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GMOseek: a user friendly tool for optimized GMO testing

BACKGROUND: With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many o...

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Autores principales: Morisset, Dany, Novak, Petra Kralj, Zupanič, Darko, Gruden, Kristina, Lavrač, Nada, Žel, Jana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138379/
https://www.ncbi.nlm.nih.gov/pubmed/25084968
http://dx.doi.org/10.1186/1471-2105-15-258
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author Morisset, Dany
Novak, Petra Kralj
Zupanič, Darko
Gruden, Kristina
Lavrač, Nada
Žel, Jana
author_facet Morisset, Dany
Novak, Petra Kralj
Zupanič, Darko
Gruden, Kristina
Lavrač, Nada
Žel, Jana
author_sort Morisset, Dany
collection PubMed
description BACKGROUND: With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many of them have already adopted the so called "matrix approach" to rationalize the resources and efforts used to increase their efficiency within a limited budget. Most of the time, the "matrix approach" is implemented using limited information and some proprietary (if any) computational tool to efficiently use the available data. RESULTS: The developed GMOseek software is designed to support decision making in all the phases of routine GMO laboratory testing, including the interpretation of wet-lab results. The tool makes use of a tabulated matrix of GM events and their genetic elements, of the laboratory analysis history and the available information about the sample at hand. The tool uses an optimization approach to suggest the most suited screening assays for the given sample. The practical GMOseek user interface allows the user to customize the search for a cost-efficient combination of screening assays to be employed on a given sample. It further guides the user to select appropriate analyses to determine the presence of individual GM events in the analyzed sample, and it helps taking a final decision regarding the GMO composition in the sample. GMOseek can also be used to evaluate new, previously unused GMO screening targets and to estimate the profitability of developing new GMO screening methods. CONCLUSION: The presented freely available software tool offers the GMO testing laboratories the possibility to select combinations of assays (e.g. quantitative real-time PCR tests) needed for their task, by allowing the expert to express his/her preferences in terms of multiplexing and cost. The utility of GMOseek is exemplified by analyzing selected food, feed and seed samples from a national reference laboratory for GMO testing and by comparing its performance to existing tools which use the matrix approach. GMOseek proves superior when tested on real samples in terms of GMO coverage and cost efficiency of its screening strategies, including its capacity of simple interpretation of the testing results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-258) contains supplementary material, which is available to authorized users.
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spelling pubmed-41383792014-08-21 GMOseek: a user friendly tool for optimized GMO testing Morisset, Dany Novak, Petra Kralj Zupanič, Darko Gruden, Kristina Lavrač, Nada Žel, Jana BMC Bioinformatics Software BACKGROUND: With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many of them have already adopted the so called "matrix approach" to rationalize the resources and efforts used to increase their efficiency within a limited budget. Most of the time, the "matrix approach" is implemented using limited information and some proprietary (if any) computational tool to efficiently use the available data. RESULTS: The developed GMOseek software is designed to support decision making in all the phases of routine GMO laboratory testing, including the interpretation of wet-lab results. The tool makes use of a tabulated matrix of GM events and their genetic elements, of the laboratory analysis history and the available information about the sample at hand. The tool uses an optimization approach to suggest the most suited screening assays for the given sample. The practical GMOseek user interface allows the user to customize the search for a cost-efficient combination of screening assays to be employed on a given sample. It further guides the user to select appropriate analyses to determine the presence of individual GM events in the analyzed sample, and it helps taking a final decision regarding the GMO composition in the sample. GMOseek can also be used to evaluate new, previously unused GMO screening targets and to estimate the profitability of developing new GMO screening methods. CONCLUSION: The presented freely available software tool offers the GMO testing laboratories the possibility to select combinations of assays (e.g. quantitative real-time PCR tests) needed for their task, by allowing the expert to express his/her preferences in terms of multiplexing and cost. The utility of GMOseek is exemplified by analyzing selected food, feed and seed samples from a national reference laboratory for GMO testing and by comparing its performance to existing tools which use the matrix approach. GMOseek proves superior when tested on real samples in terms of GMO coverage and cost efficiency of its screening strategies, including its capacity of simple interpretation of the testing results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-258) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-01 /pmc/articles/PMC4138379/ /pubmed/25084968 http://dx.doi.org/10.1186/1471-2105-15-258 Text en © Morisset et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. 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 credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Morisset, Dany
Novak, Petra Kralj
Zupanič, Darko
Gruden, Kristina
Lavrač, Nada
Žel, Jana
GMOseek: a user friendly tool for optimized GMO testing
title GMOseek: a user friendly tool for optimized GMO testing
title_full GMOseek: a user friendly tool for optimized GMO testing
title_fullStr GMOseek: a user friendly tool for optimized GMO testing
title_full_unstemmed GMOseek: a user friendly tool for optimized GMO testing
title_short GMOseek: a user friendly tool for optimized GMO testing
title_sort gmoseek: a user friendly tool for optimized gmo testing
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138379/
https://www.ncbi.nlm.nih.gov/pubmed/25084968
http://dx.doi.org/10.1186/1471-2105-15-258
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