epiACO - a method for identifying epistasis based on ant Colony optimization algorithm

Table 1 Details of 5 commonly used benchmark models of 2-SNP epistatic interactions

Models		MAF(a)	MAF(b)	Prevalence	Penetrance function
					Genotypes (SNP A)	Genotypes (SNP B)
					Genotypes (SNP A)	BB	Bb	bb
ME Models	Model 1	0.300	0.200	0.100	AA	0.087	0.087	0.087
					Aa	0.087	0.146	0.190
					aa	0.087	0.190	0.247
	Model 2	0.400	0.400	0.050	AA	0.042	0.042	0.042
					Aa	0.240	0.270	0.420
					aa	0.240	0.440	0.090
NME Models	Model 3	0.500	0.500	0.300	AA	0.470	0.230	0.270
					Aa	0.240	0.270	0.420
					aa	0.240	0.440	0.090
	Model 4	0.400	0.400	0.171	AA	0.068	0.299	0.017
					Aa	0.289	0.044	0.285
					aa	0.048	0.262	0.174
	Model 5	0.500	0.500	0.010	AA	0.000	0.000	0.100
					Aa	0.000	0.050	0.000
					aa	0.100	0.000	0.000

Prevalence is the proportion of samples that occur a disease. Penetrance is the probability of the occurrence of a disease given a particular genotype.MAF(a) is the minor allele frequency of a. AA, Aa, and aa are homozygous common genotype, heterozygous genotype, and homozygous minor genotype

ISSN: 1756-0381