POPSIM - A GENERAL-POPULATION SIMULATION PROGRAM

Motivation: The investigation of common disorders of polygenic inherit ance using both population-based association designs and non-parametri c linkage analysis within families is gaining increasing importance. W e have created a program that allows for the flexible simulation of po pulations as a tool to investigate the properties of population-based mapping approaches. Results: We have created a population simulation p rogram, POPSIM, that (i) creates a virtual representation of every ind ividual, (ii) makes no prior assumptions but the Mendelian rules and ( iii) allows populations of several million individuals in size to be g enerated and to be followed over hundreds of generations. The paramete rs of the disease model, population structure and population expansion rate can be specified. Flexible sampling options exist that allow sam ples of families and individuals to be drawn at any given point during the population history. The program may be a useful tool in the study of the influence of genetic drift, recombination and admixture on the generation and maintenance of linkage disequilibrium in populations, as well as the evaluation of stochastic sampling characteristics of fa milies and individuals conditional on a complex genetic phenotype from homogeneous and heterogeneous populations.