The gamete competition model is a likelihood version of the transmission disequilibrium test (TDT)
that is inspired by conditional logistic regression and the Bradley–Terry ranking procedure. In
family-based association studies, both the TDT and the gamete competition model apply directly to
data on a single nucleotide polymorphism (SNP). Because any given SNP has limited polymorphism,
it is tempting to collect several SNPs within a gene into a single super marker whose alleles are
haplotypes. Unfortunately, this tactic wreaks havoc with the traditional TDT, which requires
codominant markers (Spielman et al. 1993; Terwilliger & Ott, 1992). Eliminating phase ambiguities
by assigning haplotypes to individuals before conducting the TDT may give misleading results
because only the most probable haplotypes are then considered. Because pedigree implementations
of the gamete competition model can accommodate dominant as well as codominant markers,
they circumvent the phase problem by including all possible phases weighted by their estimated
frequencies.