7.5 Imputation

LD also means that we can perform imputation to improve our GWAS discovery power. If we know which variants tend to occur together on the same haplotype, we can infer the presence of variants in an individual even if those SNPs were never sequenced.

In imputation, you:

Genotype individuals using the sequencing data you have (Fig. 4A)
Use a reference panel of haplotypes to fill in variants you didn’t genotype (Fig. 4B)
Perform GWAS

Imputation can discover GWAS signals that were hidden in the original variant set (Fig. 4B vs. Fig. 4F), or further support signals you already found.

Fig. 4 (source). Imputing variants that were not actually sequenced.