For the combination of data across stages 1, 2 and 3, we also adopted these two strategies (of using GC-corrected and GC-uncorrected stage 1 data). In the first, we performed individual GC-correction of DGI, FUSION and WTCCC stage 1 data prior to meta-analysis with stage 2 and stage 3 data (an approach which may be over-conservative where, as here, none of the T2D-associated SNPs has particular hallmarks of stratification) (Supplementary Note). In the second, we combined only uncorrected data (except for the deCODE data, where we have applied GC correction given a more marked genomic control inflation [GC ~1.3] in that sample). We present the resulting data from both approaches (of using GC-corrected and GC-uncorrected stage 1 data for stage 1-3 meta-analysis) in Supplementary Table 6 and a comparison of results (showing very small differences) in the Supplementary Note. All data presented elsewhere in the manuscript reflect the GC-corrected analysis strategy outcome.
