Combining two markov chain monte carlo approaches for linkage and association studies with a complex pedigree and multi marker loci

In QTL mapping using linkage and/or linkage disequilibrium, an important process is to find the pattern of inheritance states and haplotype configurations, a process known as haplotype reconstruction. Haplotype reconstruction is routinely based upon observed pedigree information and marker genotypes for individuals in the pedigree. It is not feasible for the exact methods to use all such information for large complex pedigree especially when there are many missing genotypes. Markov Chain Monte Carlo (MCMC) approaches have been widely used to handle a complex pedigree with sparse genotypic data. However they often have reducibility problems or are slow to converge. Combining two different MCMC approaches results in improvement of computational speed and mixing properties. It allows obtaining reliable estimates such as identity by descent coefficients between individuals within a reasonable time.