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Selective Phenotyping, Entropy Reduction, and the Mastermind game

BACKGROUND: With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, the...

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Detalles Bibliográficos
Autores principales: Gagneur, Julien, Elze, Markus C, Tresch, Achim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258278/
https://www.ncbi.nlm.nih.gov/pubmed/22014271
http://dx.doi.org/10.1186/1471-2105-12-406
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author Gagneur, Julien
Elze, Markus C
Tresch, Achim
author_facet Gagneur, Julien
Elze, Markus C
Tresch, Achim
author_sort Gagneur, Julien
collection PubMed
description BACKGROUND: With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. RESULTS: Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset. CONCLUSIONS: Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping.
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spelling pubmed-32582782012-01-18 Selective Phenotyping, Entropy Reduction, and the Mastermind game Gagneur, Julien Elze, Markus C Tresch, Achim BMC Bioinformatics Research Article BACKGROUND: With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. RESULTS: Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of previously phenotyped individuals, thereby enabling an efficient incremental strategy. The effective performance of SPARE is demonstrated on simulated data as well as on an experimental yeast dataset. CONCLUSIONS: Using entropy reduction as an objective criterion gives a natural way to tackle both issues of detection and localization simultaneously and to integrate intermediate phenotypic data. We foresee entropy-based strategies as a fruitful research direction for selective phenotyping. BioMed Central 2011-10-20 /pmc/articles/PMC3258278/ /pubmed/22014271 http://dx.doi.org/10.1186/1471-2105-12-406 Text en Copyright ©2011 Gagneur 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 Research Article
Gagneur, Julien
Elze, Markus C
Tresch, Achim
Selective Phenotyping, Entropy Reduction, and the Mastermind game
title Selective Phenotyping, Entropy Reduction, and the Mastermind game
title_full Selective Phenotyping, Entropy Reduction, and the Mastermind game
title_fullStr Selective Phenotyping, Entropy Reduction, and the Mastermind game
title_full_unstemmed Selective Phenotyping, Entropy Reduction, and the Mastermind game
title_short Selective Phenotyping, Entropy Reduction, and the Mastermind game
title_sort selective phenotyping, entropy reduction, and the mastermind game
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3258278/
https://www.ncbi.nlm.nih.gov/pubmed/22014271
http://dx.doi.org/10.1186/1471-2105-12-406
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