We have assumed here that accurate genotypes are available for all SNPs on each chip. In practice some SNPs on each chip will fail QC tests and not be available for analyses. As a consequence, our study will overestimate power, though this effect is unlikely to be large. We are only able to use SNPs in HapMap as potential disease SNPs. These may not be systematically representative of all potential disease SNPs. HapMap SNPs have systematically higher MAFs than do arbitrary SNPs [2], but for SNPs within a particular range of MAF, it seems unlikely that their LD properties will differ systematically, so, for example, we would expect our results for common SNPs to extend beyond those in HapMap.
