The adequacy of case-control matching and possibility of differential genotyping of cases and controls were formally evaluated using Q-Q plots of −log10P values (based on the 90% least significant SNPs). Deviation of the genotype frequencies in the controls from those expected under Hardy-Weinberg Equilibrium (HWE) was assessed by χ2 test, or Fisher’s exact test where an expected cell count was <5. Comparison of the difference in number of associations observed and expected was made using the binomial test.
