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 geneti...

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Autores principales: Sieh, Weiva, Basu, Saonli, Fu, Audrey Q, Rothstein, Joseph H, Scheet, Paul A, Stewart, William CL, Sung, Yun J, Thompson, Elizabeth A, Wijsman, Ellen M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Proceedings
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866829/
https://www.ncbi.nlm.nih.gov/pubmed/16451566
http://dx.doi.org/10.1186/1471-2156-6-S1-S11
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author Sieh, Weiva
Basu, Saonli
Fu, Audrey Q
Rothstein, Joseph H
Scheet, Paul A
Stewart, William CL
Sung, Yun J
Thompson, Elizabeth A
Wijsman, Ellen M
author_facet Sieh, Weiva
Basu, Saonli
Fu, Audrey Q
Rothstein, Joseph H
Scheet, Paul A
Stewart, William CL
Sung, Yun J
Thompson, Elizabeth A
Wijsman, Ellen M
author_sort Sieh, Weiva
collection PubMed
description 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.
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spelling pubmed-18668292007-05-11 Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data Sieh, Weiva Basu, Saonli Fu, Audrey Q Rothstein, Joseph H Scheet, Paul A Stewart, William CL Sung, Yun J Thompson, Elizabeth A Wijsman, Ellen M BMC Genet Proceedings 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. BioMed Central 2005-12-30 /pmc/articles/PMC1866829/ /pubmed/16451566 http://dx.doi.org/10.1186/1471-2156-6-S1-S11 Text en Copyright © 2005 Sieh et al; licensee BioMed Central Ltd http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Sieh, Weiva
Basu, Saonli
Fu, Audrey Q
Rothstein, Joseph H
Scheet, Paul A
Stewart, William CL
Sung, Yun J
Thompson, Elizabeth A
Wijsman, Ellen M
Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title_full Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title_fullStr Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title_full_unstemmed Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title_short Comparison of marker types and map assumptions using Markov chain Monte Carlo-based linkage analysis of COGA data
title_sort comparison of marker types and map assumptions using markov chain monte carlo-based linkage analysis of coga data
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866829/
https://www.ncbi.nlm.nih.gov/pubmed/16451566
http://dx.doi.org/10.1186/1471-2156-6-S1-S11
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