Thirty of the 900 GWAS2 cases were excluded from further analyses due to: failed genotyping/low call rate (n=13); a genome-wide average identity by state (IBS) score of above 1.60, indicating cryptic relatedness (n=1); discrepancies between reported- and genotype-derived sex (n=2); or outlier status (n=14). Figure 1 shows the results of the PCA following the exclusion of outliers. Of the 502,276 SNPs present in the SNP set content of all samples after pooling with the GWAS1 data, 500,467 were autosomal. Of these, 92.5% passed QC. The final data set comprised 463,044 autosomal SNPs from a total of 1,333 cases and 2,168 controls. The mean CR of the final set of SNPs (cases and controls combined) was 99.94% (SD=0.12%). To visualize the outcome of the QC steps, the pre- and postQC association p-values are depicted as a quantile-quantile plot (Figure 2).
