Comparison of information-theoretic to statistical methods for gene-gene interactions in the presence of genetic heterogeneity

Table 1 Overview of simulation sets used to test power to detect GGI and type I error.

Model	Sample size	Number of SNPs	Number of Interactions	MAF	K _p	h ²
Set 1A: Comparison of KWII to MDR^a
1-GH			2	0.5	0.05	0.013
2-GH					0.025
3-GH	400	10	2	0.25	0.06	0.007
3			1			0.03
4-GH			2	0.1	0.025	0.003
4			1			0.012
Set 1B: Comparison of KWII to RPM ^b
5A					0.3	0.62
5B						0.3
5C						0.15
6A					0.1	0.22
6B	200	7	1	0.5		0.11
6C						0.056
7A					0.01	0.02
7B						0.01
7C						0.005
Set 2: Comparison of KWII to MDR, RPM, and Logistic Regression Approaches ^c
1-GH and 7C	600, 1200 & 2400	10	3	0.5	0.037	0.013
Set 3: GAW15 Problem 2 ^d
1-GH	2400	865	2	0.5	0.05	0.013
2-GH					0.025
3-GH		865	2	0.25	0.06	0.007
3			1			0.03
4-GH		865	2	0.1	0.025	0.003
4			1			0.012

GH: Genetic Heterogenity; K_p = population prevalence; h² = Broad sense heritability;
^a Penetrance is modeled as in Table 2 [16]
^b Penetrance is modeled as in Table 3 [2]
^c Kp values for Interactions 1 and 2 are each 0.05 (penetrance table from Model 1-GH from [16]) and for interaction 3 Kp is 0.01 (penetrance table from Model 7C from [2])
^d[27]

ISSN: 1471-2164