Combining the meiosis Gibbs sampler with the random walk approach for linkage and association studies with a general complex pedigree and multimarker loci

A linkage analysis for finding inheritance states and haplotype configurations is an essential process for linkage and association mapping. The linkage analysis is routinely based upon observed pedigree information and marker genotypes for individuals in the pedigree. It is not feasible for exact methods to use all such information for a large complex pedigree especially when there are many missing genotypic data. Proposed Markov chain Monte Carlo approaches such as a single-site Gibbs sampler or the meiosis Gibbs sampler are able to handle a complex pedigree with sparse genotypic data; however, they often have reducibility problems, causing biased estimates. We present a combined method, applying the random walk approach to the reducible sites in the meiosis sampler. Therefore, one can efficiently obtain reliable estimates such as identity-by-descent coefficients between individuals based on inheritance states or haplotype configurations, and a wider range of data can be used for mapping of quantitative trait loci within a reasonable time.