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GMOfinder—A GMO Screening Database

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Abstract

The development and cultivation of genetically modified crops is still increasing globally. Food and feed imports from outside the European Union (EU) will subsequently require more effort from the responsible authorities in monitoring the compliance with effective labelling regulations. The aim of this study was the development of the GMOfinder, a database for collection and interpretation of information related to the screening for genetically modified organisms (GMOs). Different genetic elements (e.g. promoters, terminators, structural genes) are artificially introduced into plants to establish new genetic modifications. The introduced elements may vary between GMO events, depending on the intended trait(s). Screening for such inserted elements with (real-time) polymerase chain reaction is a common first step to analyse samples for the presence of any genetical modification. From the pattern of detectable and nondetectable elements, valuable conclusions about the identity of putative present GMO event(s) can be drawn with the GMOfinder. Information about selected genetic elements from the literature, applications for authorisation and other (web) sources were systematically integrated in a tabular matrix format. Special care was taken to additionally record the sources of the information, thus facilitating evaluation of screening results, and tracing of possible errors in the matrix. The GMOfinder accesses data from the element matrix with implemented algorithms and facilitates to interpret the outcome of screenings. Such a preselection helps to systematically narrow down the candidates for subsequent identification reactions. Optional display of events with potentially masked elements completes the included features.

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Abbreviations

BVL:

German Federal Office for Consumer Protection and Food Safety

EFSA:

European Food Safety Authority

EURL-GMFF:

European Reference Laboratory for GM Food and Feed

GMO:

Genetically modified organism

LGL:

Bavarian Health and Food Safety Authority

QM:

Quality management

UI:

Unique identifier

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Acknowledgements

The presented work was funded by the Bavarian State Ministry of the Environment and Public Health (UGV04090803099). We thank Krimhilde Posthoff and Patrick Guertler for testing the database and for useful discussions. Andrea Harwardt, Claudia Bujotzek, Roswitha Dorfner, Ulrike Mulats, Melina Mehmedovic, and Manuela Hillen provided excellent technical assistance.

Conflict of Interest

None

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Authors and Affiliations

  1. Bavarian Health and Food Safety Authority (LGL), Veterinärstr. 2, 85764, Oberschleissheim, Germany

    Lars Gerdes, Ulrich Busch & Sven Pecoraro

Authors
  1. Lars Gerdes
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  2. Ulrich Busch
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  3. Sven Pecoraro
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Corresponding author

Correspondence to Sven Pecoraro.

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Fig. S6

Query algorithms in the GMOfinder. Schematic overview and partial screenshots of the dataset selection procedure in the GMOfinder. The user decides on the form by adjusting option groups; the value from the option group is assigned via visual basic for applications (VBA) to a global variable; a public function is set via VBA according to the global variable; the public function is then used directly as query parameter in a query (JPEG 580 kb)

High resolution image (TIFF 1.17 mb)

Fig. S7

Query parameters for the species selection. Schematic overview of the species selection procedure in the GMOfinder. The user enters experimental screening results by adjusting the species option groups (e.g. ‘Maize’) on the form; the value from the option group (e.g. ‘1’ for ‘detectable’) is assigned via VBA to a global variable (e.g. ‘MaisVorh’: ‘-1’ for ‘detectable’); a public function (e.g. ‘SpeziesMais()’) is set via VBA according to the global variable (e.g. ‘Mais’ for ‘detectable’); the public function is then used directly as parameter in the query. Query parameters: SpeziesMais() Or SpeziesSoja()… Or SpeziesTorenie(). Each of the parameters is either the German name of the species (e.g. ‘Mais’) or an empty string (‘“”’). Selection of ‘detectable’ or ‘not tested’ yields the corresponding German name, selection of ‘not detectable’ or ‘exclude’ yields the empty string as query parameter for the corresponding species (JPEG 166 kb)

High resolution image (TIFF 41.5 kb)

Fig. S8

Query parameters for the selection of genetic elements/constructs. Schematic overview of the genetic elements/constructs selection procedure in the GMOfinder. The user enters experimental screening results by adjusting the element/construct option groups (e.g. ‘p35S (a)’); the value from the option group (e.g. ‘1’ for ‘detectable’) is assigned via VBA to a global variable (e.g. ‘aVorh’: ‘1’ for ‘detectable’); two public functions [e.g. ‘Eamin()’ and ‘Eamax()’] are set via VBA according to the global variable (e.g. ‘0’ and ‘9’ for ‘detectable’); the public functions are then used as limiting parameters in the query. Query parameters: Between Exxxmin() And Exxxmax(). Each of the parameters Exxxmin and Exxxmax is -9, 9, or 0. The database value for the given element/construct is for each GMO an integer value between -9 and 9, or 0 (compare table in Fig. 2). The selection of the option with/without masking affects the public function Exxxmin() that is set to -9 independently of the selection in the option group (JPEG 194 kb)

High resolution image (TIFF 55.2 kb)

Fig. S9

Query parameters for the selection of empty datasets. Schematic overview of the selection procedure of empty datasets in the GMOfinder. The user decides on the inclusion/exclusion of empty datasets by adjusting the corresponding option group; the value from the option group (e.g. ‘1’ for ‘exclude’) is assigned via VBA to the global variable ‘leereDS’: ‘1’ for ‘exclude’; the public function ‘leerDS()’ is set via VBA according to the global variable (e.g. ‘“”’ for ‘exclude’); the public function is then used as comparison parameter in the query. Query parameters: Abs([a])+Abs([b])+…+Abs([m])>0 Or leerDS(). The database values for all elements/constructs are integer values between −9 and 9 or 0. Datasets with only 0 as value and accordingly 0 as sum of the absolute values are excluded by the presented query if the option ‘exclude’ is chosen (JPEG 137 kb)

High resolution image (TIFF 31.6 kb)

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Gerdes, L., Busch, U. & Pecoraro, S. GMOfinder—A GMO Screening Database. Food Anal. Methods 5, 1368–1376 (2012). https://doi.org/10.1007/s12161-012-9378-6

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