Our experience with the FUSION GWAS, summarized above, shows that imputation can be an effective way to estimate unobserved genotypes and/or allele counts. These genotypes can then be used in a variety of downstream analyses, including logistic regression analyses for discrete traits and linear regression analyses for quantitative traits, and to facilitate meta-analysis of studies based on different platforms. A key issue when considering imputation-based approaches is whether similarly accurate estimates of unobserved data points can be obtained with different genotyping panels or in different populations [Clark and Li, 2007], and to evaluate this we conducted two additional experiments.
