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Opening of the discussion: Overview of available Databases [#5602]
Dear Forum Participants,

Welcome to the second round of discussions of the Network of laboratories for the Detection and Identification of LMOs. This discussion will focus on the topic of compiling an "Overview of available databases for methods and sequence information".

An essential component for the successful detection and identification of LMOs using DNA based technologies is the availability of up-to-date accurate and reliable databases of LMO sequence information and databases containing reference methods for LMO analysis to facilitate the screening process within laboratories. Furthermore, the availability of LMO matrices for comparing and interpreting PCR data will facilitate the establishment of the identity of potential LMOs that may be present in a sample.

In this forum, participants are invited to share information on sources to access relevant information on genetic element sequences, reference detection methods or LMO screening matrices with the view to create, through the BCH, a pool of information on existing or developing LMOs, including regionally specific LMOs, and their respective sequence information that is easily accessible for the benefit of LMO detection and identification laboratories that may encounter these LMOs during their routine monitoring and screening processes.

We are looking forward to an enthusiastic discussion.
Dina
posted on 2014-01-20 00:25 UTC by Dina Abdelhakim, SCBD
This is a reply to 5602 RE: Opening of the discussion: Overview of available Databases [#5609]
Dear Forum Participants,

As mentioned in the introduction to this topic, there are several databases of methods for LM crops such as the “EU Database of Reference Methods for GMO Analysis” (http://gmo-crl.jrc.ec.europa.eu/gmomethods) which is maintained by the Joint Research Center of the European Commission and the “GMO Detection Method Database” (http://gmdd.shgmo.org/) which is maintained by the GMO Detection Laboratory at Shanghai Jiao Tong University.

In addition to these there are several publications that describe programs for screening matrices that can be used in the routine testing of GMO laboratories as needed.

These include, amongst others, "GMOtrack: Generator of Cost-Effective GMO Testing Strategies" (http://kt.ijs.si/software/GMOtrack/). This program generates cost-effective testing strategies for traceability of LMOs and computes the optimal set of screening assays for a two-phase testing strategy.

Additionally there is also "The GMOseek matrix a decision support tool for optimizing the detection of genetically modified plants" (http://kt.ijs.si/software/GMOtrack/GMOseek.html). The program is designed to assist in selecting the optimal combination of screening methods and interpreting the data from screening and event-specific testing.

Are there other databases that are commonly used in your laboratories? Are you familiar with databases that include regionally specific crops?

We encourage you to share additional information with the forum to work towards building a comprehensive set of technical tools for the detection of unauthorized LMOs.

Best regards,
Dina
posted on 2014-02-04 17:02 UTC by Dina Abdelhakim, SCBD
This is a reply to 5609 RE: Opening of the discussion: Overview of available Databases [#5729]
Dear colleagues,

due to the fact that the number of GMOs is increasing steadily, screening of samples under investigation is an important issue. This is usually done with element and construct-specific PCR methods for the detection of e.g. p35S, tnos, bar, pat, epsps, pnos-nptII and many others. As a result of combined screening analysis a profile of detected and non-detected elements and constructs is obtained. In order to support analysts in interpretation of such profiles an Access-based database and interpretation tool called the GMOfinder was developed in our institute. Its structure and different features have been published (Gerdes L., Busch U., Pecoraro S., 2012. GMOfinder—A GMO Screening Database. Food Anal. Methods (2012) 5:1368–1376). Selected features of the GMOfinder are:
• MS Access database for method-based collection and user-friendly interpretation of information related to the screening for GMOs.
• A main application is the interpretation of PCR screening results to systematically find candidates for subsequent identification analysis.
• Contains 350 GMO events from 29 plant species (April 2014, see attached figure).
• The underlying idea is the matrix-approach where each GMO is assigned to its specific profile of detectable and non-detectable genetic elements and constructs (see also: http://gmo-crl.jrc.ec.europa.eu/doc/2011-12-12%20ENGL%20UGM%20WG%20Publication.pdf).
• The tabular matrix can be used for external queries in other laboratories.
• The tabular matrix data in the GMOfinder is protected from unintended modifications or deletions.
• Optional display of events with potentially masked genetic elements (mixed profiles due to more than one GMO in a sample).
• Easy incorporation of further information on GMO events when available
• Results tagged with an explanatory comment if experimental findings in contradiction with theoretical information.
• False positive results due to infection with the naturally occurring plant pathogens CaMV and Agrobacterium are taken into account
• Documentation of information sources: as free text and weighed numerically by their reliability; experimental proof ranking higher than theoretical conclusions.
• Additionally, datasets can be semi-automatically exported to MS Word to record the changes over time which helps to integrate the GMOfinder into the QM system.
• Missing information on the presence or absence of a genetic element in a given GMO is denoted as such and considered by the algorithms during analysis.

We use this tool in our lab on a daily basis since 2011. The GMOfinder is free of charge and readily available on request to all non-profit laboratories that do official GMO analysis (sven.pecoraro@lgl.bayern.de).

Best regards,
Sven Pecoraro
posted on 2014-04-01 13:59 UTC by Dr. Sven Pecoraro, Bavarian Health and Food Safety Authority
This is a reply to 5729 RE: Use of methods posted in available Databases [#5730]
Thanks Sven for the post on GMOFinder.

Like the GMOfinder which is free of charge and readily available on request to all non-profit laboratories that do official GMO analysis, the methods developed by technoilogy providers are also available via the CropLife methods database, and also to seed providers that wish to test for adventitious presence.
As with GMOFinder, he posting of methods on a website does not guarantee that the methods are available and free to use irrespective of any intellectual property issues.  As discussed at the workshop in Italy in November, many of the methods posted on the EURL-GMFF website are not available without a licence from the developer.  I am therefore posting this clarification regarding the use of methods posted on the EURL-GMFF website.  These intellectual property considerations also apply to methods posted on other websiteds such as the SHGMO.

Methods are submitted to the EU-RL GMFF by the applicants in accordance with the legal requirements under Regulation (EC) No 1829/2003, to enable EU-RL GMFF to validate the method and make it available to EU Member State authorities for testing for the presence and for quantification of the targeted GM event in food and feed. All intellectual property rights to the method are retained by the applicant, but under these rights the applicant does not restrict the use under Article 30(5) of Regulation (EC) No 1829/2003 by these authorities. Any other use is prohibited unless previously agreed in writing with the applicant.

Thus although a method may be present on the EURL website, the posting of the method does not give up the rights to the method.  The same restriction is applicable to many of the event-specific methods posted on other websites or in national standards.

Should Governments and other organisations such as seed producers wish to use a method for detection of Low Level Presence of events, they can download the methods from the CropLife Detection methods Website (http://www.detection-methods.com), where you can obtain a non-transferable, limited, non-exclusive, royalty-free license to use the method(s) for detecting the transgenic event DNA.  The methods can be used to establish seed purity, grain quality, or purity or quality of other agricultural products at any stage of research, development or commercialization.  Those wishing to use a method that has intellectual property protection for fee-for service testing are advised to contact the developer of the method which can be done through this website.

I hope this clarification is useful; those using the methods as part of their regulatory compliance testing thus have a simple way of obtaining such methods directly from the developers of the methods.

Best regards,

Ray Shillito
posted on 2014-04-01 15:09 UTC by Dr Raymond Shillito, Bayer CropScience