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Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops

Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However...

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Autores principales: Fernández, Soledad A, Fernando, Rohan L, Guldbrandtsen, Bernt, Stricker, Christian, Schelling, Matthias, Carriquiry, Alicia L
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2002
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705433/
https://www.ncbi.nlm.nih.gov/pubmed/12427385
http://dx.doi.org/10.1186/1297-9686-34-5-537
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author Fernández, Soledad A
Fernando, Rohan L
Guldbrandtsen, Bernt
Stricker, Christian
Schelling, Matthias
Carriquiry, Alicia L
author_facet Fernández, Soledad A
Fernando, Rohan L
Guldbrandtsen, Bernt
Stricker, Christian
Schelling, Matthias
Carriquiry, Alicia L
author_sort Fernández, Soledad A
collection PubMed
description Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. Joint sampling of genotypes has been proposed as a strategy to overcome these problems. An algorithm that combines the Elston-Stewart algorithm and iterative peeling (ESIP sampler) to sample genotypes jointly from the entire pedigree is used in this study. Here, it is shown that the ESIP sampler yields an irreducible Markov chain, regardless of the number of alleles at a locus. Further, results obtained by ESIP sampler are compared with other methods in the literature. Of the methods that are guaranteed to be irreducible, ESIP was the most efficient.
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spelling pubmed-27054332009-07-03 Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops Fernández, Soledad A Fernando, Rohan L Guldbrandtsen, Bernt Stricker, Christian Schelling, Matthias Carriquiry, Alicia L Genet Sel Evol Research Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. Joint sampling of genotypes has been proposed as a strategy to overcome these problems. An algorithm that combines the Elston-Stewart algorithm and iterative peeling (ESIP sampler) to sample genotypes jointly from the entire pedigree is used in this study. Here, it is shown that the ESIP sampler yields an irreducible Markov chain, regardless of the number of alleles at a locus. Further, results obtained by ESIP sampler are compared with other methods in the literature. Of the methods that are guaranteed to be irreducible, ESIP was the most efficient. BioMed Central 2002-09-15 /pmc/articles/PMC2705433/ /pubmed/12427385 http://dx.doi.org/10.1186/1297-9686-34-5-537 Text en Copyright © 2002 INRA, EDP Sciences
spellingShingle Research
Fernández, Soledad A
Fernando, Rohan L
Guldbrandtsen, Bernt
Stricker, Christian
Schelling, Matthias
Carriquiry, Alicia L
Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title_full Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title_fullStr Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title_full_unstemmed Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title_short Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops
title_sort irreducibility and efficiency of esip to sample marker genotypes in large pedigrees with loops
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705433/
https://www.ncbi.nlm.nih.gov/pubmed/12427385
http://dx.doi.org/10.1186/1297-9686-34-5-537
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