One limitation of the approach we (and others [9],[10],[12],[11]) have used is that the causal SNP is assumed to be one of those SNPs in the HapMap panel and this will not always be true. Other studies [1] have shown that the majority of SNPs not in HapMap will be highly correlated with the SNPs that are in HapMap and this is especially true for the more common SNPs. This means there is a slight bias in our power results for each chip and for the use of imputation but we do not expect it to be large. A consequence of this point is that the power we estimate for the ‘complete’ chip approximates the power we might obtain if we had a chip which typed all the SNPs that exist in the human genome.
