We examine data from Klein et al. (2005), who reported a GWAS for age-related macular degeneration; being one of the first GWAS there were just 96 cases and 50 controls. We examine HWE for 116,212 SNPs in controls. We first carried out a number of quality control measures, and for comparison purposes use the same criteria as Klein et al. (2005). Specifically, SNPs were removed if they were called in less than 85% of individuals or if the MAF was less than 1%; this left 102,640 SNPs. In Klein et al. (2005), a Bonferroni correction was applied to control the FWER at 5%, to give a p-value threshold of 4.9 × 10−7. Figure 4 displays various summaries for these data. In panel (a) we plot –log10 p-values from the χ2 test versus their exact test counterparts and we see a large degree of dissimilarity, which is not surprising given the small sample sizes here. The discreteness of the p-values from the exact test is apparent also, and the distribution away from zero (which corresponds principally to null SNPs) is far
