Title: Analytes and Related PCR Primers Used for GMO Detection and Quantification
Publisher: OPOCE
Publication Year: 2007
JRC N°: JRC37001
ISBN: 978-92-79-08006-7
ISSN: 1018-5593
Other Identifiers: EUR 23059 EN
URI: http://publications.jrc.ec.europa.eu/repository/handle/JRC37001
DOI: 10.2788/5861
Type: EUR - Scientific and Technical Research Reports
Abstract: This document provides the first general overview on PCR primers used by Member State control laboratories for the detection, identification and quantification of GMOs. The data has been collected from a survey launched in 2005. The survey aimed at reviewing the PCR primers used by ENGL members for control purposes and at gathering analytical details on the corresponding PCR procedures. It further aimed to provide a catalogue of DNA sequences as a basis for the future development of plasmid standards. Participants to the survey were specifically requested to provide information on the genetic targets and if relevant, the GM event for which the primers were designed, to include the sequences of primers and the purpose (qualitative/quantitative and screening/identification analysis), type (i.e. single, multiplex, competitive, double-competitive, simplex real-time or multiplex real-time) and specificity (gene-specificity, construct specificity or event-specificity) of the corresponding PCR assay. They were further requested to provide comments and references, as well as to specify the confidentiality status of data provided. As a quality control step, the collated information was checked against the corresponding data published in the GMOs methods database (<http://bgmo.jrc.ec.europa.eu/home/ict/methodsdatabase.htm), in literature or on the CRL web site (<http://gmo-crl.jrc.it) and further edited and normalised. The survey has provided a very large amount of interconnected data. To streamline the consultation of the report, the results of the survey have been grouped in two sections according to the scope of the PCR analysis namely, GMO-specific, and Taxon-specific applications. The GMO section covers primers that are specific for transgene sequences while the Taxon section covers PCR primers that are specific for endogenous genes. The results of the survey have been further grouped according to the purpose of the PCR assay (qualitative/quantitative and screening/identification analysis) and its corresponding specificity. The data obtained from the survey was first analysed to verify representativeness of the results and identify general trends. The analysis revealed that the data set was representative since 55% of the ENGL laboratories participated. Furthermore, the participants were geographically widely distributed across the Member States. The analysis also evaluated general trends such as the frequency by which published and/or validated PCR primers were used by member laboratories and the frequency by which GM events or genetic elements were targeted in the PCR assays. The general overview revealed that 83% of the primers used by laboratories were published in peer-reviewed articles. Custom-designed primers or commercially available kits were rarely reported. The survey data further indicated that 44% of primers were used for detecting common transgenic elements and endogenous genes while the other primers were predominantly employed for identification of authorised GMO. The general overview also revealed that 46% of reported primers had been tested in collaborative studies. Further data analyses were performed on the sets of primers defined by the participating laboratories for a particular scope, purpose and specificity of the PCR assay. Strikingly, these analyses revealed a great variability of primers selection for GMOs control purposes. In general, however, a single primer pair was reported by more than 30% of the ENGL members while there was a wide distribution of primer utilisation in the remaining laboratories. The primer pairs most commonly employed were construct-specific, while for quantitative identification, ENGL laboratories tended to use primers that were event-specific. In approximately 30% of cases, primers designed for quantitative determination were also utilised for qualitative analysis.
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