A Monte Carlo approach to calculating probabilities for continuous identity by descent data

Abstract

Two related individuals are identical by descent at a genetic locus if they share the same gene copy at that locus due to inheritance from a recent common ancestor. We consider idealized continuous identity by descent (IBD) data in which IBD status is known continuously along chromosomes. IBD data contains information about the relationship between the two individuals, and about the underlying crossover processes. We present a Monte Carlo method for calculating probabilities for IBD data. The method is not restricted to Haldane's Poisson process model of crossing-over but may be used with other models including the chi-square, Kosambi renewal and Sturt models. Results of a simulation study demonstrate that IBD data can be used to distinguish between alternative models for the crossover process.