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

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