title: The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium.
abstract: We study the properties of a modified lod score method for testing linkage that incorporates linkage disequilibrium (LD-lod). By examination of its score statistic, we show that the LD-lod score method adaptively combines two sources of information: (a) the IBD sharing score which is informative for linkage regardless of the existence of LD and (b) the contrast between allele-specific IBD sharing scores which is informative for linkage only in the presence of LD. We also consider the connection between the LD-lod score method and the transmission-disequilibrium test (TDT) for triad data and the mean test for affected sib pair (ASP) data. We show that, for triad data, the recessive LD-lod test is asymptotically equivalent to the TDT; and for ASP data, it is an adaptive combination of the TDT and the ASP mean test. We demonstrate that the LD-lod score method has relatively good statistical efficiency in comparison with the ASP mean test and the TDT for a broad range of LD and the genetic models considered in this report. Therefore, the LD-lod score method is an interesting approach for detecting linkage when the extent of LD is unknown, such as in a genome-wide screen with a dense set of genetic markers.
authors.affiliation: Department of Statistics and Actuarial Science, University of Iowa, Iowa City, Iowa 52242, USA. jian-huang@uiowa.edu
authors.forename: J
authors.initials: J
authors.lastname: Huang
authors.forename: Y
authors.initials: Y
authors.lastname: Jiang
mesh_terms: D008040:Genetic Linkage; D006801:Humans; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D008126:Lod Score; D008957:Models, Genetic; D018401:Sample Size