Multiple factors will impact power of imputation-based strategies for the analysis of GWA studies, including differences in the patterns of LD and allele frequencies between the study and reference popOulations. However, for the single-marker analyses examined in our study, the impact of these factors can be measured via their effect on imputation accuracy, since the missing (unmeasured) genotypes are the quantities of interest for analysis. Different imputation algorithms will lead to slightly differential accuracies. However, our aim here was not to compare these accuracies but to condition on the sorts of accuracies that might be expected from typical marker densities and patterns of LD.
