A Hardy–Weinberg equilibrium (HWE) test (in the WTCCC2 control data) identified SNPs with large deviations (p<0.001) that were excluded from analysis, controlling for possible genotyping errors in the controls. As the cases were genotyped separately, further filtering steps were undertaken to control for possible genotyping error in the cases. See Appendix 2 (supplementary methods) for details. All QC steps were performed using PLINK [22], and 681,552 SNPs remained for analysis. A QQ plot is shown in Appendix 3.
