title: JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.
abstract: The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/.
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy mauro.petrillo@ec.europa.eu.
authors.forename: Mauro
authors.initials: M
authors.lastname: Petrillo
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Angers-Loustau
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
authors.forename: Peter
authors.initials: P
authors.lastname: Henriksson
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Bonfini
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
authors.forename: Alex
authors.initials: A
authors.lastname: Patak
authors.affiliation: Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
authors.forename: Joachim
authors.initials: J
authors.lastname: Kreysa
mesh_terms: D004247:DNA; D030561:Databases, Nucleic Acid; D030841:Food, Genetically Modified; D058977:Molecular Sequence Annotation; D030781:Organisms, Genetically Modified / Q000235:genetics*; D016133:Polymerase Chain Reaction
chemical_list: D004247:DNA