Significance testing for direct identity-by-descent mapping

Direct identity-by-descent mapping is a technique for narrowing down the lo cation of the gene or genes responsible for a given genetic disease to smal l segments of the genome. The technique involves DNA comparisons between pa irs of affected individuals. The data generated are in the form of matching segments of the genome, representing regions likely to be identical-by-des cent (IBD). Regions in the genome over which there are significantly more s egments aligned than is expected by chance are taken as candidate regions f or the disease gene or genes. Due to the complex geometric nature of the da ta, significance testing involves certain mathematical difficulties. We pre sent here a new method for measuring this significance. This method introdu ces a novel stat ist ic and is appropriate whether or not the relationships between the paired individuals are known, We give examples that we have ca lculated implementing this method, including an application to real data.