University of Washington - Statistics
Segments of genome inherited from a common ancestor by multiple individuals are said to be identical by descent (IBD). Dense genotyping platforms permit the detection of IBD segments less than 5 centiMorgans long, which arise due to coancestry on the order of dozens of generations ago. Generalizations of classical pedigree-based linkage methods use this inferred IBD and can be applied in situations where pedigree data is incomplete. We present a method for inferring IBD in groups of individuals without pedigrees. The core of the method is a hidden Markov model, motivated by population genetics, for the IBD process on two individuals. This model is intractable for larger groups of individuals, and analyzing pairs independently produces invalid IBD configurations on the group level. We introduce a Monte Carlo method which samples consistent IBD configurations by conditionally sampling pairwise configurations.
The procedure can build on a preexisting IBD configuration, so IBD can be sampled in separate families using standard pedigree methods, then merged into a single analysis.
We also show how to decouple the
haplotype phase of the genotype data from the underlying model, permitting the use of both unphased and (perhaps incompletely) phased data.