ABSTRACT
The models for genetic haplotyping described in Chapters 2 and 3 are based on two critical assumptions. One is that the population chosen to haplotype a complex trait should be at Hardy-Weinberg equilibrium (HWE). As a fundamental assumption in general population genetic studies (Lynch and Walsh, 1998), this allows the diplotype frequency to be expressed as the product of the frequencies of two pairing haplotypes. The second is that one haplotype composed of alleles at multiple SNPs is different from the remaining haplotypes in terms of genetic effects on a trait. This assumption allows the direct use of a traditional biallelic quantitative genetic model (Lynch and Walsh, 1998) and facilitates the definition and estimation of genetic effects triggered by different haplotypes.
