GMO testing with microarrays

OBJECTIVES:

The goal of this project is to develop guidelines to validate microarrays as a method for detecting GMOs. Appropriate statistical methods are developed to design microarray tests and interpret resulting data.


APPROACH:

A new method based on the use of microarray for the detection of the amplicons produced by PCR was developed allowing the detection and identification of GMOs. This report outlines validation data of the method that was validated in the framework of a European project (Co-Extra project) and with the assistance of the scientific community working on GMOs. The validation was coordinated by the JRC and organised by Eppendorf Array Technologies. The validation study was performed according to international ISO norms with the participation of twelve laboratories having quality assurance systems in place. The goal of the study was to assess the performance of the DualChipĀ® GMO assay as a screening method for EU approved GMOs through a collaborative study. The detection method is commercially available as a detection kit (Eppendorf, Hamburg, Germany). The technology is based on the identification of GMO specific DNA sequences first amplified by PCR, followed by hybridisation on a predefined microarray, labelling, detection, data acquisition and data analysis. The interest of the microarray lies with the possibility to obtain multiple detections within one assay due to the presence of multiple capture probes specific for the different targets. In addition, the microarray is not limited by the number of detection probes. The present method is a qualitative multiple targets detection tool adapted for the screening of multiple GMOs. The validation was preceded by a pre-validation study performed in five laboratories.


SHORT RESULTS:

The overall method performance has been evaluated with respect to the expected method acceptance criteria set before the validation study. All seven criteria were fulfilled, with the main criteria as detection of the different elements at 0.1% concentration of GM and 1% plant with a 95% accuracy rate fully satisfied.

The results obtained during the collaborative trial indicate that the tested microarray can be considered as fit for purposes of screening with respect to its intra and inter laboratory accuracy.

The results demonstrate the validity of the DualChip GMO (Eppendorf, Hamburg, Germany) as an array multiplex approach for the screening of GMO. The results showed that the technology is robust, practical and is suitable as a screening tool.

When performed on samples, the detection of the targeted elements leads to the confirmation of the presence or not of a GM. Moreover, using a matrix of the genetic composition of GM events, the identity of the GM can be proposed as the outcome of the data analysis.

The presently validated array can be extended and updated with the growing number of approved and unapproved GMOs for which a detection method is needed.

The performance of the method was assessed on raw material samples; its applicability can be evaluated on and extended to complex samples.The present work represents, to our knowledge, the first example of inter-laboratory validation of a multiplex assay.


More information:

Prototype multiplex assays developed
This deliverable is a review of the work that has been performed under task T6.1 (development of multiplex screening methods) to identify candidate prototype assay(s) that may be subjected to optimisation and validation.

Compilation of target sequences suitable for inclusion in multiplex GMO screening assays
The purpose of this deliverable is primarily to provide an overview on suitable target sequences and to facilitate the sharing of sequence information and also to initiate relevant discussions and actions that ensure the availability and appropriateness of sequence information.



PARTICIPANTS:

NAME / ORGANISATIONCONTACT INFORMATION
Arne Holst-Jensen
National Veterinary Institute, Norway
Email: info@coextra.eu