title: On the use of haplotype phylogeny to detect disease susceptibility loci.
abstract: BACKGROUND
  The cladistic approach proposed by Templeton has been presented as promising for the study of the genetic factors involved in common diseases. This approach allows the joint study of multiple markers within a gene by considering haplotypes and grouping them in nested clades. The idea is to search for clades with an excess of cases as compared to the whole sample and to identify the mutations defining these clades as potential candidate disease susceptibility sites. However, the performance of this approach for the study of the genetic factors involved in complex diseases has never been studied.
  
  
  RESULTS
  In this paper, we propose a new method to perform such a cladistic analysis and we estimate its power through simulations. We show that under models where the susceptibility to the disease is caused by a single genetic variant, the cladistic test is neither really more powerful to detect an association nor really more efficient to localize the susceptibility site than an individual SNP testing. However, when two interacting sites are responsible for the disease, the cladistic analysis greatly improves the probability to find the two susceptibility sites. The impact of the linkage disequilibrium and of the tree characteristics on the efficiency of the cladistic analysis are also discussed. An application on a real data set concerning the CARD15 gene and Crohn disease shows that the method can successfully identify the three variant sites that are involved in the disease susceptibility.
  
  
  CONCLUSIONS
  The use of phylogenies to group haplotypes is especially interesting to pinpoint the sites that are likely to be involved in disease susceptibility among the different markers identified within a gene.
authors.affiliation: Unité de recherche en Génétique Epidémiologique et structure des populations humaines, INSERM U535, Villejuif, France. bardel@vjf.inserm.fr
authors.forename: Claire
authors.initials: C
authors.lastname: Bardel
authors.forename: Vincent
authors.initials: V
authors.lastname: Danjean
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Hugot
authors.forename: Pierre
authors.initials: P
authors.lastname: Darlu
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Génin
mesh_terms: D003424:Crohn Disease / Q000235:genetics; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005820:Genetic Testing / Q000379:methods*; D006239:Haplotypes; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics; D015810:Linkage Disequilibrium; D009154:Mutation; D053473:Nod2 Signaling Adaptor Protein; D010802:Phylogeny; D011110:Polymorphism, Genetic
chemical_list: D005819:Genetic Markers; D047908:Intracellular Signaling Peptides and Proteins; C429018:NOD2 protein, human; D053473:Nod2 Signaling Adaptor Protein