Computing probabilities of homozygosity by descent

A person is autozygous at a locus if the person inherits the same allele tw ice identical by descent along two distinct paths from the same ancestor. A utozygosity is a common cause of recessive diseases in inbred populations. Homozygosity mapping uses this fact to locate the genes that cause recessiv e diseases. The probability of autozygosity can be used to estimate the pro bability of a true positive and of a false positive in homozygosity mapping . Thompson [1994] and Cuo [1997] therefore studied the problem of computing the prior, unconditional (multilocus) probability of autozygosity (MPA). I consider a different quantity: the interval probability of autozygosity ( IPA). The two measures are identical in the single-locus case. IPA has two notable advantages over MPA: 1. IPA does not include the possibility of heterozygous regions between the homozygous markers. 2. IPA can be computed in time that is polynomial in the pedigree size. My polynomial-time algorithm for the single-locus case solves a problem men tioned by Guo. I implemented a program to compute the IPA. The contribution of this work is the application of basic, abstract methods from computer s cience to address a problem in genetics. Genet. Epidemiol. (C) 1999 Wiley-L iss, Inc.