ABSTRACT
The association between haplotype diversity and phenotypic variation has been detected by several pharmacogenetic studies (Judson et al., 2000; Bader, 2001; Rha et al., 2007) and will shape our recognition of the genetic control of drug response. However, since haplotypes (comprising diplotypes) cannot be directly observed, the effects of different haplotypes on the phenotype need be postulated from observed zygotic genotypes. The inference of diplotypes for a particular genotype is statistically a missing data problem that can be formulated by a finite mixture model. Liu et al. (2004) proposed a statistical model for estimating and testing haplotype effects at a QTN in a random sample drawn from a natural population. This model is based on the population genetic properties of gene segregation. Through the implementation of the EM algorithm, population genetic parameters of SNPs, such as haplotype frequencies, allele frequencies, and linkage disequilibria, and quantitative genetic parameters, such as haplotype effects of a QTN, are estimated with closed forms.
