Much like conducting a meta-analysis, genotype imputation must be conducted with great care. The reference panel (i.e. the 1000 Genomes data or the HapMap project) must contain haplotypes drawn from the same population as the study sample in order to facilitate a proper haplotype match. If a study was conducted using individuals of Asian descent, but only European descent populations are represented in the reference panel, the genotype imputation quality will be poor as there is a lower probability of a haplotype match. Also, the reference allele for each SNP must be identical in both the study sample and the reference panel. Finally, the analysis of imputed genotypes should account for the uncertainty in genotype state generated by the imputation process.
