Chromosome-based method for rapid computer simulation in human genetic linkage analysis

Computer-based simulation has been an important method in human linkage analysis for a long time. Typically, such analyses have been performed by simulating a set of linked markers according to the intermarker recombination fractions, under the assumption of no genetic interference. A novel approach is proposed in which such simulations can be performed using chromosome-based methods, rather than traditional recombination fraction-based methods. We propose simulating pedigree data using a crossover formation (CF) process to generate the number of crossovers and their locations in Morgans along the entire length of a chromosome. By this method, one can generate simulated multilocus data for any number of loci on a chromosome much more efficiently than with the currently available methods like those used in the SLINK or SIMLINK programs. Further, interference can be incorporated directly in this method, which is not possible with existing packages.