We genotyped the prioritized SNPs in three stage 2 case-control samples1 (Supplementary Table 1; Supplementary Methods). The prioritized SNPs were genotyped in all DGI stage 1 and 2 samples using the iPLEX Sequenom MassARRAY platform (http://www.sequenom.com/Assets/pdfs/appnotes/8876-006.pdf). 63 SNPs passing QC (>94% call rate, MAF>0.01 and HWE p value >0.001) were used for association testing. We tested for T2D association in each DGI stage 2 case-control set using a chi-squared analysis (assuming an additive genetic model). Results from the three DGI stage 2 samples were combined using Cochran-Mantel-Haenszel meta-analysis.
