Multiple Gene Risk Prediction Performance

This package supports simulations of large groups of independent markers each conferring (multiplicative) risk of disease, where the risk conferred by each genotype is assumed to be known. For each simulation, various summary measures of the performance of the risk prediction algorithm are calculated.

Given an odds ratio, a frequency of the risk allele (in the population) and an overall disease prevalence, a disease likelihood ratio can be calculated (assuming Hardy-Weinberg equilibrium, and that each instance of the risk allele confers the same multiplicative risk).

Genetic profiles can be simulated given the overall frequency of the risk allele for a panel of genes. Assuming a known correct risk model (1) disease states can be simulated and (2) the performance of the panel of genes as a combined marker for risk prediction can be assessed.

The package can be downloaded here.

Documentation on how to use the package is here.

Additionally, Pepe MS, Gu W, Morris DE (2010) has results from the package. The appendix also describes the software.


Pepe MS, Gu W, Morris DE (2010). The Potential of Genes and Other Markers to Inform about Risk. Cancer Epidemiology, Biomarkers and Prevention 19(3):655-665.