To conduct a meta-analysis properly, the effect of the same allele across multiple distinct studies must be assessed. This can prove difficult if different studies use different genotyping platforms (which use different SNP marker sets). As this is often the case, GWAS datasets can be imputed to generate results for a common set of SNPs across all studies. Genotype imputation exploits known LD patterns and haplotype frequencies from the HapMap or 1000 Genomes project to estimate genotypes for SNPs not directly genotyped in the study [50].
