In the experiments described so far, we illustrated the accuracy of genotype imputation that relies on existing resources (such as the Phase II HapMap) and genotyping technologies (including a variety of commercial genotyping chips). It is likely that both these resources and technologies will continue to evolve rapidly and it is interesting to consider how these developments might impact imputation-based approaches. For example, it is clear that genotyping chips of the future will be able to examine an ever larger number of tag SNPs in a cost-effective manner. Extrapolating from Table III, it is clear these should provide improved genomic coverage, eventually allowing investigators to impute nearly all HapMap SNPs with near perfect accuracy. Nevertheless, it is also clear from Table III that when coupled with imputation-based analyses even relatively low-density SNP chips can provide excellent coverage of the genome in populations with LD patterns similar to the CEU, JPT, and CHB. Thus, we expect the main advantages of new higher-density chips will be in the study of populations with less extensive LD, such as the YRI, and in the analysis of rarer variants.
