Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Database

The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants

Annette Block1, Frédéric Debode2*, Lutz Grohmann3, Julie Hulin2, Isabel Taverniers4, Linda Kluga5, Elodie Barbau-Piednoir6, Sylvia Broeders6, Ingrid Huber1, Marc Van den Bulcke56, Petra Heinze3, Gilbert Berben2, Ulrich Busch1, Nancy Roosens6, Eric Janssen2, Jana Žel7, Kristina Gruden7 and Dany Morisset7

Author Affiliations

1 Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany

2 Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium

3 Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany

4 Institute for Agricultural and Fisheries Research (EV ILVO), Merelbeke, Belgium

5 European Commission, Directorate General Joint Research Centre, Institute for Health and Consumer Protection (EC JRC-IHCP), Ispra, Italy

6 Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium

7 National Institute of Biology (NIB), Ljubljana, Slovenia

For all author emails, please log on.

BMC Bioinformatics 2013, 14:256  doi:10.1186/1471-2105-14-256

Published: 22 August 2013

Abstract

Background

Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs’ molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information.

Description

The GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available.

Conclusions

The GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms.

Keywords:
Genetically modified organism (GMO); GMO screening; Matrix approach; Genetically modified plant