Other approaches for genotype imputation have been developed independently [Marchini et al., 2007; Servin and Stephens, 2007]. We expect that our results demonstrating the utility of larger reference panels, showing that the three HapMap analysis panels can be combined to better impute genotypes in populations that are genetically distant from the HapMap analysis panels, illustrating the ability of imputation-based approaches to estimate LD between untyped markers, and comparing the relative performance of imputation-based approaches for different commercial marker panels will apply when these alternative approaches for genotype imputation are used. The approaches differ in the precise details of how they search for shared haplotype stretches and also in the efficiency of their computational implementations. For example, whereas [Marchini et al., 2007] rely on recombination rates generated by the HapMap Consortium and assume a uniform mutation/error rate for all markers, we estimate “recombination rates” within each dataset and allow “mutation rates” to vary. These parameters capture not only intrinsic characteristics of the markers and regions being examined, but also—for example—the genetic distance between the samples being imputed and the reference panel
