The GENEVA T2D projects were genotyped on the Affymetrix 6.0 array with Birdseed v1.33 calling by plate. A total of 28 (NHS) and 26 (HPFS) low quality samples were found with high heterozygosity, a high level of relatedness to other samples, and poor BAF plots (see Supporting Information for more details). However, important differences from the situation described by Pluzhnikov et.al [2008] are that the samples are distributed across many plates and we did not find evidence of spurious associations. The QQ plots show low genomic inflation (Figure S14) and genotypic cluster plots for the top hits (after SNP filtering described below) are generally of good quality. Nevertheless, the possible effect of low quality samples was investigated in two ways.
