Table 4.

Average computing times (in seconds) over 10 (in the case of gene–gene interactions, 5) applications of the gTDT based on both analytic (or numerical) parameter estimates using log-likelihoods of the form (2) and the conventional iterative fitting procedure as well as score tests based on (2) to the 569,187 autosomal SNPs from the case–parent trio study of the International Cleft Consortium (Beaty et al., 2010), interactions of each of these SNPs with gender, and all 499,500 interactions between two of 1000 randomly selected SNPs (considering a model consisting of one parameter for the interaction term)

	Individual SNPs
	Additive	Dominant	Recessive	MAX
Analytic	525	474	472	690
Score	525	437	435	698
Conventional	43,318	42,740	42,726	128,784
	SNP–Gender Interaction
	Additive	Dominant	Recessive
Analytic	545	455	454
Score	556	465	462
Conventional	51,600	51,834	53,237
	SNP–SNP Interaction
	Additive	Dominant	Recessive
Analytic	–	–	335
Numerical	1,182	497	469
Score	785	324	283
Conventional	126,748	124,753	124,425