Bayes estimates of haplotype effects

We describe a Markov chain Monte Carlo implementation of a Bayesian approac h to estimating associations of a trait with a large set of haplotypes rece ntly introduced by Clayton and Jones [Am J Hum Genet 65:1161-9, 2000]. The model uses the length of the longest segment in common between any two hapl otypes to define the prior correlation structure for the set of haplotype e ffects, using an intrinsic autocorrelation model. When applied to the Genet ic Analysis Workshop 12 data for trait Q1, we found highly significant vari ation between haplotypes, using either a structured or unstructured covaria nce matrix. (C) 2001 Wiley-Liss, Inc.