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Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests
Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization metho...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236755/ https://www.ncbi.nlm.nih.gov/pubmed/22174739 http://dx.doi.org/10.1371/journal.pone.0027320 |
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author | Mourad, Raphaël Sinoquet, Christine Dina, Christian Leray, Philippe |
author_facet | Mourad, Raphaël Sinoquet, Christine Dina, Christian Leray, Philippe |
author_sort | Mourad, Raphaël |
collection | PubMed |
description | Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data. |
format | Online Article Text |
id | pubmed-3236755 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32367552011-12-15 Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests Mourad, Raphaël Sinoquet, Christine Dina, Christian Leray, Philippe PLoS One Research Article Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data. Public Library of Science 2011-12-13 /pmc/articles/PMC3236755/ /pubmed/22174739 http://dx.doi.org/10.1371/journal.pone.0027320 Text en Mourad et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Mourad, Raphaël Sinoquet, Christine Dina, Christian Leray, Philippe Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title | Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title_full | Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title_fullStr | Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title_full_unstemmed | Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title_short | Visualization of Pairwise and Multilocus Linkage Disequilibrium Structure Using Latent Forests |
title_sort | visualization of pairwise and multilocus linkage disequilibrium structure using latent forests |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236755/ https://www.ncbi.nlm.nih.gov/pubmed/22174739 http://dx.doi.org/10.1371/journal.pone.0027320 |
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