title: GMOseek: a user friendly tool for optimized GMO testing.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia. dany.morisset@nib.si.
authors.forename: Dany
authors.initials: D
authors.lastname: Morisset
authors.forename: Petra Kralj
authors.initials: PK
authors.lastname: Novak
authors.forename: Darko
authors.initials: D
authors.lastname: Zupanič
authors.forename: Kristina
authors.initials: K
authors.lastname: Gruden
authors.forename: Nada
authors.initials: N
authors.lastname: Lavrač
authors.forename: Jana
authors.initials: J
authors.lastname: Žel
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003657:Decision Making; D007753:Laboratories; D030821:Plants, Genetically Modified; D060888:Real-Time Polymerase Chain Reaction; D012984:Software; D014584:User-Computer Interface
references.citation: Anal Bioanal Chem. 2010 Mar;396(6):2065-72
references.pmid: 19855963
references.citation: Biotechnol Adv. 2009 Nov-Dec;27(6):1071-1082
references.pmid: 19477261
references.citation: Anal Bioanal Chem. 2010 Mar;396(6):2073-89
references.pmid: 19937431
references.citation: Anal Bioanal Chem. 2003 Apr;375(8):985-93
references.pmid: 12733008
references.citation: Anal Bioanal Chem. 2010 Mar;396(6):1991-2002
references.pmid: 19876618
references.citation: J AOAC Int. 2009 Nov-Dec;92(6):1739-46
references.pmid: 20166592
references.citation: Nat Biotechnol. 2010 Jan;28(1):23-5
references.pmid: 20062032
references.citation: Biotechnol Adv. 2012 Nov-Dec;30(6):1318-35
references.pmid: 22333321
references.citation: Anal Biochem. 2008 May 15;376(2):189-99
references.pmid: 18346452
references.citation: BMC Bioinformatics. 2013 Aug 22;14:256
references.pmid: 23965170
references.citation: J Agric Food Chem. 2013 Oct 30;61(43):10293-301
references.pmid: 23971699
references.citation: Anal Bioanal Chem. 2010 Mar;396(6):2113-23
references.pmid: 19960341