Despite favorable design scores, the SNP assay design process failed at Illumina for 480 SNPs. An additional 237 SNPs failed genotyping and genotypes for 5,851 SNPs were delivered. Quality control (QC) filters were then applied and a total of 700 SNPs failed for the following reasons (note that a SNP could fail for more than one reason): minor allele frequency (MAF) <0.01 (538 SNPs); AN Trios (affected individual with two parents, parents only used for QC) with ≥2 Mendel errors (1 SNP); duplicate samples with ≥2 disagreements (111 SNPs); missing genotypes in >0.05 of cases or controls (24 SNPs); differential genotype missingness in cases versus controls at P <0.01 (4 SNPs); and Hardy–Weinberg equilibrium (HWE) exact P <0.01 in controls (47 SNPs). The total number of SNPs passing all QC steps was 5,151. The total number of genes with SNPs passing all QC steps was 182. In addition, the plot of homozygosity over all SNPs showed no significant differences between cases and controls (P = 0.35) and no individual had marked elevated homozygosity. Finally, population stratification was assessed through genomic control [Devlin and Roeder, 1999]: lambda (λ) = 1.035 is consistent with an acceptably small amount of population stratification.
