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MCMC IN THE ANALYSIS OF GENETIC DATA ON PEDIGREES

This chapter provides a tutorial introduction to the use of MCMC in the analysis of data observed for multiple genetic loci on members of extended pedigrees in which there are many missing data. We introduce the specification of pedigrees and inheritance, and the structure of genetic models defining the dependence structure of data. We review exact computational algorithms which can provide a partial solution, and can be used to improve MCMC sampling of inheritance patterns. Realization of inheritance patterns can be used in several ways. Here, we focus on the estimation of multilocus linkage lod scores for the location of a locus affecting a disease trait relative to a known map of genetic marker loci.