TABLE 3.

Type I error rates (percentage) of test statistics F_AB,ad, F_AB,a, and F_HTR of the haplotype trend regression (HTR) method at a 0.05 significance level when two markers A and B are used in the analysis

LD measure			Error Rates
	Sample size	Test case	FAB,ad	FAB,a	FHTR
0	N = 200	Null	4.90	5.22	5.39
Additive	5.09	4.75	4.77
Dominant	4.62	4.87	4.79
Recessive	5.36	5.12	4.81
0.08	N = 200	Null	5.09	5.23	5.55
Additive	4.92	4.74	4.71
Dominant	4.63	4.84	4.71
		Recessive	5.04	5.02	4.94

The total variance is fixed as σ² = 1.0 and the trait allele frequency is taken as q₁ = q₂ = 0.5. The numbers m and n of alleles = 2. The allele frequencies are given by and . Four test cases are considered: null, no major gene effect a = d = 0; additive, additive mode of inheritance a = 1, but no dominant effect d = 0; dominant, dominant mode of inheritance a = d = 1; recessive, recessive mode of inheritance a = 1 and d = –0.5. In each test case, linkage equilibrium is assumed between the QTL Q and the markers A and B; i.e., . No linkage disequilibrium of third order is assumed among markers A and B and the QTL Q; that is, D_AQB = 0.