and controls from three UK replication sets (RS1, RS2 and RS3, described in4; Supplementary Table 1; Supplementary Methods). Genotyping of prioritized SNPs in RS1, RS2 and RS3 was performed by Kbiosciences (Herts., UK). All assays were validated prior to use, using a standard 96-well validation plate used by Kbiosciences and up to 296 samples from the WTCCC study (see Comparison of genotypes from imputation and direct genotyping; Supplementary Methods). Concordance rates between the Affymetrix and KASPar/TaqMan genotypes (based on up to 296 replicate stage 1 samples) were 97.5% on average. All genotyped SNPs had genotype call frequency rates >94% in the replication sets and no SNPs had HWE p value<0.001 in cases or controls. We tested for association with T2D using the Cochran-Armitage test for trend. Results from the 3 replication sets were combined in a Cochran-Mantel-Haenszel meta-analysis framework.
