Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data.
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.
Sieh
Weiva
W
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA. wsieh@u.washington.edu
Basu
Saonli
S
Fu
Audrey Q
AQ
Rothstein
Joseph H
JH
Scheet
Paul A
PA
Stewart
William C L
WC
Sung
Yun J
YJ
Thompson
Elizabeth A
EA
Wijsman
Ellen M
EM
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