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

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 Thompson^2,3 and Ellen M Wijsman^1,3

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

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

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

author email corresponding author email

BMC Genetics 2005, 6(Suppl 1):S11doi:10.1186/1471-2156-6-S1-S11

Published:	30 December 2005

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.