Minor differences in haplotype frequency estimates can produce very large differences in heterogeneity test statistics

Table 1 Table showing haplotype frequency estimates and likelihood ratio statistics obtained from MLOCUS and GENECOUNTING for polymorphisms around DRD2

Haplotype	MLOCUS			GENECOUNTING
	Cases	Controls	Combined	Cases	Controls	Combined
111111	0.005	0.000	0.011	0.021	0.000	0.012
111112	0.006	0.007	0.007	0.008	0.007	0.008
111121	0.499	0.470	0.480	0.482	0.472	0.479
111221	0.029	0.043	0.034	0.027	0.043	0.033
112111	0.001	0.000	0.002	0.004	0.000	0.002
112112	0.392	0.376	0.385	0.384	0.370	0.379
112121	0.021	0.026	0.021	0.021	0.025	0.023
112122	0.001	0.000	0.000	0.000	0.000	0.000
112221	0.001	0.000	0.001	0.001	0.000	0.001
221112	0.043	0.074	0.055	0.050	0.078	0.061
222112	0.001	0.004	0.003	0.000	0.004	0.002
222212	0.001	0.000	0.001	0.001	0.000	0.000
Log likelihood	-820.072	-573.826	-1458.75	-931.20	-601.13	-1548.8
Likelihood ratio statistic			129.7			33.0
Asymptotic P value assuming 11 df			1.8*10^-15			5.4*10^-4
Empirical P value from permutation test						2.8*10^-4

ISSN: 2730-6844