title: A sparse transmission disequilibrium test for haplotypes based on Bradley-Terry graphs.
abstract: BACKGROUND
  Linkage and association analysis based on haplotype transmission disequilibrium can be more informative than single marker analysis. Several works have been proposed in recent years to extend the transmission disequilibrium test (TDT) to haplotypes. Among them, a powerful approach called the evolutionary tree TDT (ET-TDT) incorporates information about the evolutionary relationship among haplotypes using the cladogram of the locus.
  
  
  METHODS
  In this work we extend this approach by taking into consideration the sparsity of causal mutations in the evolutionary history. We first introduce the notion of a Bradley-Terry (BT) graph representation of a haplotype locus. The most important property of the BT graph is that sparsity of the edge set of the graph corresponds to small number of causal mutations in the evolution of the haplotypes. We then propose a method to test the null hypothesis of no linkage and association against sparse alternatives under which a small number of edges on the BT graph have non-nil effects.
  
  
  CONCLUSIONS
  We compare the performance of our approach to that of the ET-TDT through a power study, and show that incorporating sparsity of causal mutations can significantly improve the power of a haplotype-based TDT.
authors.affiliation: Department of Statistical Science, Duke University, Durham, N.C. 27708-0251, USA. li.ma@duke.edu
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
authors.forename: Art B
authors.initials: AB
authors.lastname: Owen
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005787:Gene Frequency; D008040:Genetic Linkage; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic