Improved IBD detection using incomplete haplotype information

In this paper we describe an improved method for identifying genetic regions shared identical-by-descent (IBD) from recent common ancestors. This method improves existing methods by taking advantage of phase information even if it is less than fully accurate or missing. We present an analysis of how using phase information increases the accuracy of IBD detection compared to using only genotype information.Our algorithm should have utility in a wide range of genetic studies that rely on identification of shared genetic material in large families or small populations.Genetic studies designed to identify the location of loci that influence phenotypes depend on identifying regions of the genome that are shared among different individuals. This is true for both identification of rare, highly penetrant monogenic disease loci via linkage analysis or for common alleles that influence disease susceptibility via linkage disequilibrium as revealed by genome-wide association studies (GWAS). The use of very dense panels of single-nucleotide polymorphisms (SNPs) via microarrays makes direct identification of disease-associated variation possible in some study designs. However, in family-based studies of monogenic or oligogenic phenotypes, causal alleles are expected to have non-trivial penetrance and be relatively rare, thus making identification of disease-associated chromosomal regions a necessary prerequisite for identifying causal variation.There has been tremendous recent progress at both ends of the spectrum for finding disease-influencing variants. There are useful techniques for identifying rare, but highly penetrant, monogenic disorders as well as for uncovering common variation conferring small but reproducibly increased risk. However, the middle ground of variants of moderate risk and moderate frequency is less well explored. Studies in large complex extended families and isolated populations with a high rate of specific phenotypes provide one method for approaching su