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

Weiva Sieh; Saonli Basu; Audrey Q. Fu; Joseph H. Rothstein; Paul A. Scheet; William C.L. Stewart; Yun J. Sung; Elizabeth A. Thompson; Ellen M. Wijsman

doi:10.1186/1471-2156-6-S1-S11

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

Weiva Sieh, Saonli Basu, Audrey Q. Fu, Joseph H. Rothstein, Paul A. Scheet, William C.L. Stewart, Yun J. Sung, Elizabeth A. Thompson, Ellen M. Wijsman

Biostatistics

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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.

Original language	English (US)
Article number	S11
Journal	BMC genetics
Volume	6
Issue number	SUPPL.1
DOIs	https://doi.org/10.1186/1471-2156-6-S1-S11
State	Published - Dec 30 2005

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AU - Sieh, Weiva

AU - Basu, Saonli

AU - Fu, Audrey Q.

AU - Rothstein, Joseph H.

AU - Scheet, Paul A.

AU - Stewart, William C.L.

AU - Sung, Yun J.

AU - Thompson, Elizabeth A.

AU - Wijsman, Ellen M.

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Y1 - 2005/12/30

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

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