Our previous publication details numbers of SNPs genotyped and quality controlled in Phase 1(4). Briefly, a total of 552,974 SNPs were satisfactorily genotyped (99.7%). Of the SNPs satisfactorily genotyped, 524,714 were common to both cases and controls. Several quality control processes were sequentially applied to these SNPs (Figure 1a), leaving 511,919 SNPs for which genotype data were informative. For the informative SNPs mean individual sample call rates (the percentage of samples for which a genotype was obtained for each SNP) were 99.8% and 99.6% in cases and controls, respectively. Comparison of the observed and expected distributions showed little evidence for an inflation of the test statistics (inflation factor λ= 1.02, based on the 90% least significant SNPs), thereby excluding systematic bias. Of the 1978 cases, 1958 were successfully genotyped and following quality control, 1952 cases were used in the analysis (Figure 1a).
