title: Comparison of measures for haplotype similarity.
abstract: Measuring the association of haplotype similarities with phenotype similarities has been used to develop statistical tests of genetic association. Previously, we applied the general approach of Mantel statistics to correlate genetic and phenotype similarity, where genetic similarity was defined by the number of intervals flanked by markers identical by state for pairs of haplotypes. Here we investigated in the case-control study design the effect on power of the Mantel statistics for five different measures of genetic similarity based on haplotypes: 1) the number of shared intervals, 2) the physical length of the shared intervals, 3) the genetic length of the shared intervals in centimorgans, 4) the genetic length of the shared intervals in linkage disequilibrium units (LDU) and 5) Yu's measure that attaches more weight to the sharing of rare than common alleles. With prior knowledge of the answers of Genetic Analysis Workshop 15 Problem 3, we analyzed the simulated data sets in two genomic regions surrounding the disease loci on chromosomes 6 and 18. For the dense map on chromosome 6, all methods showed a very high power of comparable magnitude. For chromosome 18, we observed a power between 19% and 99% at the pointwise 5% significance level using 1000 cases and 1000 controls for all methods except Yu's measure. While it yielded a much lower power, Yu's measure had 80% power around the disease locus.
authors.affiliation: Cancer Epidemiology, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Vivien
authors.initials: V
authors.lastname: Marquard
authors.affiliation: Cancer Epidemiology, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Beckmann
authors.affiliation: Molecular Genetic Epidemiology, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Justo L
authors.initials: JL
authors.lastname: Bermejo
authors.affiliation: Institute of Human Genetics, University of Heidelberg, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany.
authors.forename: Christine
authors.initials: C
authors.lastname: Fischer
authors.affiliation: Cancer Epidemiology, German Cancer Research Center DKFZ, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
authors.forename: Jenny
authors.initials: J
authors.lastname: Chang-Claude