SNP imputation procedures use haplotype information on genotyped SNPs in the study population and predict untyped SNPs based on linkage disequilibrium (LD) patterns between SNPs, as estimated from reference panels of much denser genotyping, usually from HapMap (Altshuler et al. 2010) and more recently the 1000 Genomes project (Durbin et al. 2010). See Marchini and Howie for a review of this literature (Marchini and Howie 2010).
