All GWA studies were genotyped using the Affymetrix GeneChip 500K array set, and genotypes were called using the BRLMM algorithm. Each study applied genotyping quality control criteria and conducted tests for population stratification: 352,700 SNPs passed quality control in EPIC-Norfolk and 390,631 in the CoLaus cohort. In CoLaus correction for population substructure was done by principal components. The genomic control inflation factors (lGC) for each GWA study were <1 for EPIC-Norfolk control cohort and obese cases and 1.016 in CoLaus, indicating that the extent of residual population substructure is modest, and no further genomic control corrections were applied.
