Estimation of conditional multilocus gene identity among relatives

resolution of the genetic factors affecting complex traits. These include analysis with multipoint methods, use of extended pedigrees, and selective sampling of pedigrees. By sampling the affected individuals in an extended pedigree, we obtain individuals who have an increased probability of sharing genes identical by descent (IBD) at marker loci that are linked to the trait locus or loci. Given marker data on specified members of a pedigree, the conditional IBD status among relatives can be assessed, but exact computation is often impractical for multiple linked markers on complex pedigrees. The use of Markov chain Monte Carlo (MCMC) methods greatly extends the range of models and data sets for which analysis is computationally feasible. Many forms of MCMC have now been implemented in the context of genetic analysis. Here we propose a new sampler, which takes as latent variables the segregation indicators at marker loci, and jointly updates all indicators corresponding to a given meiosis. The sampler has good mixing properties. Questions of irreducibility are also addressed.