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This article is part of the supplement: Genetic Analysis Workshop 14: Microsatellite and single-nucleotide polymorphism

Open Access Proceedings

Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data

Weiva Sieh1, Saonli Basu2, Audrey Q Fu2, Joseph H Rothstein3, Paul A Scheet2, William CL Stewart2, Yun J Sung1, Elizabeth A Thompson23 and Ellen M Wijsman13*

Author Affiliations

1 Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, 98195, USA

2 Department of Statistics, University of Washington, Seattle, Washington, 98195, USA

3 Department of Biostatistics, University of Washington, Seattle, Washington, 98195, USA

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BMC Genetics 2005, 6(Suppl 1):S11  doi:10.1186/1471-2156-6-S1-S11

Published: 30 December 2005


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.