Physical Sciences and Mathematics Commons^™

Association Testing By Haplotype-Sharing Methods Applicable To Whole-Genome Analysis, Ilja M. Nolte, Andre R. De Vries, Geert T. Sijker, Ritsert C. Jansen, Dumitru Brinza, Alexander Zelikovskiy, Gerard J. Te Meerman

Computer Science Faculty Publications

We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS test, which tests whether a case and a control haplotype show less sharing than two random haplotypes. The significance of the HSS is determined using a variance estimate from the theory of U-statistics, whereas the significance of the CROSS test is estimated from a sequential randomization procedure. Both methods are fast and hence practical, even for whole-genome screens with high marker densities. We analyzed data sets of Problems 2 and 3 of …