Petrillo Mauro, Angers-Loustau Alexandre, Henriksson Peter, Bonfini Laura, Patak Alex, Kreysa Joachim
Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy
Molecular Biology and Genomics Unit, Joint Research Centre, European Commission, Ispra, Italy.
Database (Oxford). 2015 Sep 30;2015. doi: 10.1093/database/bav101. Print 2015.
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/.
DNA目标序列是设计转基因生物（GMO）检测方法的关键要素。遗憾的是，此类信息常常缺失，尤其是对于未经授权的转基因生物。此外，专利序列通常注释不佳，深藏于复杂繁多的文档中，难以与相应的转基因事件相关联。在此，我们推出了JRC转基因生物扩增子数据库，该数据库通过利用转基因生物分析的参考方法进行计算机模拟PCR扩增，对公共核苷酸序列数据库进行筛选，从而收集扩增子。欧盟转基因食品和饲料参考实验室（EU-RL GMFF）在GMOMETHODS数据库中提供了这些方法，以支持欧盟法规的执行和转基因食品/饲料的管控。JRC转基因生物扩增子数据库由超过24万个扩增子组成，可通过网络界面轻松访问和筛选。据我们所知，这是首次尝试汇总和收集与食品和饲料中转基因生物相关的公开可用序列。JRC转基因生物扩增子数据库为检测实验室在转基因生物方法的设计和评估方面提供支持，尤其提供引物特异性的计算机模拟预测和转基因目标覆盖率。这个新工具可协助实验室分析复杂问题，如未经授权的转基因生物的检测和鉴定。值得注意的是，JRC转基因生物扩增子数据库允许检索和表征专利文件中包含的与转基因生物相关的序列。最后，它有助于注释描述欠佳的转基因序列，并在公共数据库中识别新的相关转基因生物相关序列。可通过欧盟转基因食品和饲料参考实验室网站上托管的基于网络的门户免费访问JRC转基因生物扩增子数据库。数据库网址：http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/
