Relationship estimation can be extended to inbred populations by estimating probabilities of Jacquard’s nine IBD modes instead of three k-coefficients [Jacquard, 1972; Anderson and Weir, 2007; Weir et al., 2006]. The inbreeding coefficient, f, which is the probability that a person carries two alleles IBD at a locus, can also be estimated by maximizing the likelihood using the EM algorithm [Dempster et al., 1977; Thompson, 2000]. In human genetic isolated populations, it is rare to have inbreeding within an individual even though there are higher kinships among individuals [Agarwala et al., 2001].
