Imputation (genetics)

Imputation in genetics refers to the statistical inference of unobserved genotypes. 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"). 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.