Association results from the two GWAS cohorts were combined using the inverse variance weighted method implemented in METAL (http://www.sph.umich.edu/csg/abecasis/metal/). Inflation factor was calculated as the ratio of median of the observed vs. expected individual SNP χ2 statistics. It was adjusted for each GWAS cohort before meta-analysis. Meta-analyses of the four replication cohorts, as well as the six GWAS and replication cohorts were also conducted using the inverse variance weighted method. In order to account for modest relatedness between the GWAS (cohorts 1 and 2) and the replication samples (cohorts 3 and 4), BMI Z-scores of all six cohorts were pooled and analyzed together using variance component method for comparison with the meta-analysis method. To evaluate the potential confounding effect of disease, 2,111 community nondiabetic subjects from cohorts 1, 3, and 6, 1,516 T2DM-ESRD subjects from cohorts 2 and 4, and 1,362 T2DM subjects from cohorts 4, 5, and 6 were separately analyzed using linear regression and variance component methods as appropriate. The association results were then combined using METAL to assess the overall SNP association in nondiabetic, T2DM-ESRD, and T2DM subjects separately.
