Imputation (genetics)

In genetics, imputation is the statistical inference of unobserved genotypes.^[1] It is achieved by using known haplotypes in a population, for instance from the HapMap or the 1000 Genomes Project in humans, thereby allowing to test for association between a trait of interest (e.g. a disease) and experimentally untyped genetic variants, but whose genotypes have been statistically inferred ("imputed").^[2] Genotype imputation is usually performed on SNPs, the most common kind of genetic variation.

Genotype imputation hence helps tremendously in narrowing down the location of probably causal variants in genome-wide association studies, because it increases the SNP density (the genome size remains constant, but the number of genetic variants increases) and thus reduces the distance between two adjacent SNPs.