We describe here in brief the application of meta-analysis to GWA studies of T2D [42]. Three T2D GWA scans (WTCCC, DGI, FUSION) [43-46] were combined in a meta-analysis framework. Details for the design of these studies can be found in their original publications [43-46]. Genotypes at untyped SNPs were imputed across the HapMap in each of the 3 individual studies. Stringent quality control was carried out for directly typed and imputed variants, and individual studies were corrected for population stratification before combining summary results across a total of 10,128 samples. Approximately 2.2 million SNPs survived quality control. To combine the data, both fixed effects OR-based and p value-based meta-analysis approaches were used.
