Samples from the HapMap project have been genotyped for a very large number of SNPs. Under the assumption that these samples (e.g., the northern European subset) are comparable to members of a case-control collection, the combination of these datasets can be used to estimate (impute) genotypes in the case-control collection by treating it as a missing data problem. Thus, it is possible to increase the number of available genotypes from, for example, 500,000 directly assessed SNPs to 2 million directly genotyped and imputed SNPs. A major use of imputation is to allow direct comparison of case-control studies that were genotyped using different GWAS platforms. For many of the Affymetrix and Illumina platforms, the number of SNPs directly genotyped on both platforms is < 20%. Imputation is often an essential precursor for meta-analysis.
