title: Bayesian linkage analysis of categorical traits for arbitrary pedigree designs.
abstract: BACKGROUND
  Pedigree studies of complex heritable diseases often feature nominal or ordinal phenotypic measurements and missing genetic marker or phenotype data.
  
  
  METHODS
  We have developed a Bayesian method for Linkage analysis of Ordinal and Categorical traits (LOCate) that can analyze complex genealogical structure for family groups and incorporate missing data. LOCate uses a Gibbs sampling approach to assess linkage, incorporating a simulated tempering algorithm for fast mixing. While our treatment is Bayesian, we develop a LOD (log of odds) score estimator for assessing linkage from Gibbs sampling that is highly accurate for simulated data. LOCate is applicable to linkage analysis for ordinal or nominal traits, a versatility which we demonstrate by analyzing simulated data with a nominal trait, on which LOCate outperforms LOT, an existing method which is designed for ordinal traits. We additionally demonstrate our method's versatility by analyzing a candidate locus (D2S1788) for panic disorder in humans, in a dataset with a large amount of missing data, which LOT was unable to handle.
  
  
  CONCLUSIONS
  LOCate's accuracy and applicability to both ordinal and nominal traits will prove useful to researchers interested in mapping loci for categorical traits.
authors.affiliation: Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA. agb36@cornell.edu
authors.forename: Abra
authors.initials: A
authors.lastname: Brisbin
authors.forename: Myrna M
authors.initials: MM
authors.lastname: Weissman
authors.forename: Abby J
authors.initials: AJ
authors.lastname: Fyer
authors.forename: Steven P
authors.initials: SP
authors.lastname: Hamilton
authors.forename: James A
authors.initials: JA
authors.lastname: Knowles
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Jason G
authors.initials: JG
authors.lastname: Mezey
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D008040:Genetic Linkage; D006801:Humans; D008957:Models, Genetic; D010375:Pedigree; D019655:Quantitative Trait, Heritable; D012984:Software