A SNP streak model for the identification of genetic regions identical-by-descent

The availability of very dense genetic maps is changing in a fundamental way the methods used to identify the genetic basis of both rare and common inherited traits. The ability to directly compare the genomes of two related individuals and quickly identify those regions that are inherited identical-by-descent (IBD) from a recent common ancestor would be of utility in a wide range of genetic mapping methods. Here, we describe a simple method for using dense SNP maps to identify regions of the genome likely to be inherited IBD by family members. This method is based on identifying obligate recombination events and examining the pattern of distribution of such events along the genetic map. Specifically, we use the length of a consecutive set of biallelic markers that have a high probability of having avoided such obligate recombination events. This ;;SNP streak" is derived from subsets of samples within a pedigree and allows us to make statistical inferences about the ancestry of the region(s) containing stretches of markers with these properties. We show that the use of subsets of more than two samples has the advantage of identifying shorter shared subsegments as significant. This mitigates the effects of errors in SNP calls. We provide specific examples of microarray-based SNP data, using a family with a complex pedigree and with a rare form of inherited kidney disease, to illustrate this approach.