Multipoint mapping under genetic interference.

Genetic chiasma interference occurs when one crossover influences the probability of another crossover occurring nearby. While interference is known to occur in humans, it is typically ignored when computing multipoint likelihoods for genetic mapping. This biologically unsound assumption of no interference facilitates the calculation of the likelihoods at the expense of reduced power to accurately construct a genetic map. We have developed a computer program that calculates multipoint likelihoods of three-generation nuclear families while taking interference into account. In our program, interference is modelled by using a map function to convert genetic distances into recombination fractions. We can determine which of several map functions best fits the data by comparing the multipoint likelihoods of the data under each map function. Since the distribution of the difference between likelihoods is unknown, we use a simulation approach to determine the statistical significance of our results. When our program is applied to six loci, D10S34, D10S19, D10S16, D10S14, D10S4, and D10S20, from the CEPH consortium map of chromosome 10, we find significant evidence in favor of positive interference as modelled by the Sturt map function.