title: Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data.
abstract: We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations.
authors.affiliation: Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA. wsieh@u.washington.edu
authors.forename: Weiva
authors.initials: W
authors.lastname: Sieh
authors.forename: Saonli
authors.initials: S
authors.lastname: Basu
authors.forename: Audrey Q
authors.initials: AQ
authors.lastname: Fu
authors.forename: Joseph H
authors.initials: JH
authors.lastname: Rothstein
authors.forename: Paul A
authors.initials: PA
authors.lastname: Scheet
authors.forename: William C L
authors.initials: WC
authors.lastname: Stewart
authors.forename: Yun J
authors.initials: YJ
authors.lastname: Sung
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Thompson
authors.forename: Ellen M
authors.initials: EM
authors.lastname: Wijsman
mesh_terms: D000437:Alcoholism / Q000235:genetics*; D001499:Bayes Theorem; D002874:Chromosome Mapping; D020090:Chromosome Segregation / Q000235:genetics*; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics; D003198:Computer Simulation; D003299:Cooperative Behavior; D030541:Databases, Genetic; D008040:Genetic Linkage; D006801:Humans; D008390:Markov Chains; D018895:Microsatellite Repeats / Q000235:genetics*; D009010:Monte Carlo Method; D019655:Quantitative Trait, Heritable