Initially, many approaches implicitly imputed missing genotypes based on the potential genotype distribution in a family [56]–[58]. In practice, the genetic linkage implied that family members share a certain degree of similarity through their “identical-by-descent” (IBD) regions on the chromosomes. In this way, genotypes of the non-typed markers for these family members can be inferred according to their shared IBD with the other relatives. Figure 1 illustrates the procedure of this genotype inference. As shown in the figure, a subset of microsatellite markers has been typed for all the family members except the founders (red), whereas both microsatellite and SNP markers have been typed in only a few selected common individuals (black). Genotypes of the dense SNPs for missing individuals can be inferred by comparing the haplotypes that are IBD with the other individuals in the family. Several studies have been published on the genotype imputation procedures described above [59], [60]. These procedures are implemented in programs such as MERLIN [55], [61] and MENDEL [62], [63], using one of the pedigree analysis algorithms such as the Lander-Green [64] or Elston-Stewart
