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A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family
BACKGROUND: Unlike a pedigree initiated with two inbred lines, a full-sib family derived from two outbred parents frequently has many different segregation types of markers whose linkage phases are not known prior to linkage analysis. RESULTS: We formulate a general model of simultaneously estimatin...
Autores principales: | , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2004
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC509239/ https://www.ncbi.nlm.nih.gov/pubmed/15274749 http://dx.doi.org/10.1186/1471-2156-5-20 |
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author | Lu, Qing Cui, Yuehua Wu, Rongling |
author_facet | Lu, Qing Cui, Yuehua Wu, Rongling |
author_sort | Lu, Qing |
collection | PubMed |
description | BACKGROUND: Unlike a pedigree initiated with two inbred lines, a full-sib family derived from two outbred parents frequently has many different segregation types of markers whose linkage phases are not known prior to linkage analysis. RESULTS: We formulate a general model of simultaneously estimating linkage, parental diplotype and gene order through multi-point analysis in a full-sib family. Our model is based on a multinomial mixture model taking into account different diplotypes and gene orders, weighted by their corresponding occurring probabilities. The EM algorithm is implemented to provide the maximum likelihood estimates of the linkage, parental diplotype and gene order over any type of markers. CONCLUSIONS: Through simulation studies, this model is found to be more computationally efficient compared with existing models for linkage mapping. We discuss the extension of the model and its implications for genome mapping in outcrossing species. |
format | Text |
id | pubmed-509239 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2004 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-5092392004-08-12 A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family Lu, Qing Cui, Yuehua Wu, Rongling BMC Genet Methodology Article BACKGROUND: Unlike a pedigree initiated with two inbred lines, a full-sib family derived from two outbred parents frequently has many different segregation types of markers whose linkage phases are not known prior to linkage analysis. RESULTS: We formulate a general model of simultaneously estimating linkage, parental diplotype and gene order through multi-point analysis in a full-sib family. Our model is based on a multinomial mixture model taking into account different diplotypes and gene orders, weighted by their corresponding occurring probabilities. The EM algorithm is implemented to provide the maximum likelihood estimates of the linkage, parental diplotype and gene order over any type of markers. CONCLUSIONS: Through simulation studies, this model is found to be more computationally efficient compared with existing models for linkage mapping. We discuss the extension of the model and its implications for genome mapping in outcrossing species. BioMed Central 2004-07-26 /pmc/articles/PMC509239/ /pubmed/15274749 http://dx.doi.org/10.1186/1471-2156-5-20 Text en Copyright © 2004 Lu 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 | Methodology Article Lu, Qing Cui, Yuehua Wu, Rongling A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title | A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title_full | A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title_fullStr | A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title_full_unstemmed | A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title_short | A multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
title_sort | multilocus likelihood approach to joint modeling of linkage, parental diplotype and gene order in a full-sib family |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC509239/ https://www.ncbi.nlm.nih.gov/pubmed/15274749 http://dx.doi.org/10.1186/1471-2156-5-20 |
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