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A complete classification of epistatic two-locus models

BACKGROUND: The study of epistasis is of great importance in statistical genetics in fields such as linkage and association analysis and QTL mapping. In an effort to classify the types of epistasis in the case of two biallelic loci Li and Reich listed and described all models in the simplest case of...

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Autores principales: Hallgrímsdóttir, Ingileif B, Yuster, Debbie S
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2289835/
https://www.ncbi.nlm.nih.gov/pubmed/18284682
http://dx.doi.org/10.1186/1471-2156-9-17
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author Hallgrímsdóttir, Ingileif B
Yuster, Debbie S
author_facet Hallgrímsdóttir, Ingileif B
Yuster, Debbie S
author_sort Hallgrímsdóttir, Ingileif B
collection PubMed
description BACKGROUND: The study of epistasis is of great importance in statistical genetics in fields such as linkage and association analysis and QTL mapping. In an effort to classify the types of epistasis in the case of two biallelic loci Li and Reich listed and described all models in the simplest case of 0/1 penetrance values. However, they left open the problem of finding a classification of two-locus models with continuous penetrance values. RESULTS: We provide a complete classification of biallelic two-locus models. In addition to solving the classification problem for dichotomous trait disease models, our results apply to any instance where real numbers are assigned to genotypes, and provide a complete framework for studying epistasis in QTL data. Our approach is geometric and we show that there are 387 distinct types of two-locus models, which can be reduced to 69 when symmetry between loci and alleles is accounted for. The model types are defined by 86 circuits, which are linear combinations of genotype values, each of which measures a fundamental unit of interaction. CONCLUSION: The circuits provide information on epistasis beyond that contained in the additive × additive, additive × dominance, and dominance × dominance interaction terms. We discuss the connection between our classification and standard epistatic models and demonstrate its utility by analyzing a previously published dataset.
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spelling pubmed-22898352008-04-08 A complete classification of epistatic two-locus models Hallgrímsdóttir, Ingileif B Yuster, Debbie S BMC Genet Methodology Article BACKGROUND: The study of epistasis is of great importance in statistical genetics in fields such as linkage and association analysis and QTL mapping. In an effort to classify the types of epistasis in the case of two biallelic loci Li and Reich listed and described all models in the simplest case of 0/1 penetrance values. However, they left open the problem of finding a classification of two-locus models with continuous penetrance values. RESULTS: We provide a complete classification of biallelic two-locus models. In addition to solving the classification problem for dichotomous trait disease models, our results apply to any instance where real numbers are assigned to genotypes, and provide a complete framework for studying epistasis in QTL data. Our approach is geometric and we show that there are 387 distinct types of two-locus models, which can be reduced to 69 when symmetry between loci and alleles is accounted for. The model types are defined by 86 circuits, which are linear combinations of genotype values, each of which measures a fundamental unit of interaction. CONCLUSION: The circuits provide information on epistasis beyond that contained in the additive × additive, additive × dominance, and dominance × dominance interaction terms. We discuss the connection between our classification and standard epistatic models and demonstrate its utility by analyzing a previously published dataset. BioMed Central 2008-02-19 /pmc/articles/PMC2289835/ /pubmed/18284682 http://dx.doi.org/10.1186/1471-2156-9-17 Text en Copyright © 2008 Hallgrímsdóttir and Yuster; 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
Hallgrímsdóttir, Ingileif B
Yuster, Debbie S
A complete classification of epistatic two-locus models
title A complete classification of epistatic two-locus models
title_full A complete classification of epistatic two-locus models
title_fullStr A complete classification of epistatic two-locus models
title_full_unstemmed A complete classification of epistatic two-locus models
title_short A complete classification of epistatic two-locus models
title_sort complete classification of epistatic two-locus models
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2289835/
https://www.ncbi.nlm.nih.gov/pubmed/18284682
http://dx.doi.org/10.1186/1471-2156-9-17
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