Power of multipoint identity-by-descent methods to detect linkage using variance component models

Multipoint linkage analysis gives increased power over single-point analysis to detect linkage for quantitative trait loci (QTL). Besides increased power, the use of multipoint methods makes it possible to estimate not only the location but also the magnitude of the QTL. Currently, two methods are commonly used for calculating multipoint identity-by-descent (IBD) allele-sharing estimates for pedigrees of moderate sizes. The method of Fulker et al. is based on multiple regression of the IBD status at the observed marker loci, whereas the hidden Markov model approach of Kruglyak and Lander estimates the true inheritance distribution at each chromosomal location. Simulation studies of full sibs and nuclear pedigrees show that the two methods for estimating multipoint IBD scores may give very different estimates for a pair of relatives and that a small increase in power to detect linkage can be obtained by using the hidden Markov model compared with the regression method.