PedGenie performs single SNP association tests in family study designs. When performing an association analysis using family data, one must account for the fact that individuals within a family are related; hence data are correlated. Standard test statistics are unbiased in families, but the variance of those test statistics are underestimated due to correlations between related individuals, and hence the significance of a test may be overestimated. To overcome this, PedGenie calculates an empirical null distribution to establish the significance of the test and provides an empirical p-value. The simulation procedure uses a genedrop.
Genotypes for individuals in a pedigree are simulated by assigning genotypes (at appropriate population frequencies) to the pedigree founders, and Mendelian inheritance rules are used to segregated these through the pedigree structure. For more than one SNP, a genetic recombination map is used to simulate expected recombinations. PedGenie can analyze dichotomous and quantitative dependent variables. Single study and meta analysis can be performed. PedGenie is available within our umbrella Genie tool.