In the replication stages of a multi-stage GWAS, it would be impractical to genotype the entire list of 12,898 SNPs for the correction of PS. In the process of selecting a fixed number of SNPs for the follow-up study that would typically involve 10,000 to 50,000 SNPs, there is always a trade-off between the number of SNPs allocated for population structure inference and the number of candidate disease-associated SNPs chosen for the validation/replication. Recently, Price et al. [32] and Tian et al. [33] identified panels of SNPs that are informative for discerning major European ancestries in European American populations. For example, Price et al. [32] designed a panel of 300 SNPs that aims to distinguish northwest European, southeast European, and Ashkenazi Jewish ancestry. These panels of ancestral informative SNPs are potentially useful in replication studies with a similar anticipated population substructure, but may not be as robust in studies where the population sub-structure may be different or unknown. Rapid accumulation of GWAS and their replication studies should provide ample opportunities for designing and validating panels of ancestral informative markers targeting various stratified or admixed populations.
