The maximum of a function of a Markov chain and application to linkage analysis

One method of linkage analysis in humans is based on identity-by-descent of pairs of relatives who share a phenotype of interest (for example, a particular disease). We replace the convenient assumption of continuous specification of regions of identity by descent by the more realistic, although still artificially simple, assumption of data from a discrete set of equally spaced infinitely polymorphic markers. We generalize the continuous time Markov chain analysis of Feingold (1993b) and compare the accuracy of the new approximation with that of the simpler Gaussian approximation of Feingold, Brown and Siegmund (1993) under a variety of assumptions about the composition of the pedigrees to be studied. We also suggest a perturbation of the Gaussian approximation as a compromise to achieve reasonable accuracy with minimal computational effort.