JRC GMO-Amplicons, a collection of nucleic acid sequences related to genetically modified organisms

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 unauthorised GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hardly associable 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 of GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed of the European Commission (EU-RL GMFF) provides these methods in the GMOMETHODS database for supporting 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 of 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 may assist the laboratories in the analysis of complex issues, such as detection and identification of unauthorised GMOs. Notably, the JRC GMO-Amplicons database may allow the retrieval and characterisation of GMO-related sequences also included in patents documentation. Finally, it could 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 EURL-GMFF web-site.

PETRILLO Mauro;  ANGERS Alexandre;  HENRIKSSON Peter;  BONFINI Laura;  PATAK DENNSTEDT Alexandre;  KREYSA Joachim; 

2015-10-19

OXFORD UNIV PRESS

JRC96087

1758-0463,   

http://database.oxfordjournals.org/content/2015/bav101,    https://publications.jrc.ec.europa.eu/repository/handle/JRC96087,   

10.1093/database/bav101,