The expanded reference panel we considered was constituted by controls genotyped on multiple SNP chips, but other kinds of new reference panels will also become available in the near future. For example, the HapMap Project has recently augmented its Phase II data with additional samples from both the original HapMap locations and new locations aimed at capturing more human genetic diversity. These samples have all been genotyped on multiple, largely non-overlapping SNP chips, and could be used for imputation in the same way as the controls in our Scenario B. In addition, the 1,000 Genomes project is currently pursuing whole-genome sequencing of hundreds of individuals sampled from broad geographic regions in Africa, East Asia, and Europe. One aim of the project is to generate high-quality haplotypes for these individuals, including near-complete coverage of SNPs with population MAFs of 1% or more. This resource will increase the utility of imputation approaches by expanding both the number of chromosomes in the reference set and the number of SNPs that can be imputed.
