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Table 1 The epidemiologic parameters that were used for the sample simulation

From: Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2

Task Required parameters Description
1) Starting data (Hap Map) Chromosomes, or chromosome regions, or markers and marker distance. The genomic regions containing the loci that will be simulated
  Population (ethnicity) The starting frequency and linkage data to be used in the sumulation
2) Simulation of sample’s genetic data DPLs (Disease Predisposing Loci) Loci that will influence the disease risk.
  Target allelic frequency Final allelic frequencies at the end of simuPOP simulation
  Final sample size Number of individuals that compose the population by simuPOP
Starting sample simuPOP generated sample Sample data generated with simuPOP
  Disease prevalence The expected disease prevalence in the whole sample
Environment Environmental factor distribution Distribution of the environmental exposure in the whole sample
  Environmental factor OR Odds ratio associated with one-unit-increase of the environmental exposure
  Noisy Environmental variables As many as desired confounding environmental exposures not associated with the disease risk (gaussian, binomial or uniform distributed)
Genetics DPLs These are the same DPLs as selected in the simuPOP simulation
  High risk alleles The allele, for each DPL, associated with the highest disease risk
  DPLs genotypic RR The relative risk of the high risk homozygote versus low risk homozygote, for each DPL
  Dominance The relationship of the risk associated with the heterozygote with that associated with the homozygotes (recessive, dominant, codominant)
  Epistasis model (G×G) Percent increase of the risk associated with each combined genotype
Gene Environment interaction G×E model One of the four predefined interaction models