Table of Contents

1.0        General Information. 8

1.1 System Overview.. 9

1.2 User Access Levels. 9

1.2.1 Public (euginius.eu) 9

1.2.2 Authorised Users. 9

1.3 Points of Contact. 10

1.4 Organisation of the Manual 11

1.5 Nomenclature. 11

1.6 Abbreviations. 12

2.0        Getting Started. 14

2.1 Access and Login. 15

2.1.1 Access. 15

2.2 System Menu. 15

2.2.1 Homepage. 15

2.2.2 GMO.. 16

2.2.3 Detection. 17

2.2.4 Analysis. 17

2.2.5 Authorisation. 18

2.2.6 Search. 18

2.3 Homepage Search section. 19

2.3.1 GMO Search. 19

2.3.2 Literature Search. 19

2.4 Help. 20

3.0        Using the System.. 21

3.1 GMO.. 22

3.1.1 List with GMOs and their Identifiers. 22

3.1.2 List with GMOs and Traits. 23

3.1.3 List with GMOs and Genetic Element 24

3.1.4 GMO Detailed information. 27

3.1.5 Detail Pages. 30

3.2 Detection. 33

3.2.1 Detection Methods -> PCR methods for GMO detection and identification. 33

3.2.2 GMO/method matrix. 36

3.2.3 Reference Material 39

3.3 Analysis. 40

3.3.1 Entering Screening Data. 40

3.3.2 Importing Screening Data. 41

3.3.3 Analysis Results. 42

3.4 Authorisation. 44

3.4.1 Authorisation Symbols. 44

3.4.2 Search for Generic Approval 45

3.4.3 Custom Search - EU applications. 46

3.4.4 Authorisation Free-text Search. 50

3.5 Search. 51

3.5.1 Search GMO.. 52

3.5.2 Search Literature. 53

3.5.3 Element Search. 56

3.5.4 Navigating Search Results. 57

3.6 Exporting data. 58

4.0        Workflow.. 59

4.1 Detection: search workflow for detection methods. 60

4.1.1 Searching for a method targeting an endogenous maize gene (Taxon-Specific method) 60

4.1.2 Does the method currently used in my laboratory, correspond to one of the methods registered in EUginius?. 63

4.2 GMO/method matrix: Optimisation of a screening strategy. 64

4.2.1 Coverage check of the current set of methods. 65

4.2.2 Identification of the not detected events (screening gap) 68

4.2.3 Search for methods able to close the screening-gap. 69

4.2.4 Conclusion. 70

4.3 GMO/method matrix: Designing a Screening strategy. 70

4.3.1 Finding methods. 70

4.3.2 Selecting Methods. 71

4.3.3 Conclusion. 74

4.4 Analysis Tool 74

4.4.1 Screening Results. 74

4.4.2 Confirmed Output 76

4.4.3 GMO Prediction View.. 76

4.4.4 Detection of Predicted GMO.. 78

4.4.5 Conclusion. 79

5.0        Input and Feedback. 80

5.1 Input and Feedback. 81

5.1.1 Suggest New GMO.. 81

5.1.2 Give Feedback. 81

6.0        Terms and Conditions of Use. 82

6.1 Terms of Use. 83

6.2 Conditions of Use For Registered Users. 83

 


 

 

 

 

 

 

 

 

 

 

1.0                          General Information


 


1.1 System Overview

EUginius, the European GMO Reference Database

EUginius (EUropean GMO INItiative for a Unified Database System) is an initiative of BVL - the Federal Office of Consumer Protection and Food Safety (Berlin, DE) and Wageningen Food Safety Research (Wageningen, NL) to support competent authorities and private users who seek accurate information on GMOs. EUginius is supported by the Austrian Agency for Health and Food Safety Ltd. (AGES) (www.ages.at), the Plant Breeding and Acclimatization Institute (IHAR) (www.ihar.edu.pl) and the Experimental Zooprophylactic Institute of Lazio and Tuscany (IZSLT) (www.izslt.it).

EUginius provides accurate information of major and relevant issues regarding the presence, detection and identification of GMOs with a focus on the situation in the European Union as well as world-wide coverage.

 

1.2 User Access Levels

  

1.2.1 Public (euginius.eu)

Access to the EUginius.eu database is open for use by anyone and is intended to support competent authorities as well as private users.

 

1.2.2 Authorised Users

For unrestricted access to EUginius you must have an account with proper authorisations. For the terms and conditions regarding authorised use consult 6.1 Terms of use. Access can be granted by BVL staff and can be requested via databasemanager@euginius.eu.

EUginius has 3 authorised access levels.

1.2.2.1 Read-only

Read Only grants additional access to confidential information as well as modules that are under construction. This includes:

·        BLAST Module

·        Safety Literature Module

1.2.2.2 Data entry

Data entry users have access to all levels which Read Only covers, plus access to the Data Entry module. They are able to enter new data or initiate modification or deletion of existing entries. This is part of EUginius’ 6-eyes data entry system.

1.2.2.3 Expert

Expert users have access to all levels which Read Only covers, plus access to the Data Entry module. They are able to validate new data, modification and deletion of existing entries. This is part of EUginius’ 6-eyes data entry system.

1.2.2.4 Administrator

The administrator has access to all modules, and can edit these. For any help, information or feedback contact an administrator via databasemanager@euginius.eu.

 

1.3 Points of Contact

General

For general questions about EUginius you can contact Wageningen Food Safety Research via email euginius.wfsr@wur.nl or at +31(0)317480256 or the BVL via email 405@bvl.bund.de or at +49(0)301844440503.

Input or Feedback

For any input find the hyperlinks on the homepage or consult 5.1 Input and Feedback.

Database

In case of questions about the database, contact database@euginius.eu

Website

In case of questions about the website, contact webmaster@euginius.eu

Relevant Institutions
EUginius is a collaborative effort between BVL - the Federal Office of Consumer Protection and Food Safety (Berlin, DE) and
Wageningen Food Safety Research (WFSR).

 

Wageningen Food Safety Research
Department Statutory Tasks

Federal Office of Consumer Protection and

Food Safety
Department Genetic Engineering

T +31 (0)317 480256
euginius.wfsr@wur.nl
www.wur.eu/wfsr

T +49-(0)3018-444-40000
gentechnik@bvl.bund.de
www.bvl.bund.de

Visiting address:
Akkermaalsbos 2
Building no. 123
6708 WB WAGENINGEN
The Netherlands

Visiting address:
Gerichtstraße 49
13347 BERLIN
Germany

 

Mail address:
PO Box 230
6700 AE WAGENINGEN
The Netherlands

Mail address:
PO Box 11 02 60
10832 BERLIN
Germany

 

1.4 Organisation of the Manual

This manual offers internal hyperlinks that allow you to travel through it more efficiently. These are written as 1.4 Organisation of the Manual (italic and underlined). They will take you to the place in the manual which the text references. The hyperlinks in blue font lead you to the EUginius website.

The manual is divided into 6 major sections:

1.0

General Information

Basic information about EUginius, such as functions performed and a description of the program.

2.0

Getting Started

General walk-through of the system including getting into EUginius.

3.0

Using the System

Detailed description of the system’s functions from start to finish.

4.0

Workflow

An example for using the analysis tool, finding detailed information and designing your own screening.

5.0

Input and Feedback

The standard procedure for system malfunction or improvement opportunities.

6.0

Terms and Condition of Use

Additional data to assist you when working in EUginius.

 

1.5 Nomenclature

 

GMO

Genetically Modified Organism

Event

Used when describing one particular GMO derived from a transformation process as well as genome edited organisms (GE-GMO)

UID

Unique Identifier which is given to events for standardisation between databases

Stack

A traditional crossing of two GMO events to create a plant that exhibits both features

Element

A DNA sequence that can be inserted into an organism where it will perform a specific function. In case of GE-GMO, DNA sequence which has been modified.

Coding Sequence

An element that consists of DNA coding for a protein

Promoter

An element that initiates transcription of a particular coding sequence

Terminator

An element that marks the end of a particular coding sequence, ending transcription

Construct

Two or more genetic elements aligned next to each other

BLAST

Basic Local Alignment Search Tool

Authorisation

Official permission for the use of specific GMOs

Food

Product for human consumption

Feed

Product for animal consumption

Cultivation

Growing the GMO as crop

Transformation

Genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material

Insert

DNA sequence that has integrated into the genome of a species during transformation

Vector

DNA fragment that was used in the process of transformation

Free-text search

A search which allows for manual entry of any word/phrase you choose

Query-building search

A search which allows for multiple keywords which can be selected from a drop-down list

 

1.6 Abbreviations

General

BLAST

Basic Local Alignment Search Tool

GE

Genome Edited

GMO

Genetically Modified Organism

PCR

Polymerase Chain Reaction

UID

Unique IDentifier

Genetic Elements

CS

Coding Sequence

E

Enhancer

I

Intron

L

Leader

O

Other sequences

P

Promoter

R

Regulatory element

T

Terminator

TP

Transit Peptide

V

Vector fragment

Detection Methods

QL-

Qualitative (PCR method)

QT-

Quantitative (PCR method)

-CON-

Construct-specific method

-ELE-

Element-specific method

-EVE-

Event-specific method

-TAX-

Taxon-specific method

Institutions

EUginius

EUropean GMO INItiative for a Unified database System

BCH

Biosafety Clearing-House

NCBI

National Center for Biotechnology Information

ISO

International Organization for Standardization

CEN

European Committee for Standardization (Comité Européen de Normalisation)

EURL

European Union Reference Laboratory

 


 

 

 

 

 

 

 

 

2.0                          Getting Started


 


2.1 Access and Login

  

2.1.1 Access

Public (euginius.eu)

Access to EUginius.eu is public and does not require an account. Terms of use can be found in EUginius’ footer under 6.1 Terms of Use. This public version has the following modules:

·       Home

·       GMO

·       Detection

·       Analysis

·       Authorisation

·       Search

·       Help

Private

An account is required to access the private version of EUginius.

In addition to the publically available modules, the private version offers the following modules:

·       BLAST

·       Safety Literature

·       Data Entry

 

2.2 System Menu

  

2.2.1 Homepage

Figure 1 - EUginius menu (public version)

Upon launching the system, you are presented with the homepage with a blue menu bar (Figure 1). By clicking the labelled tabs, you can move to the following sections:

·       GMO

·       Detection

·       Analysis

·       Authorisation

·       Search

·       Help

Below the labelled tabs there are three central sections and a toolbar. At the very bottom of the page are hyperlinks to the Disclaimer, Terms of use, Contact information.

2.2.1.1 Homepage toolbar (left)

The toolbar is comprised of an overview of news and articles related to EUginius. Below this article overview you can see the total number of GMOs, methods and reference materials, with links to all of them.

[GMO count] GMOs (incl. stacks) links to the List with GMOs and their identifiers page. For more information on this page, consult 3.1.1 List with GMOs and their identifiers.

[method count] methods links to the Detection methods search result page, with no search criteria. For more information on this page, consult 3.2.1 Detection Methods.

[reference material count] reference materials links to the Reference material search result page, with no search criteria. For more information on this page, consult 3.2.3.2 Reference material search result.

Genetic elements links to the List with GMOs and genetic elements page, with the element tree expanded and detailed element information. For more information on this page consult 3.1.3 List with GMOs and genetic element.

Below the Genetic elements link you can find a link to an up-to-date list of GMO-related websites.

A link to a list of GMO-related websites is found below this. At the bottom of the taskbar are hyperlinks for giving input or feedback (see 5.1 Input and Feedback).

2.2.1.2 Homepage body (center)

The top section, titled The European GMO database, gives general information on EUginius.

The section titled Free-text search has two different modes of use, GMO search and Literature search. Both work with the same search bar. Additionally, advanced searches are available at the links below the search buttons. For more information on this section, consult 2.3 Homepage Search section.

EUginius is a collaboration between institutes. The section titled About the partners lists all members of the EUginius consortium. The more about the partners... hyperlink in this section brings you to a separate page with more detailed information on the members.

2.2.2 GMO

Figure 2 - GMO module sections

The GMO module provides you with four different sections (Figure 2). They all allow you to search for GMOs using different criteria.

List with GMOs and their identifiers lets you view, sort and filter GMOs by their identifiers. It shows the name, UID, species, traits, companies, developers, tradenames and EU authorisation of GMOs.

List with GMOs and traits provides you with GMOs and their associated traits. It shows the name and traits of a GMO and offers additional filtering for these traits. The traits are organized in a hierarchical tree (Trait thesaurus).

List with GMOs and genetic elements provides you with GMOs and their genetic elements. It shows the name and all genetic elements of GMOs while offering additional filtering for these genetic elements. The genetic elements are organized in a hierarchical tree (DNA thesaurus).

The Search for GMO section is a free-text search which scans the List with GMOs and their identifiers section for any matching terms. All other sections use a query-building search.
For more information on this module, consult 3.1 GMO.

 

2.2.3 Detection

Figure 3 - Detection module sections

The Detection module provides you with three different sections (Figure 3). All sections in this tab provide you with information regarding GMO detection.

Detection methods lets you search PCR methods designed for GMO screening, identification and quantification.

GMO/method matrix lets you find information on the specificity of PCR methods and their abilities to detect GMOs. A set of methods can be selected and filtered by specific criteria. You are then given a table displaying the verification data.

Reference material lets you search for GMO reference materials and provides concentrations, percentages and catalogue numbers with sources.


For more information on this module, consult 3.2 Detection.

 

2.2.4 Analysis

Figure 4 - Analysis module

The Analysis module (Figure 4) consists of fourteen input fields containing information on GMO detection results. It supports you in sample analysis and provides explanations for detected elements.
Import result file lets you import an Excel file with screening outcomes, saving you from entering data manually.
For more information on this module, consult 3.3 Analysis.

 

2.2.5 Authorisation

Figure 5 - Authorisation module sections

The Authorisation module provides you with three different sections (Figure 5). All sections in this tab provide you with information regarding GMO approval status.

Search for generic approval is a query-building search which lets you find information on the approval status of a specific GMO for use in food, feed, cultivation or other uses.

Custom Search - EU applications is a query-building search which lets you find detailed information on applications that were submitted for GMOs with information on intended use, legal status, and legislation.

The Search term section is a free-text search which works independently of the other two sections. Result table shows application reference number, species, GMO, UID, intended use and EU authorisation status, applicants, commission decision number, expiry date, decision date, legislation, traits, genetic elements, tradenames, and companies/institutions. The matching search terms are highlighted.

 

2.2.6 Search

The Search module lets you do a free-text keyword search on GMOs and literature. An advanced search option is also available for GMOs and literature. Additional search options are available for authorisation, methods, reference material and genetic elements with an extra free-text search being possible for genetic elements.

For more information on searching in EUginius, consult 3.5 Search.

 

2.3 Homepage Search section

The homepage free-text search section has two different modes of use, GMO search and Literature search. Both work with the same search bar but advanced searches are available at the links below the search buttons. More search types are available on the Search module tab in the menu, for information on this tab or on search results consult 3.5 Search.

 

Tip:

In the Search module tab, you can click on Element search to find GMOs, DNA inserts, donors and traits which are attributed to certain elements. For more information on this consult 3.5.3 Element Search

 

 

  

2.3.1 GMO Search

The standard free-text GMO search can find GMO, UID, tradename, species, company and traits.

Advanced GMO search presents you with seven fields, these correlate to the above mentioned six features and also genetic elements.
The main advantage of the advanced search is filtering out unwanted results, as it allows exclusion of stacked events and closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search.
Some examples of free-text searches and search terms are listed below:

 

Search Term(s)

Finds GMOs with

Bt*

names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.

305423

with UID "DP-3Ř5423-1"

MON 00810 6

UID "MON-ŘŘ81Ř-6"

RRS

alias "RRS" (=GTS 40-3-2)

zea

species "Zea mays"

soybean

species "Glycine max"

syngenta

UID "Syngenta Seeds, Inc"

yieldgard

tradename "YieldGard VT PRO", "Yieldgard™", "Maxguard/Yieldgard", etc.

bt11

name "Bt11" and stacks containing Bt11

insect

trait "Insect resistance"

 

For more information on search functions or tips for search strategies, consult 3.5 Search.

 

2.3.2 Literature Search

The standard free-text literature search can find GMO name, abstract, citation and keywords.

The advanced Literature search presents you with three search options: GMO, Genetic Element and DNA search. Each of these include a search field for name, publishing authority and publication date. Keywords entered in other sections will not be taken into account when you click the search button (see example). The main advantage of the advanced search is filtering out unwanted results, as it allows closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search.

 

Example:

If you hit search on the DNA search section, only data in this section will be taken into account. Any data entered in GMO or Genetic Element search will be ignored.

 

 

For more information on search functions or tips for search strategies, consult 3.5 Search.

 

2.4 Help

The Help module provides you with this user manual. It can be accessed from several modules by clicking the blue help button in the top right corner.

Clicking the blue help button while in a module will take you to the matching section of this manual.


 

 

 

 

 

 

 

3.0                          Using the System


 


3.1 GMO

Figure 6 - GMO module sections

When entering the GMO module, you are presented with four different sections (Figure 6). All sections in this tab allow you to filter and search for GMOs using differing criteria. The Search for GMO function is identical to the homepage GMO search function. For more information on this search function consult 3.5.1 GMO Search.

 

3.1.1 List with GMOs and their Identifiers

List with GMOs and their identifiers lets you view, sort and filter GMOs by their identifiers. It shows the name, UID, species, traits, companies, developers, tradenames and EU authorisation of GMOs (Figure 7).

Figure 7 - Result of list with GMOs and their identifiers

1.

GMO

Most commonly used name for the GMO
Clicking the GMO name will lead you to the GMO detailed information page. For more information on this page consult
3.1.4 GMO detailed information.

2.

UID

The (UID) Unique Identifier which is given to the GMO.
This is useful in gathering information from other databases

3.

Species

Species which the organism belongs to.

4.

Traits

A list of traits expressed by the GMO which are not found in the wild species.

5.

Companies

All companies producing the GMO.

Clicking the company name will lead you to the list of all GMOs related to  (or produced or sold by) this company

6.

Developers

The institute(s) or company(ies)that developed the GMO, if available.

7.

Tradenames

The name which the GMO is commonly sold under by companies.

8.

EU Authorisation

Approval status of the GMO for food, feed, cultivation and other uses.
Clicking the icon in the table will lead you to a list with the EU applications
   of this GMO (if available)

   Additional information on EU authorisation can be found in the
   Authorisation tab. For more information on this, consult
3.5 Authorisation.

Applying a filter can be done by clicking the apply filter hyperlink at the top of the page. This will take you to the Advanced GMO search. For more information on this consult 3.5.1.1 Advanced GMO Search.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

 

3.1.2 List with GMOs and Traits

List with GMOs and traits provides you with GMOs and their associated traits. It shows the name and traits of a GMO and offers additional filtering for these traits.

1.

GMO

Most commonly used name for the GMO
Clicking the GMO name will lead you to the GMO detailed page. For more information on this page consult
3.1.4 GMO detailed information.

2.

Traits

A list of traits expressed by the GMO that are not found in the wild species.

 

3.1.2.1 Navigating the traits page

 

Figure 8 - Defining filter criteria to find GMOs with specific traits.

 

Filtering Data can be done through the select a trait field (Figure 8). When clicking the field, you are presented with a drop-down list. A trait from this drop-down list can be selected by clicking it, adding it to the query. By typing text into the field, the shown traits will be limited to traits matching the search term. One or more traits from the drop-down list can be selected.

A selection of traits can also be made through the traits tree.

The Traits Tree is opened by clicking the show tree hyperlink at the top of the page. This presents you with a list of categories with   next to them (Figure 9). Clicking the   will add the category to the searched traits, clicking the category will expand it, showing subcategories or specific traits. See example below:

Example:

Here the main category (1) has been expanded by clicking it. The subcategory under this (2) was also opened, displaying the traits (3).

Any of these parts can be filtered for by clicking the plus symbols next to them. This will add them to the filter field

Figure 9 - Part of traits tree

 

Filter options can be adjusted by selecting either AND or OR. AND will filter for GMOs that possess all specified traits while OR will filter for GMOs that possess any of the traits. By default, stacks are excluded. Including stacked events can be done by unchecking the box next to Exclude stacked events.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

3.1.2.2 Search Results

 

Figure 10 - Search results GMOs and traits

After filtering you get a list of GMOs and traits (Figure 10). Clicking the GMO name will bring you to the GMO details tab, for more information on this consult 3.1.4 GMO detailed information. In the traits-column each row of text in a cell represents one trait exhibited by the GMO.

 

Example:

EF2-114 expresses two traits as result of genetic modification: reduced ethylene synthesis, which falls in the category altered ripening or flowering within the category alteration in growth, development or product quality, and Altered carotenoid biosynthesis which is in the Colour modification category within the main category Composition alteration.

 

 

3.1.3 List with GMOs and Genetic Element

List with GMOs and genetic elements provides you with GMOs and their genetic elements. It shows the name and all genetic elements of GMOs while offering additional filtering for these genetic elements.

1.

GMO

Most commonly used name for the GMO
Clicking the GMO name will lead you to the GMO detailed information page. For more information on this page consult
3.1.4 GMO detailed information.

2.

Genetic Elements

A list of all elements involved in genetic modification of the GMO.

  

3.1.3.1 Navigating the Genetic Elements page

 

Figure 11 - Define filter criteria to find GMOs containing specific genetic elements

Filtering Data can be done through the select a genetic element field (Figure 11). When clicking the field, you are presented with a drop-down list. An element from this drop-down list can be selected by clicking it. Limiting the list of shown elements in this drop-down list can be done by entering text into the field.

A selection of elements can also be made through the genetic elements tree.

The Genetic Element Tree is opened by clicking the show tree hyperlink at the top of the page. This presents you with a list of categories with   next to them (Figure 12). Clicking the   will add the category to the searched traits, clicking the category will expand it, showing subcategories. See example below:

Example:

Here the main level (1) has been expanded by clicking it. A corresponding Level 2 below (2) was also opened, displaying the genetic elements (level 3).

Any of these parts can be filtered for by clicking the plus symbols next to them. This will add them to the filter field

Figure 12 - Part of genetic elements tree

By clicking show tree details next to hide tree EUginius will display more information about the elements in the tree (Figure 13). Synonyms displays other names for the element, Donor shows the organism from which the element is taken, Trait shows the trait that the element confers to the GMO, Function gives the element’s function in the GMO and Definition gives the unabbreviated name of the element. BCH gives record IDs of the corresponding elements in the Biosafety Clearing-House (http://bch.cbd.int).

 

Figure 13 - Details of a genetic element

Filter options can be adjusted by selecting either AND or OR. AND will filter for GMOs that possess all specified elements while OR will filter for GMOs that possess any of the elements. By default, stacks are excluded. Including stacked events can be done by unchecking the box next to Exclude stacked events.

Please note: The tree has a hierarchical structure where lowest levels are related to a unique higher level.

The highest level (level_1) describes the general functional types of the genetic element. The next level (level_2) is composed of an abbreviation of the element type plus a generally comprehensive long name referring to the detailed biological function. Below level_2, genetic elements of common/homologous origin and/or with comparable/analogous features are grouped. Those level_3 terms serve as a label for the actual genetic elements.

When you select a higher level, all the elements belonging to lower linked levels will be considered in the search.

3.1.3.2 Search Results

  

Figure 14a - Search results GMOs and genetic elements

After filtering you get a list of GMOs and genetic elements (Figure 14a). Clicking the GMO name will take you to the GMO details tab, for more information on this consult 3.1.4 GMO detailed information. By default, only the filtered genetic elements are shown, but by pressing show in the heading of the table you can bring up all genetic elements associated with the GMOs in alphabetical order (Figure 13b).

Example:

Above, filtering happened for CS-accD-PSECL (which is related to Coding Sequence > CS-1-amino-cyclopropane-1-carboxylic acid deaminase). By default, the genetic element column only shows the filtered element. By hitting show all associated elements for the GMO can be shown (below).

Figure 14b – Part of Search results GMOs and genetic elements with the activated show function

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

3.1.4 GMO Detailed information

When clicking the name of a GMO in any of the EUginius sections, you will be redirected to GMO detailed information tab (Figure 15). This tab presents you with all information which is linked to the selected GMO. Displayed tables can be exported into MS-Excel.

3.1.4.1 Navigating GMO Detailed Information

Figure 15 - GMO detailed information

The basic information on the GMO is always shown at the top. This information includes GMO name, Alias, UID, Tradename, Company, Developer, Species, Traits and EU authorisation. Company also provides a link which brings you to the GMO Identifier List. This list will exclusively show GMOs which the company has produced. Clicking the traffic light authorisation symbols takes you to the GMO-specific authorisation details, which provides the same information as EU Application Details Search, with your GMO as filter. For more information on the application details, consult 3.5.3 Search for EU Application details.

By clicking the arrows, text or blue bar the sections described below will expand, revealing additional information.

GMO detailed information tab

General Information

General information on GMO

 

Inserts / Modification

Modification of the GMO on the molecular level / Sequence information when available

Transformation vectors

Vectors used to transform the GMO

Detection Methods

Methods to detect the GMO

 

Reference Materials

Material with known concentrations of the GMO

 

Authorisation

Approval status of the GMO in the European Union

 

Literature reference

Literature describing the GMO

 

3.1.4.2 General Information

General Information provides basic information on the nature of the genetic modification and provides links to sources of information regarding the GMO (Figure 16). For an explanation of the module consult the image and table below.

Figure 16 - Explanation of general information about a GMO

1.

Description

General overview of the GMO.

2.

Links regarding to this GMO

Hyperlinks to sources, relevant documents and databases regarding the GMO.

3.

Transformation /Modification technique

The transformation or modification technique used to develop an organism may differ. EUginius currently includes 15 techniques.
For more information on these techniques consult for example: Ramkumar T.R., Lenka S.K., Arya S.S., Bansal K.C. (2020) A Short History and Perspectives on Plant Genetic Transformation. In: Rustgi S., Luo H. (eds) Biolistic DNA Delivery in Plants. Methods in Molecular Biology, vol 2124. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0356-7_3

3.1.4.3 Inserts / Modification

Inserts / Modification provides more detailed information on the nature of the genetic modification (Figure 17). Here you can find elements in the composite DNA and all of EUginius’ sequences associated with the GMO. For an explanation of the module, consult the image and table below.

Figure 17 - Explanation of the inserts/modification section

1.

Name

DNA called insert_ has been confirmed in the GMO. DNA starting with vector_ describes the vector that was used for the transformation. DNA ending with (putative) describes information about the insert, based on the transformation vector.

2.

Comment

Contains more detailed information on the insert/insertion site.
e.g. deletion, rearrangements, insertion etc.

3.

Map

If a DNA map is available this will be inserted here in a picture format. Please note that this function is not used until now due to copyright issues.

4.

Genetic Elements

Information following this header regards the elements contained in the insert/vector

4.1

Reference

The source used for obtaining information about the insert which the element belongs to.
e.g. scientific journal or organisation

4.2.

Elements

All elements in the insert/vector with general data.

 

4.2.1 – 4.2.8

A summary of the element, as also described on the Genetic Element Information page. If available the order of elements in the insert/vector is also provided 4.2.1).
Clicking the element name (4.2.2) will take you to Genetic Element Information, for more information on this consult 3.1.5.1 Genetic Element details.

5.

DNA Sequences

All sequences associated with the GMO and general data.

 

5.1 – 5.5

A summary of the available sequences, as also described on the Sequence String Information page. The Sequence column (5.1) can link you to additional information. This either says No if no sequence is available, or Yes if a sequence is available. If it says Yes this is also a hyperlink to said sequence.

If you click Yes it will take you to the sequence string page. For more information on this consult 3.1.5.2 Sequence String.

3.1.4.4 Transformation vectors

Transformation Vectors provides more detailed information on the vector used for the development of the GMO. For an explanation of the module consult the paragraph above: 3.1.4.3 Inserts / Modification.

3.1.4.5 Detection Methods

Detection Methods provides a detection search, with your GMO as filter. The additional column Verification is added on the right and displays method verification for your GMO. Values in this table can range from 1 to 3 with the following meaning:

1:       Detection of the target is based on other information in EUginius (database, plasmid map etc.)

2:       Detection of the target is verified by sequence alignment

3:       Detection of the target is experimentally verified using reference material

For more information on the detection methods table, consult 3.2.1 Detection Methods. For more information about the verification values, consult 3.2.2 GMO/method matrix.

3.1.4.6 Reference Materials

Reference Materials provides a smaller version of the Reference Material search with your GMO as filter. For more information on the Reference Material search section, consult 3.2.3 Reference Material. Clicking the catalogue number will bring you to the GMO reference material page, which provides you with extra information on the reference material.  For more information on the GMO reference material page, consult 3.1.5.3 Reference Material Details.

3.1.4.7 Authorisation

Authorisation provides detailed information on applications that were submitted for the GMO with information on intended use, legal status and legislation.

Clicking the Application reference number will take you to the GMO application page. For more information on this, consult 3.1.5.4 Application Details.

3.1.4.8 Literature reference

Literature reference provides the same information as advanced Literature search, with your GMO as filter.

Clicking the article citation will take you to the GMO literature details page. For more information on this, consult 3.5.2.3 Literature Details. For more information on the Literature search section, consult 3.5.2 Literature Search.

3.1.5 Detail Pages

3.1.5.1 Genetic Element details

Clicking the element name will take you to the tree with genetic elements, with the selected element in focus. More information about the tree can be found on the 3.1.3.1 Navigation the genetic elements page.

3.1.5.2 Sequence String

Clicking Yes in the Sequence column in the Related DNA Sequences table of Inserts / Modification or Vector brings you to the Sequence string page (Figure 18), this gives information on the sequence and provides the Sequence String.

Figure 18 - Explanation of sequence information

1.

DNA Name

DNA called insert_ has been confirmed in the GMO.
DNA starting with vector_ describes the vector which was used for the transformation. DNA ending with (putative) describes information about the insert, based on the transformation vector.

2.

Comment

This field is often used for description of the source of the information/detailed information on nucleotide changes in the insert.

3.

Accession Number

This is a unique code for genetic sequences, it can be used to search for genetic sequences online
e.g. GenBank

4.

Reference

The source used for entering the composite DNA into EUginius.
e.g. NCBI – GenBank, BCH, BVL or WFSR

5.

Annotation

The name under which the sequence is annotated in the reference database/source.

6.

Size

The size of the sequence in base pairs (bp).

7.

Sequence String

The full sequence as given in the reference.

3.1.5.3 GMO Reference Material

The GMO Reference Material page displays the GMO detailed information header with general information on the GMO.
Below this is a smaller version of the Reference Material search with your GMO as filter. For more information on the Reference Material search section, consult 3.2.3 Reference Material.

Clicking the catalogue number will bring you to the material details page (Figure 19), which provides you with extra information on the reference material.

Figure 19 – Explanation of GMO reference material

1.

Catalogue number

A unique identifier given to the reference material by the material provider. This identifier is used for ordering the material.

2.

Description

A description of the reference material stating material amount and type.

3.

Material Type

The type of material.

Reference material can vary from dried powder to DNA or even bacterial strains.

4.

Concentration

Concentration of the reference material.
 cp/µl is the measure for DNA concentration, it refers to genome copies (or haploid genome equivalents) per microliter

5.

Certified

Certified material comes with a certificate proving the material’s quality and composition.

6.

Available

Indicates availability of the reference material at the source provider.

7.

Source Provider

The institution which provides the reference material.
This can be AOCS, EURL (JRC), Eurofins GeneScan, IRMM/ERM, SIGMA -          ALDRICH or the Pasteur Institute.

8.

Comment

Any additional notes which EUginius staff have about the DNA are added here. This field is often used for hyperlinks/references.

9.

Extra Comment

The Extra Comment field is to indicate issues with the material in combination with specific method(s) (e.g. unexpected positive signal).

3.1.5.4 Application Details

The GMO application page can be accessed by clicking the Application reference number hyperlink in the Authorisation table. It displays the GMO Details header with general information on the GMO.
Below this, there are three sections: Application details (Figure 20), a Use/Status table and Documents.

Application Details shows general information on the application.

Figure 20 - Explanation of application details

1.

Application reference number

A unique identifier for the application, assigned to it by the institute which received the application.
e.g. for applications under Regulation (EU) No 1829/2003: EFSA-GMO-Country-Year-Number

2.

Country

The country/region for which the approval applies.

3.

Applicant

Company/institution which submitted the application.

4.

Legislation

Legislation under which the ruling was made.

5.

Comment

Any notes which EUginius staff have about the application are added here. This field is often used for short summaries on related applications.

6.

Decision date /Expiry date

The period in which the decision applies.

7.

Related applications

Hyperlinks or application references for previous applications of this GMO and use-combination.

 

 

 

The Use and Status table shows intended uses and approval status for said uses.

Attached Documents can be found below in the Documents table, this generally includes the summary of application, EFSA or EU Scientific Panel and EFSA risk assessments and decision documents with any other documents the EUginius staff deemed relevant.

 

3.2 Detection

 

Figure 21 - Functions in the Detection module

When entering the Detection section, you are presented with three different functions (Figure 21). All functions in this tab provide you with information regarding GMO detection.

 

3.2.1 Detection Methods -> PCR methods for GMO detection and identification

3.2.1.1 All methods for one GMO

Figure 22 - Search All methods for one GMO with GMO drop-down list

The methods search for one GMO (Figure 22) enables finding methods, related to a specific GMO, out of the pool of species-, element-, construct- and event-specific methods by selecting this GMO in the drop-down list.

Names of detection methods in EUginius have a specific syntax. Methods designed for quantification have the prefix QT- (quantitative), methods starting with QL- (qualitative) have been designed for qualitative analysis. This prefix is followed by a three-letter code: -CON- stands for construct-specific, -ELE- is an element-specific method, -EVE- indicates an event-specific method, and -TAX- is a taxon-specific method. If relevant, the species code (e.g. ZM – Zea mays, GM – Glycine max, and 00 if species is not relevant) is added to the method’s name. The last part indicates the primers used, or, for methods that are common with GMOMETHOD database (https://gmo-crl.jrc.ec.europa.eu/gmomethods/), only consist of a three-digit number.

3.2.1.2 Free-text search for methods

The standard free-text detection method enables searching for detection methods based on the name of the method, the primers or the probe or based on the sequence of the primers, of the probe or of the amplicon. The search results will also provide you with the Amplicon Size, but this is not a searchable metric.

In EUginius’ free-text searches at least one word will need to match the search term. Parts of a word matching will not be picked up. e.g. searching for “VW0” will not show MON810 primers VW01 or VW03. Searching for ”event”, however, will show all event-specific methods, as EUginius views phrases with hyphens as two separate words.

Wildcards give you results when you only know part of a keyword. The wildcard symbol in EUginius is *.
For example, searching for “VW*” will show all data containing “VW” even without a full word match (i.e. VW01, VW03). Wildcards can be added to both left and right sides of the word. A wildcard on the left will only apply to additional characters to the left, a wildcard on the right will only apply to the right.

Clicking advanced search on the search results page will take you to the main Detection Methods page.

3.2.1.3 All methods corresponding to defined criteria

Based on the selected search and dependent on filter criteria chosen you can find PCR methods for your specific query and your desired applications: GMO screening, identification and quantification (Figure 23).

Figure 23 - Preselect a method set

 

Figure 24 - Define a query for specific methods

 

For filtering, EUginius makes use of Boolean operators, specifically AND and OR.
   AND requires all provided keywords to match the search results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

The Target fields Events, Constructs, Elements and Species are all OR operators. The fields Target type, Validation and Standardisation are AND operators to restrict the list. If multiple keywords are entered in fields Target type, Validation and Standardisation at least one of those keywords have to be present (Figure 24).

 Any method entered in the Method field will automatically show up in the search results additionally to the methods of the set (Screening or ABC). If no method set has been selected (=ALL) only the method(s) selected in the Method field will show up.

Below, you can find the meaning of all keywords that can come up in your detection methods searches (Figures 23 and 24).

ALL

Entire pool of methods.

SCREENING

A set of methods which is restricted to methods designed to detect GMOs.

 ABC

Set of screening methods which is constantly checked and adjusted by the German National Reference Laboratory (NRL) in collaboration with the national network of GMO laboratories.

 

EventS

One or more events from this drop-down list can be selected by clicking. Limiting the list of shown events in said drop-down list can be done by entering text into the field.

The drop-down list contains all events that EUginius has detection methods for.

ConstructS

One or more constructs from this drop-down list can be selected by clicking. Limiting the list of shown constructs in said drop-down list can be done by entering text into the field.

The drop-down list contains all constructs that EUginius has detection methods for.

ElementS

One or more elements from this drop-down can be selected by clicking. Limiting the list of shown elements in said drop-down list can be done by entering text into the field.

The drop-down list contains all elements contained in EUginius.   

Species

One or more species from this drop-down list can be selected by clicking. Limiting the list of shown methods in said drop-down list can be done by entering text into the field.

The drop-down list contains all species that EUginius has detection methods for.

TARGET Type

One or more target types from this drop-down list can be selected by clicking.

Construct-specific

Specific for detecting the presence of two elements that are in proximity.

Element-specific

Specific to a single element.

Event-specific

Specific to a single GMO.

Taxon-specific

Specific to an entire taxon.

Validation

One or more validations from this drop-down list can be selected by clicking.

In-house validation

The method has been validated in one laboratory using reference materials as sample.

Ring validation

The method's performance (sensitivity, specificity, repeatability, reproducibility) has been evaluated using identical samples in several laboratories under control of a supervising laboratory.

Unknown

Validation of the method is unknown or the method is not validated.

  

Standardisation

One or more standardisations from this drop-down list can be selected by clicking.

CEN standard

Standardised by the European Committee for Standardisation (CEN).

EU reference method

Standardised by the Joint Research Centre of the European Commission or the EU-RL GMFF.

ISO standard

Standardised by the International Organization for Standardization.

National standard

Performed according to national standards (country not specified).

 

 

Method

One or more methods from this drop-down list can be selected by clicking. Limiting the list of shown methods in said drop-down list can be done by entering text into the field.

The drop-down list contains all methods in EUginius.

Detection Methods Search Result

Figure 25 shows an example of the result of a specific query. For more explanation about the different columns see above. The content of the table can be exported as an Excel file (see section 3.6 Exporting data).

Figure 25 - Result of detection method search

­Detailed examples on how to use the functions in the detection module can be found in 4.1 Detection: search workflow for detection methods.

3.2.2 GMO/method matrix

The GMO/method matrix section lets you find information on the specificity of a PCR method and its ability to detect GMOs (Figure 27). A set of methods can be selected and filtered by specific criteria. You can also select specific GMOs and/or species of interest or filter for GMOs with a specific authorisation status in the EU. If no GMOs are selected and no status filter applied the matrix will contain all GMOs present in EUginius.

3.2.2.1 Select methods foR the GMO/method matrix

The Filter Criteria for Select methods for the GMO/method matrix section lets you limit the detection methods which are shown in the verification matrix.

A detailed explanation of keywords and combining them with AND or OR in the detection methods filter/search was given in 3.2.1.3 All methods corresponding to defined criteria.

3.2.2.2 select GMOs for the GMO/method matrix

The Filter Criteria for Select GMOs for the GMO/method matrix section lets you limit the GMOs which are shown in the verification matrix. You can select specific GMOs, species of interest or filter for GMOs with a specific authorisation status in the EU.

 

Figure 26 - Define a query for the GMOs for the GMO/method matrix

For filtering EUginius makes use of Boolean operators, specifically ‘AND’ and/or ‘OR’.
   AND requires all provided keywords to match the results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

The list of GMOs to be shown in the matrix (Figure 27) can be restricted by different filters (Figure 26).

Specific GMOs or Species can be selected.

Stacks can be excluded (default) or included. 

The list of GMOs can be restricted by authorisation status. The authorisation options are combined with AND. This means that GMOs in the list should comply with all the options.

By hitting search EUginius will open up the option to show three result matrices, which all can be exported as an Excel file (see section 3.6 Exporting data).

·       GMOs detected by selected methods

·       GMOs not detected by selected methods

·       All GMOs

3.2.2.3 Navigating The Matrix

Figure 27 - Verification matrix

Except for GMO, Authorisation, Species and Reference material (RM) available, all column headers are detection methods in EUginius. This list of detection methods can be limited by using filters in the Select methods for the GMO/method matrix section of the search page. For more information on this section consult 3.2.2.2 Select methods for the GMO/method matrix.

All row headers are GMOs in EUginius. This list of GMOs can be limited by using filters in the Select GMOs for the GMO/method matrix section of the search page. For more information on this section consult 3.2.2.3 Select GMOs for the GMO/method matrix.

The matrix crosses filtered GMOs with filtered detection methods, assigning a value to each GMO-method combination. The values indicate the reliability with which a method will detect a certain GMO. These values mean the following:

3

Detection of the target is experimentally verified using reference material

2

Detection of the target is verified by sequence alignment

1

Detection of the target is based on other information in EUginius (literature, plasmid map etc.)

-1

No expected target detection, based on other information in EUginius (literature, plasmid maps etc.)

-2

No expected target detection, based on sequence alignment

-3

No target detection is experimentally confirmed using reference material

In the GMO column, clicking a GMO’s name will take you to the respective GMO details tab. For more information on this tab consult 3.1.4 GMO detailed information.

Authorisation uses coloured symbols to display the approval status of the GMO for food, feed, cultivation and other uses. For more information on this, consult 3.5.1 Authorisation Symbols.

RM available tells you about reference material availability. If it says Yes, this means reference material is available, at this point the text is a hyperlink. Clicking the hyperlink will take you to the Reference Material tab of GMO Details. For more information on this tab, consult 3.1.4.5 Reference Materials.

Specific examples on how to use the functions in the GMO/method matrix module can be found in 4.2 GMO/method matrix: Optimisation of a screening strategy and 4.3 GMO/method matrix: Designing a Screening strategy .

 

3.2.3 Reference Material

The Reference material section allows to perform searches on the availability and on the source of GMO reference materials (Figure 28), providing you with the information you need to validate or perform your experiments.

3.2.3.1 Searching

Figure 28 - Define a query for reference materials

For its searches EUginius makes use of Boolean operators, specifically AND and OR.
   AND requires all provided keywords to match the search results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

In the reference material search all fields need to match reference material for it to be shown in the search results. The search fields in this section are query-building searches. Selecting two values in one field means EUginius puts an OR between the keywords. This means that only one of the keywords has to match.

Below is a list with descriptions of the search parameters.

1.

GMO

The name(s) of GMOs for which you want to find reference material.

2.

Species

The species for which you want to find reference material.

3.

Source

The institution which provides the reference material.
This can be AOCS, EURL (JRC), Eurofins GeneScan, IRMM/ERM, SIGMA-ALDRICH or the Pasteur Institute.

4.

Material Type

The type of material you would like to have as reference material.
Reference material can vary from dried powder to DNA or even bacterial strains.

5.

Certified

Checking this box will mean only certified materials are shown.

3.2.3.2 reference material search result

Figure 28 shows an example of the result of a specific query. For more explanation about the different columns, see the search criteria above (Figure 29). The column Value is not a search criterion but indicates the concentration of the GMO in the sample. The content of the table can be exported as an Excel file (see section 3.6 Exporting data). Clicking catalogue number takes you to the details. For more information on this page, consult 3.1.5.3 GMO reference material.

Figure 29 - Reference material search result

 

3.3 Analysis

The Analysis module consists of 14 input fields containing information on GMO detection results (Figure 30). It supports you in sample analysis and can provide explanations for detected events. Import result file lets you import an Excel file with screening outcomes from your laboratory, saving you from entering data manually. ­A detailed example workflow showing how to use the functions can be found in 4.4 Analysis Tool.

 

3.3.1 Entering Screening Data

Figure 30 - Manually entering screening data for Analysis module

The fields can be filled with the following information:

1.

Species

Species detected with a taxon-/species-specific method.

2.

GMO

GMOs detected with an event-specific method.

3.

Promoter

Promoters detected with an element-specific method.

4.

Terminator

Terminators detected with an element-specific method.

5.

Coding Sequence

Coding sequences detected with an element-specific method.

6.

Other elements

Other elements detected with an element-specific method.

7.

Construct

Constructs detected with a construct-specific method.

8.

Step 2, NOT detected

Here you should enter any species-, GMO-, promoter-, terminator, coding sequence, other element-, construct-specific methods that you used but that did not yield positive results.

 

 

 

3.3.2 Importing Screening Data

 

Import result file lets you import an Excel file with screening outcomes to save time entering data.

Figure 31 - Importing screening data for Analysis module

The Excel file which can be imported (Figure 31) has a layout especially designed for easy entry in either EUginius or a LIMS (laboratory information management system).

Row 1

Row 1 is redundant for data analysis purposes; it purely provides the user of the Excel sheet with a name for the method.

Row 2

EUginius’ method abbreviation. This is required for EUginius’ analysis module. For finding the EUginius method abbreviation that corresponds to your method(s) (see 4.1.2.1 Which method in EUginius corresponds to the P-35S method from my laboratory?).

Row 3

LIMS’ method abbreviation. This is required for LIMS’ data management.

Rows 4+

Each row from 4 onwards is a separate screening. Once the analysis has been run you can switch between screening results by moving pages.
This allows you to run multiple analyses at the same time.

 

 

Column A

A legend describing the contents of the rows behind them.

Columns B+

A matrix of screening information showing test results per method for the different screening samples.

 

 

D

Detected, the test showed a positive result.

ND

Not Detected, the test showed no result.

-

Blank, this test was not performed.

 

3.3.3 Analysis Results

After clicking the Analyse button, EUginius will begin to calculate which parts of your screening data coincide with the detected GMOs and which other GMOs may be present that have not been accounted for in your screening. When you have used an import file with results, the samples will be shown one by one on separate pages.

GMO Information is provided in a matrix with colour coding and symbols. These colours and symbols have the following meanings:

Unexplained detected target (detected target not present in any of the identified GMOs)

Confirmed not-detected target (tested but not detected)

Explained detected target (detected target present at least in one of the identified GMOs)

3.3.3.1 Confirmed output

The parameters which EUginius used in the analysis are displayed first (Targets detected by used methods/ Targets not detected by used methods).

Then, the analysis report shows the GMOs which were identified with the event specific method(s) as well as the elements which were detected. Additionally, it is indicated if the presence of the detected elements can be explained by the GMOs identified (green underlined) or not (red underlined).

In the table, complementary information on the identified GMOs are displayed (Figure 32).

Figure 32 - Confirmed output

1.

Targets detected by used method/Targets not detected by used method

Parameters which were used in the analysis are listed in this section.

2.

Analysis Report

Lists targets which were detected (GMOs/ constructs/ elements).
This should match what you entered in step 1 of the module

3.

Refine Search

Brings you back to the GMO analysis module
All entered values should be preserved

4.

Species

Species of the GMO

5.

GMO

GMOs name
Clicking the GMO name will lead you to the GMO detailed information section. For more information on this section consult
3.1.4 GMO Detailed information-

6.

Promoter

All Promoters which are present in the GMO

7.

Terminator

All Terminators which are present in the GMO

8.

Coding Sequence

All Coding Sequences which are present in the GMO

9.

Construct

All Constructs which can be detected in the GMO

10.

EU authorisation

Approval status of the GMO for food, feed, cultivation and other uses. Additional information on EU authorisation can be found in Authorisation tab. For more information on this, consult 3.4
   Authorisation

3.3.3.2 GMO prediction view

The GMO Prediction views shows GMOs which may explain targets  detected in the sample but not present in be the GMOs identified (Figure 33). The GMOs are sorted in alphabetical order of the species by default.

Note: It is your choice to restrict the outcome. EUginius can only make calculations based on your input.

Figure 33 - GMO prediction view (note that the importance sorting was used in this example)

1.

Detected Species Only

Ticking this box means only GMOs will be shown from species that you detected.

This is especially useful if you are sure what kind of material you   have.

2.

Verified Methods Only

Ticking this box means EUginius will analyse based purely on +3 (practically) verified methods for GMOs.

Theoretical matches between method and GMO will not be considered.

3.

Exclude Undetected

This will exclude any GMOs that contains target(s) which you tested for but did not detect.

This also counts for species.

4.

Species

Species of the GMO

5.

GMO

GMOs name

Clicking the GMO name will lead you to the GMO detailed information section. For more information on this section consult 3.1.4 GMO Detailed information

6.

Importance sorting

Shows the number of unexplained targets over the amount of explained targets (in prediction view only).
Checking the box will put the most likely GMOs on top.

7.

Promoter

All Promoters which are present in the GMO

8.

Terminator

All Terminators which are present in the GMO

9.

Coding Sequence

All Coding Sequences which are present in the GMO

10.

Construct

All Constructs which can be detected in the GMO

11.

EU authorisation

Approval status of the GMO for food, feed, cultivation and other uses. Additional information on EU authorisation can be found in Authorisation tab. For more information on this, consult 3.4  Authorisation

 

3.4 Authorisation

Figure 34 - Authorisation sections

When entering the Authorisation module, you are presented with three different sections: Search for generic approval, Custom search – EU applications, and Free-text search (Figure 34). All sections in this tab provide you with information regarding GMO approval.

 

3.4.1 Authorisation Symbols

Many of EUginius’ sections have columns for EU authorisation. These use coloured symbols to display approval status of the GMO for food, feed, cultivation and other uses. These symbols indicate the following:

Not Approved

Food

Not approved for human consumption in the EU

Feed

Not approved for animal consumption in the EU

Cultivation

Not approved for cultivation in the EU

Other uses

Not approved for any other uses in the EU

Approved with Restrictions or Phasing Out

Food

Approved for human consumption in the EU with restrictions or phasing out

Feed

Approved for animal consumption in the EU with restrictions or phasing out

Cultivation

Approved for cultivation in the EU with restrictions or phasing out

Other uses

Approved for any other uses in the EU with restrictions or phasing out

Approved

Food

Approved for human consumption in the EU

Feed

Approved for animal consumption in the EU

Cultivation

Approved for cultivation in the EU

Other uses

Approved for any other uses in the EU

Not submitted

Food

Approved for human consumption in the EU

Feed

Approved for animal consumption in the EU

Cultivation

Approved for cultivation in the EU

Other uses

Approved for any other uses in the EU

 

As of 2023:

MON810 maize is the only GMO with limited approval for EU cultivation. All other GMOs are not approved for cultivation in the EU.

 

 

3.4.2 Search for Generic Approval

Search for Generic Approval section lets you find information on the approval status of a specific GMO for use in food, feed, cultivation or other uses (Figure 35).

3.4.2.1 Searching

Figure 35 - Search for generic approval

For its searches EUginius makes use of Boolean operators, specifically AND and OR. All searches in this module use AND meaning that all provided keywords have to match the search results, narrowing down the number of results.

Below you can find the meaning of all keywords that can come up in your searches for generic approval.

1.

GMO

The name(s) of GMOs of which you want to know the authorisation status.

2.

Species

The species for which you want to know the authorisation status.

3.

Country

The country/region for which the authorisation applies.
For regulatory reasons, EU is considered a “country” in EUginius.

4.

Country-Zone

A larger region which the authorisation applies for.
 e.g. Europe

5.

Authorisation

Section that lets you specific your search based on authorisation status of GMOs.

  

3.4.2.2 Search Results

Figure 36 - Generic approval search results

Changing your search can be done by clicking Refine Search at the top of the page (Figure 36). When clicking the link, you are taken back to the generic approval search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

1.

GMO

The name of the GMOs which the approval is for.
Clicking the GMO name will take you to GMO details, for more information on this consult 3.1.4 GMO detailed information

2.

Species

The species for which you want to know the authorisation status.

3.

Continent

Continent in which the shown authorisation status applies.

4.

Country

Country in which the shown authorisation status applies.
This can also be EU for EFSA decisions

5.

National authorisation

Authorisation of the GMO for food, feed, cultivation and other uses. For regulatory reasons, the EU is seen as one nation.

EUginius uses symbols to indicate authorisation status, for more information on this consult 3.4.1 Authorisation Symbols

 

 

 

3.4.3 Custom Search - EU applications

Here you can use a set of search parameters which are specific to EU applications or which describe the specificity of the GMO(s) subject of EU applications (Figure 37).

The criteria are included when selected under positive criteria and excluded when selected under negative criteria.

You can expand the list of search parameters for both, positive and negative criteria, by adding optional filters. There are seven filters which can be added to or removed from the selection.

Stacks can be included (default) or excluded from the search. 

 

 

3.4.3.1 Searching – positive criteria

Figure 37 – Explanation custom search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. All fields are combined in the query with AND, meaning that all provided keywords have to match the search results, narrowing down the number of results. Multiple selections in one field are combined with OR, meaning the result should match one of the keywords in this field unless you can choose between AND and OR (fields Traits and Genetic Elements).

Below, you can find the meaning of all keywords that can be used in the EU applications searches. Numbers in parentheses correspond to optional criteria.

1.

Application reference number

A unique identifier for the application, assigned to it by the institute which received the application.

2.

Species

Species for which you want to find information.

3.

GMO

Name(s) of GMOs for which you want to find information.

 

 

 

(4.)

UID

Unique Identifier code for GMOs.

5.

Intended use

Use(s) and EU authorisation status for the GMO(s).

6.

Applicant

The company / institution which submitted the application.

7.

Country

Country in which the authorisation applies.

8.

Commission decision number

Number of the Commission Implementing Decision.

9.

Expiry date

Date on which the authorisation expires.

(10.)

Decision date

Date of the European Commission decision.

(11.)

Legislation

Legislation under which the application was submitted / the authorisation is granted

(12.)

Traits

Traits which can be exhibited by GMOs

(13.)

Genetic Elements

Elements which can be inserted in GMOs

(14.)

Tradenames

The name(s) which the GMO is commonly sold under

(15.)

Companies/Institutions

The company/institution which developed the GMO as well as companies producing or selling the GMO.

All values entered here will be considered in the results.

3.4.3.2 Searching – Negative criteria

Below the section Search for positive criteria you can select negative criteria (Figure 37), which will exclude search results from your query. The fields and queries function as within the positive criteria search (Figure 37).

3.4.3.3 Search Results

EUginius opens up the option to show three result tables, which all can be exported as an Excel file (see section 3.6 Exporting data):

·       All applications: all applications that meet the search criteria (Figure 38a),

·       Valid applications: applications that meet the search criteria and have at least one authorisation status currently set to approved, approved with restrictions, phasing out or pending,

·       Further applications: applications that meet the search criteria and do not have any authorisation status set to approved, approved with restrictions, phasing out or pending.

Figure 38a - Custom search results

Changing your search can be done by clicking Refine Search at the top of the page. When clicking the link, you are taken back to the custom search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

 

1.

Application reference number

Number from the European Food Safety Authority (EFSA) assigned to the application

2.

Species

Species for which you want to find information.

3.

GMO

Name(s) of GMOs for which you want to find information.

Clicking the GMO name will lead you to the GMO Detailed information section. For more information on this section consult 3.1.4 GMO Detailed information.

e.g.  “+2 GMOs” indicates that there are two more GMOs covered by the application. Clicking on the blue arrow symbol  (    ) in the first column expands the list with the additional GMOs.

(4.)

UID

Unique Identifier code for GMOs.

5.

Intended use

Use(s) and EU authorisation status for the GMO(s).

6.

Applicant

The company / institution which submitted the application.

7.

Commission decision number

Number of the Commission Implementing Decision.

8.

Expiry date

Date on which the authorisation expires.

9.

Decision date

Date of the European Commission decision.

(10.)

Legislation

Legislation under which the application was submitted / the authorisation is granted

(11.)

Traits

Traits which can be exhibited by GMOs

(12.)

Genetic Elements

Elements which can be inserted in GMOs

(13.)

Tradenames

The name(s) which the GMO is commonly sold under

(14.)

Companies/Institutions

The company/institute which developed the GMO as well as companies producing or selling the GMO.

 

The blue arrow symbol (   ) in the first column indicates that there are more GMOs covered by the application. When you click on the symbol these additional GMOs are displayed as well (Figure 38b).

Figure 38b - Custom search results – expanded GMOs display

3.4.4 Authorisation Free-text Search

The authorisation free-text search lets you find all applications submitted in the European Union for authorisation of GMO(s). It allows the use of application related terms (name of the applicant, the name of the EFSA application file reference, the Commission Decision Number), as well as GMO related terms (GMO name, GMO alias, UID, species name (Latin name or common name), trade name(s), company/institution). The search terms are highlighted in the result table.

Some examples of free-text searches and search terms are listed below:

Search Term(s)

Search result(s)

*

Finds all applications in EUginius

Bt*

names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.

305423

GMO “DP305423” and its’ UID "DP-3Ř5423-1"

Ms8 OR Rf3

GMOs “Ms8” and “Rf3” or stacks with one or both (e.g. “Ms11 x Rf3” or “Rf3 x GT73”)

Moon*

Tradenames “Moonlite” and “Moonberry”; additionally, Carnation lines which contain “Moon*” in their Alias – please note that the latter results are not highlighted in yellow as the GMO alias is not displayed.

Gossypium

species "Gossypium hirsutum”

Cotton

species " Gossypium hirsutum”

syngenta

Applicant or Companies/Institutions e.g. "Syngenta Seeds SAS", “Syngenta Crop Protection”

“Syngenta Seeds SAS”

Specifically finds “Syngenta Seeds SAS”

EFSA*

Finds all Application reference numbers containing “EFSA”

“EFSA-GMO-RX-GA21”

Specifically finds application “EFSA-GMO-RX-GA21”

Directive 90/220/EEC

All applications submitted under legislation “Directive 90/220/EEC”

98/292 OR 2017/1207

Applications with the respective Commission decisions “(EU) 2017/1207” OR  “(EC) 98/292”

98/292 AND 2017/1207

No result – no application decided with both Commission decisions “(EU) 2017/1207” AND  “(EC) 98/292”

 

The display of the result table can be amended using the box on the right of the page (Figure 39). It allows you to show/hide some of the columns.

 

Figure 39 - Results of authorisation free-text search

 

3.5 Search

Figure 40 - Collected search options

In the Search module (Figure 40) you can do a free-text keyword search on GMOs and literature.

An advanced search option is also available for GMOs and literature. Clicking the hyperlink for advanced GMO search will bring you to a new page, for more information on this consult 3.5.1.1 Advanced GMO Search.

Clicking the hyperlink for advanced Literature search will also take you to a new page, for more information on this consult 3.5.2.1 Advanced Literature Search.

Element Search can only be accessed through this module and it allows you to search for genetic elements based on GMO, Donor, Species, Elements and Traits. For more information consult 3.5.3 Element Search.

All other links and functions from this page can be accessed from outside this module as well. Information on these other functions and pages was previously discussed in this manual. The free-text search for detection methods is explained in Chapter 3.2.1.2 Free-text search for methods. The Table of Contents lists all other chapters and can help you navigate to the specific search functions.

 

3.5.1 Search GMO

The standard free-text GMO search can find GMO, UID, Tradename, Species, Company, Traits and Genetic Elements.

Some examples of free-text searches and search terms are listed below:

Search Term(s)

Finds GMOs with

Bt*

names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.

305423

with UID "DP-3Ř5423-1"

MON 00810 6

UID "MON-ŘŘ81Ř-6"

RRS

alias "RRS" (=GTS 40-3-2)

zea

species "Zea mays"

soybean

species "Glycine max"

syngenta

UID "Syngenta"

yieldgard

tradename "YieldGard VT PRO", "Yieldgard™", "Maxguard/Yieldgard", etc.

bt11

name "Bt11" and stacks containing Bt11

insect

trait "Insect resistance"

 

3.5.1.1 Advanced GMO Search

The advanced GMO search (Figure 41) presents you with seven fields, these correlate to the seven features mentioned above.
The main advantage of the advanced search is filtering out unwanted results, as it allows exclusion of stacked events and closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search. Advanced GMO Search has two search sections: Select GMOs and Stacks, Search GMOs.

Select GMOs and Stacks lets you filter for specific GMOs by picking event-specific GMO names or UIDs.

 

Example:

Entering MON810 will show MON810 and all stacks containing MON810. These results will be the same as a search for MON810’s UID (MON-ŘŘ81Ř-6)

 

 

Checking “Exclude stacked events” means only one GMO shows up per entered keyword, this would be the GMO which you entered. No stacks of this GMO will be shown in the result list. Exclude stacked events is selected by default.

Search GMOs lets you search for GMOs using attributes instead of names or identifiers.

Figure 41 - Advanced GMO search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. Searching for traits or genetic elements allows to choose between the two search operators.

1.

Tradename

The name which the GMO is commonly sold under.

2.

Species

Species for which you want to find reference material.

3.

Company

Company which produces/sells the GMO.

4.

Exclude stacked events

Checking this stops any stacks from being shown.
   Stacks are crosses between two different GMOs

5.

Traits

Traits which can be exhibited by GMOs.

6.

Genetic Elements

Elements which may be integrated/present in GMOs.

 

Search Results from the advanced GMO search serve the same function as a filter for the GMO list of identifiers. For any questions regarding the search results we recommend you consult 3.1.1 List with GMOs and their Identifiers.

 

3.5.2 Search Literature

The standard free-text literature search is capable of searching for GMO name, abstract, citation and keywords.

The advanced literature search presents you with three search options, GMO search, Genetic Element search and DNA search. Each of these include a name search, publishing authority specifier and a publication date. Keywords entered in other sections will not be taken into account when clicking the search button (see example). The main advantage of the advanced search is filtering out unwanted results, as it allows for a closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search.

3.5.2.1 Advanced Literature Search

Advanced GMO Search has three search sections: GMO search, Genetic Element search and DNA Name search.

Searching by GMO allows for specification of GMO, publishing authority and publication date.

Useful when you want to know more about a specific GMO

Searching by Genetic Element allows for specification of genetic element, publishing authority and publication date.

 

Searching by DNA name allows for specification of genetic element, publishing authority and publication date.

 

Publishing authority usually refers to one specific institution, though “Research Group” can also be picked here. Picking Research Group will show any scientific publication matching your criteria.

Publication date may differ from the application or decision date. Keep this in mind when searching for literature.

3.5.2.2 Literature Search Results

Figure 42 - Literature search results

Changing Search Criteria can be done by clicking Refine Search at the top of the page (Figure 42). When clicking the link, you are taken back to the literature search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

1.

Citation

Literature citation as generally used in references

Research groups publications are cited in APA 6th edition

Clicking the citation will lead you to the Literature details section.

For more information on this section consult 3.5.2.3 GMO Literature Details

2.

Publication year

Year in which the literature was published

3.

Publishing authority

Authority which published the literature

4.

Publication type

This shows the type of publication and can show you what the purpose of the publication is.
e.g. application document, patent, decision or peer-reviewed article

5.

Content types

This is a tagging system for EUginius literature with multiple content types being assigned to literature for different reasons.
e.g. application, decision, detection, environment, risk assessment and safety

3.5.2.3 GMO Literature Details

GMO literature details gives information about the literature citation and provides links to the literature. For an explanation of the module consult Figure 43 and table below.

Figure 43 - GMO literature details

1.

Citation

Literature citation as generally used in references.
Research groups publications are cited in APA 6th edition.
Most other documents also stick to a similar standard.

2.

Publication type

This shows the type of publication and can show you what the purpose of the publication is.

e.g. application document, patent, decision or peer-reviewed article

3.

Comment

Notes of the EUginius staff about the literature are added here.

This is generally left empty.

4.

Content type

This is a tagging system for EUginius literature with multiple content types being assigned to literature for different reasons.
e.g. Application, decision, detection, environment, risk assessment and safety

5.

Keyword

Any words which EUginius staff deemed relevant are added here, in order to aid you in finding the right document.

6.

Publication Year

Year in which the literature was published.

7.

Authority

Authority which published the literature.

8.

View PDF

If available, a .pdf file of the literature can be downloaded here.

9.

View Url

A hyperlink to the citation where you can find the text.
Clicking the hyperlink will open it in a new tab.

 

3.5.3 Element Search

The Element Search presents you with six fields that contribute to one query (Figure 44). This allows specification of GMO, Element Donor, Species and Element or Trait.

With similar fields exclusion of certain known GMOs, genetic elements or traits is also possible. This helps in the analysis of detected GMOs when several events are tested for.

3.5.3.1 Element Search

Figure 44 - Explanation of Element search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. AND means the result needs to contain all entered keywords. OR means all GMOs matching the keyword will be shown regardless of other keywords.

1.

GMO

GMO name
Using this in a search will show all elements inside your GMO

2.

Donor

Species which the genetic element was taken from.
The element may also be synthetic, this option is also listed

3.

Species

Species in which the genetic element has been inserted.

4.

Genetic Elements

A query-building search of all elements in EUginius element thesaurus.
Using this in a search will show all GMOs and inserts that carry the selected element

5.

Traits

Traits that are attributed to elements in the thesaurus.

  

 

Searching for information on one specific element:

If you have an element’s name and you would like more information about it, you can type the name in the Genetic Elements query-building field.

 

 

 

3.5.3.2 Element Search Results

Figure 45 - Element search results

Changing your search can be done by clicking Refine Search at the top of the page (Figure 45). When clicking the link, you are taken back to the element search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

1.

GMO

GMO wherein the element is found in

Clicking the GMO name will take you to GMO details, for more information on this consult 3.1.4 GMO detailed information

2.

Species

Species of the GMO

3.

DNA

Insert or vector which was used to insert the element into the GMO Clicking the DNA name will take you to DNA details, for more information on this consult 3.1.5.1 Genetic Element details

4.

Element

The element which matched your search criteria

5.

Donor

Species which the genetic element was taken from

Elements can also be synthetic.

6.

Trait

Trait that was introduced into the GMO
This is only available for coding sequences.

 

3.5.4 Navigating Search Results

Figure 46 - Navigating search results

Sorting allows you to arrange your filtered results in alphabetical order

Sort

The sort symbol indicates that the feature is not being sorted for

Ascending

The ascending symbol indicates that the feature is currently being sorted for

Descending

The descending symbol indicates that the feature is currently being sorted for

Navigating Pages lets you go through your results or limit the amount of results you see.

Next Page

Navigate to the next page

Last Page

Navigate to the last page (e.g. page 25 out of 25)

Previous Page

Navigate to the previous page

First page

Navigate to the first page (page 1)

 

3.6 Exporting data

Several sections in EUginius allow you to export data using the                         button.

After clicking this button EUginius will generate an Excel (.xls) file for you with all information that is presented in the matrix. All pages are included in the export.
This may take a while depending on the amount of data you want to export. Your browser will then prompt you with the option to download the exported file.

Exported files adhere to a set format in EUginius:
   Exportpage_YearMonthDay_HourMinuteSecond_Millisecond.xlsx

 


 


 

 

 

 

 

 

 

4.0                          Workflow


 


 

4.1 Detection: search workflow for detection methods

4.1.1 Searching for a method targeting an endogenous maize gene (Taxon-Specific method)

In this example, we are looking for a taxon-specific method to be used as reference PCR method for quantification of GM-maize.

We would like to know:

·       Which methods are available?

·       Which method is suitable to quantify genetically modified maize?

 

4.1.1.1 Available maize-specific methods

For this purpose, go to the Detection methods section under the Detection module.

On this page, there are three different options for a method search. The result tables of each search contain different type of information.

If we are searching for maize-specific methods, we can use two of the available search functions (Figure 47a/ 47b).

Figure 47 – PCR methods for GMO detection and identification: Examples a and b show how to screen for maize-specific methods.

a.       Using the Free text search for methods gives you a result table with technical information.

As the search term enter the maize Latin name ‘Zea mays’ and perform the search (Figure 47 (a)).

NB: In this section, always use the Latin name from species.

You get a list of all the taxon-specific methods present in EUginius which target a maize specific sequence. The results table displays the method name (code used in EUginius and further databases) and all information about the primers/probe and amplicon sequences (Figure 48).

 

Figure 48 - Search results – free-text search for maize-specific methods (example a).

There are currently 10 methods available for the detection of maize.

QT-TAX-ZM-001 and QT-TAX-ZM-014 use the same primers and probe, QT-TAX-ZM-003 use nearly the same primer (forward primer has one additional base).

QT-TAX-ZM-002 and QT-TAX-ZM-005 use the same primers but have different probes.

b.       Using the All methods corresponding to defined criteria search gives you a result table with qualitative information.

Here you first indicate if you want to search in a specific set of methods. For our purpose, we use the entire pool of methods and check ‘All’ (Figure 47 (b)).

Then, you select suitable filter(s). To look for maize-specific methods, select Zea mays in the filter ’Species‘ and perform the search (common names are also usable; e.g. maize or corn).

You get a list with the same maize-specific methods as found previously. However, instead of the sequence information, the results table displays a short description of the method with indication of the number of target copies per haploid genome (when available) as well as information about the type of validation and standardisation (Figure 49).

Figure 49: Search results - All methods corresponding to defined criteria: in this case all maize-specific methods (example b).

There are currently 10 methods available for the detection of maize. They were all validated through a ring trial validation. All but one belongs to the ISO standard methods or the EU reference method.

Six methods target the maize alcohol dehydrogenase 1 (adh1) gene and two other methods the maize high-mobility-group (hmg) gene.

The estimated number of target copies per haploid genome are indicated for four of the methods, (QT-TAX-ZM-014, QT-TAX-ZM-004, QT-TAX-ZM-002, QT-TAX-ZM-001).

4.1.1.2 Best method(s) for quantification analysis of genetically modified maize

When using a taxon-specific method for quantification purposes, several criteria may be of importance:

·       the validation status of a method as well as the standardisation give indication on the reliability of the method

·       the number of target copies per haploid genome has a direct effect on the calculation.

Therefore, when looking for a taxon-specific method which should fit for quantification, the All methods corresponding to defined criteria should be used (see 4.1.1.1.b). In the results table, (Table 2) you get all necessary information to choose the appropriate method(s).

Moreover, in EUginius methods designed for quantification have the prefix QT- (for quantitative), the methods starting with QL- have been designed for qualitative analysis.

For maize, the methods QT-TAX-ZM-001, QT-TAX-ZM-014 are both targeting the single copy gene adh1, both are of high standard (respectively ISO and EU reference method) and can be used for quantification purposes. Similarly, the method QT-TAX-ZM-002 which targets the single copy gene hmgA and belongs to the ISO standard methods is suitable for quantification.

When using the QT-TAX-ZM-004 method which targets the maize aldolase (ald1) gene (EU reference method), the two copies of ald1 per haploid genome have to be considered in the calculation.

 

4.1.2 Does the method currently used in my laboratory, correspond to one of the methods registered in EUginius?

EUginius uses a specific syntax for the naming of the methods (mostly shared with the GMOMETHODS application from JRC  -  https://gmo-crl.jrc.ec.europa.eu/jrcgmomatrix/). This specific name is used in different tools of the EUginius application (e.g. GMO/method matrix, analysis tool). It could therefore be useful for the user, which may have registered the methods with an own naming system, to find the corresponding method (and official method name) in EUginius.

4.1.2.1 Which method in EUginius corresponds to the P-35S method from my laboratory?

In EUginius there are 8 methods registered that target the promoter from the Cauliflower mosaic virus (P-35S-CaMV; see table below).  If you would like to use the analysis module of EUginius you have to enter the EUginius method name to select the target detected (or not detected) in your laboratory analysis. Therefore, finding the correct method name is mandatory.

Target

EUginius' method name

Type

P-Cauliflower mosaic virus

(P-35S)

QL-ELE-00-001

element-specific

P-Cauliflower mosaic virus

(P-35S)

QL-ELE-00-004

element-specific

P-Cauliflower mosaic virus

(P-35S)

QL-ELE-00-005

element-specific

P-Cauliflower mosaic virus

(P-35S), P-scp1-SYNTH, E-35S-CaMV

QL-ELE-00-012

element-specific

P-Cauliflower mosaic virus

(P-35S)

QL-ELE-00-017

element-specific

P-Cauliflower mosaic virus

(P-35S)

QT-ELE-00-001

element-specific

P-Cauliflower mosaic virus

(P-35S), P-scp1-SYNTH, E-35S-CaMV

QT-ELE-00-004

element-specific

P-Cauliflower mosaic virus

(P-35S)

QT-ELE-P35S 1-5'

/P35S 1-3'

element-specific

 

To check which one corresponds to the method you use, go to the Detection methods section under the Detection module (Figure 1).

Here, use the Free text search for methods.

·       Use the sequence of one primer/probe (for example GCCTCTGCCGACAGTGGT; Figure 50), or

·       use the primer/probe name: EUginius enters the primer/probe name as published in literature.

Figure 50: Search results – in this case the result of a free-text search using a specific primer sequence.

The search result (Figure 50) shows that two methods, QT-ELE-00-004 and QL-ELE-00-012, use the specific primer used in the free-text search.

Keep in mind to check further sequences (reverse primer/probe) to identify/confirm the corresponding method.

 

4.2 GMO/method matrix: Optimisation of a screening strategy

In this example we would like to know if the pool of screening methods we currently apply allows to detect all soybean single events authorised in the EU, and whether it provides a good coverage on non-authorised single events. Finally, we would like to know if there are methods that we could add to our pool of screening methods in order to increase the coverage.

Our approach consists therefore of the following steps:

·       Check the coverage of the current set of methods – does the set detect all soybean single events authorised in the EU?

·       Identify events that are not detected by the methods (screening-gap)

·       Search for methods able to close the screening-gap

 

4.2.1 Coverage check of the current set of methods

To check the coverage of the current set of methods, go to the GMO/method matrix section under the Detection tab.

On the left under Restrict method list by: select, under ’method’, the methods currently used for the analysis of soybean (pool of 9 screening methods currently used, see table below):

Target

EUginius code

construct: ctp2/cp4-epsps

   QL-CON-00-008

construct: P-35S/pat

   QL-CON-00-011

element: P-nos-RHIRD

   QL-ELE-00-008

element: T-nos-RHIRD

   QL-ELE-00-011

element: CS-bar-STRHY

   QL-ELE-00-014

element: E-FMV, P-34S FMV

   QL-ELE-00-015

element: CS-cry1Ab-BACTU, CS-cry1Ab_1Ac_tr-SYNTH, CS-cry1Ac-BACTU

   QL-ELE-00-016

element: T-rbcS_E9-PEA

   QL-ELE-00-024

element: E-35S-CaMV, P-Cauliflower mosaic virus

   QT-ELE-00-004

 

Select on the right under Select GMOs for the GMO/method matrix the species of interest:

Glycine max (soybean)

Select all authorisation status (selected by default) and perform a search (Figure 51).

Figure 51– Example workflow to check the coverage of 9 screening methods to detect all soybean single event

GMO/method matrix search result gives us matrices assigning verification values to the combinations of GMOs and detection methods, displayed are:

·       under the banner GMOs detected by selected methods the GMOs that are detected by at least one of the selected methods (first matrix),

·       under the banner GMOs not detected by selected methods the GMOs that do not contain any of the target of the selected methods; they constitute our screening-gap (second matrix).

.

Figure 52 – Result matrix with 26 soybean events detected by the selected methods.

For an explanation of this matrix consult 3.2.2.3 Navigating the matrix.

The first matrix indicates that 26 soybean events are detected by the selected methods (Figure 52). Moreover, the matrix allows to identify if there are redundancies in our current strategy (methods that detected events already covered/detected by other methods).

NB: Methods that detected only a part of events already detected by another method do not enlarge the coverage; they can, in some cases, help by the identification of the events.

In this example, one method is not adapted to the screening of soybean events (indicated by the red background), and four methods do not enlarge the coverage (indicated by the red frame).

The use of a pool reduced to four methods (T-nos-RHIRD (QL-ELE-00-011), CS-cry1Ab-BACTU, CS-cry1Ab_1Ac_tr-SYNTH, CS-cry1Ac-BACTU (QL-ELE-00-016), CS-pat-STRVR (QL-ELE-00-025), E-35S-CaMV, P-Cauliflower mosaic virus (QT-ELE-00-004)) would allow to detect the 26 events currently depicted.

 

4.2.2 Identification of the not detected events (screening gap)

The second matrix (‘GMOs not detected by selected methods’) indicates that 9 single events are not detected by the selected method (Figure 53).

Figure 53 – Result matrix showing GMOs which were not detected by the search query using selected methods.

Four out of nine events are genome edited GMOs (recognisable through the prefix GE in their names). For this type of GMOs, no screening based on element or construct specific method is applicable so far. Therefore, those events will not be further considered by the optimisation of the screening strategy; we will concentrate on the five remaining GMOs (indicated by the green frame).

 

4.2.3 Search for methods able to close the screening-gap

To identify methods that could allow us to detect more of the soybean events, we proceed to a second search.

For this purpose, we go to the GMO/method matrix section using refine search.

We reset the previous filter parameters.

We select under Select methods for the GMO/method matrix “all”.

We select under Select GMOs for the GMO/method matrix the five previously identified as not detected GMOs (see green box in Figure 53) and perform a search.

The results indicate in the first matrix that the 5 events previously identified as screening-gap are detected by the selected methods (all), which means that there is at least one method for each of these events which allows to detect it.

The matrix contains all the detection methods present in EUginius (258 as of July 2021) and is therefore very wide. Only details with positive values are displayed here. Taxon-specific methods are not relevant for our screening purpose and will not be considered.

Figure 54 – Methods with positive values (indicating possibility to detect these GMOs with the respective method).

Three methods can be used to close screening-gap (green boxes). Three of the events are detected by four element-specific methods targeting two different elements. These events get a verification value of +3 with one of these methods (targeting both T-orf23-RHIRD and T-transcript 7 (QL-ELE-T-g7-F/T-g7-R)), which means that the detection of the events has been experimentally verified. This method would be preferred to complete our screening strategy.

Two events are detected only by their event-specific methods (DP305423 (QT-EVE-GM-008) and CV127 (QT-EVE-GM-011)). In order not to miss these events in the screening, these two methods should be added to the previously mentioned method.

 

4.2.4 Conclusion

Using the GMO/method matrix we were able to check our screening strategy. In the first step we identified four methods that are not necessary for the strict detection of soybean events. In a second step we were able to find three additional methods to complete our strategy and close the screening gap.

With a pool of 7 methods, we would be able to detect 31 soybean events including the 16 events that are authorised in the EU.

 

4.3 GMO/method matrix: Designing a Screening strategy

In this example we would like to design a screening test which allows to detect, on the basis of the elements they contain, at least the following GMOs:

·       Bt11

·       DAS59122

·       DAS40278

·       GA21

·       MIR162

·       MIR604

·       MON87427

·       NK603

 

4.3.1 Finding methods

For this purpose, we go to the GMO/method matrix section under the Detection tab. Here, we set the method set to SCREENING and enter the GMOs we would like to detect (Figure 55).

Figure 55 – Example of a screening for methods to detect specific GMOs in the GMO/method matrix module.

 

4.3.2 Selecting Methods

 

Figure 56 – GMO/method matrix search result. Note that this is only a part of the matrix.

GMO/method matrix search result gives us a matrix of GMOs and detection methods showing which methods can detect which GMOs (Figure 56). For an explanation of this matrix consult 3.2.2.3 Navigating the matrix.

When designing a screening we want to pick methods in such a way that all GMOs are detected at least once with as few as possible methods in the screening. Here method-GMO verifications of category +3 are preferred as they are most reliable.

Zoomed in, we see that several methods detect six of our nine GMOs and could be utilized. T-nos-RHIRD (QL-ELE-00-011) offers the highest reliability here as its effectiveness for these GMOs has been confirmed (Figure 57, red box).

Figure 57 – The method marked in red (QL-ELE-00-011) offers the highest reliability to detect 6 out of the selected 9 GMOs.

Now we need to find a method that fills in most of the gaps. The more additional GMOs are detected here the better. Having two matches will make identification easier. Several GMOs have a total of five matches and fill two of the three gaps. Here E-35S-CaMV, P-35S CaMV (QT-ELE-00-004) has the highest reliability to detect MON810 and DAS59122 (Figure 58, red box).

Figure 58 – An additional method (QT-ELE-00-004) marked in red can be used to detect two of the three remaining GMOs (MON810 and DAS59122).

After this, there is only one GMO that our screening cannot detect yet (DAS40278). There is only one method listed that can detect DAS40278 (P-ubi1-MAIZE (QL-ELE-P-Ubi-F/P-Ubi-R); Figure 59, red box), which we will also add to the screening.

 

Figure 59 – A third method (QL-ELE-P-Ubi-F/P-Ubi-R) marked in red fills the last gap to detect the remaining GMO (DAS40278).

 

4.3.3 Conclusion

Using EUginius’ GMO/Method matrix function we determined the optimal screening test for Bt11, DAS59122, DAS40278, GA21, MIR162, MIR604, MON87427 and NK603. This is composed of:

·       T-nos-RHIRD (QL-ELE-00-011)

·       E-35S-CaMV, P-35S CaMV (QT-ELE-00-004)

·       DAS40278 (P-ubi1-MAIZE (QL-ELE-P-Ubi-F/P-Ubi-R))

 

4.4 Analysis Tool

In this example we are given a feed sample of Zea mays which is presumed to contain the genetically modified maize event MON810.

We would like to know:

·       Are there other species in the sample?

·       Is MON810 really present in this sample?

o   Which detected elements can be explained by its presence?

·       Are there elements detected that are not explained?

·       Which GMOs can explain the detected elements not present in the identified GMOs?

o   Are these GMOs authorised in the EU?

o   How do we detect these GMOs?

·       What can we conclude?

4.4.1 Screening Results

In this example, we analysed the feed sample XD2210-1 with a set of five taxon-, two event-, one construct- and nine element-specific methods. The results presented in the table below can be entered manually or with the input file (excel-file containing the table as formatted here, note that wording of the headers as it is given below is mandatory).

Here we manually inserted the results into EUginius’ analysis module (Figure 60):

Figure 60 – Example of a search query in the analysis module. The search parameters can either be inserted manually or uploaded using an excel-file.

Clicking “Analyse” makes EUginius analyse your entered screening results. For an upload of an excel file, you would need to use “Choose file” and “Analyse result file” (Figure 60).

 

4.4.2 Confirmed Output

Confirmed output tells us which elements can be explained by the GMOs that we have detected (Figure 61).

Figure 61 – Results of the analysis described above. MON810 can explain the presence of the element P-Cauliflower mosaic virus.

The element P-Cauliflower mosaic virus as well as all the elements affiliated to it are targets of the selected method (QT-ELE-P35S 1-5'/P35S 1-3'). In this case, the element P-Cauliflower mosaic virus can be explained with the presence of MON810 which contains the element P-e35S-CaMV (affiliated to P-Cauliflower mosaic virus).

Two other elements, P-act1-ORYSA and T-nos-RHIRD could not be explained by the presence of MON810 in the tested sample. This means there must be another GMO in the mixture that was not tested for. The GMO Prediction view can help us figure out which GMO this might be.

 

4.4.3 GMO Prediction View

In this case, GMO Prediction View presents us with 170 different GMOs that might be in our sample (Figure 62; note that the numbers of possible GMOs can vary; the numbers in this example are from August 2021). We obviously want to reduce the list of possible candidates.

Please realise that the next steps will reduce the number of likely candidates based on your own assumptions/expectations.

Figure 62 – GMO prediction view shows all GMOs which might be contained in the analysed feed sample.

Many of the listed GMOs come from different species, in this sample however, we do not expect other species than the five we have tested. Checking the “Restrict list to GMOs from detected species” box will remove all GMOs from species that we did not detect (Figure 63). In this case we are only left with Zea mays GMOs after applying this filter.

After restricting to detected species we are left with 36 GMOs.

Figure 63 – GMO prediction view with the restriction to only show species which were part of the analysis (see green box).

 

We could test for the presence of these 36 GMOs, but since we are confident that we correctly performed our screening, we can eliminate a few more GMOs from this list.

Checking the “Exclude GMOs from the list that contain targets that could not be detected” box, will remove all GMOs with elements that we tested for but could not be detected (Figure 64). These are GMOs with elements that are underlined in yellow.

After filtering out not-detected species and not-detected elements, there are 8 GMOs left. One of them was already identified in the sample (MON810).

By checking “Importance sorting” we move GMOs to the top that best explain the elements which were not explained by MON810 (P-act1-ORYSA, T-nos-RHIRD). In this example GA21 would be the first listed candidate GMO. Here, 2/0 means that:

·       two (2) elements that are not explained by the presence of the identified GMO (MON810 in this case) are contained by the GMO listed. Such elements are red underlined.

·       none (0) of the already explained elements is contained by this GMO. Such an element would be green underlined.

Figure 64 – GMO prediction view with the restriction to exclude GMOs that contain targets which were not detected as well as the activated “importance sorting” function.

In this particular case, events GA21 best explains the unexplained elements as it contains the two elements which were detected but are not present in MON810. GA21 is authorised for food and feed in the EU.

Six more events (3272, 5307, MIR162, MIR604, MON87403, PY203) could be in the sample, but would not suffice to explain all unexplained elements. All but two (3272 and PY203) are authorised for food and feed in the EU.

In the next step, we would test for GA21 with an event-specific method.

 

4.4.4 Detection of Predicted GMO

Clicking the GMO name will take you to Detection Method GMO Details, which provides you with a list of all detection methods that will give a positive result for your GMO.

In the case of GA21 we are presented with 22 methods that will show positive for GA21, but not all 22 methods are useful to us. Since we want a method that is specific to GA21 it should be an event-specific method. There are two options for GA21: QT-EVE-ZM-007 and QT-EVE-ZM-014 (the abbreviation -EVE- in the method name indicates an event-specific method). Both are ring trial validated EU reference methods that are specific to GA21 and therefore best suitable for our purpose.

 

4.4.5 Conclusion

In doing this analysis we found out that:

·       Maize is present in the sample.

·       There are none of the other tested species in the sample.

·       Event MON810 is effectively present in the sample and can explain the detected target P-Cauliflower mosaic virus.

·       Most likely, GA21 is in the sample since it contains both unexplained elements.

·       GA21 can be detected with QT-EVE-ZM-007 and QT-EVE-ZM-014.

·       Further events could be present in the sample, but none of them is able to explain alone the unexplained elements.

·       MON810 is approved for animal feed in the EU, as is GA21. When GA21 would explain the presence of P-act1 and T-nos and the sample is marketed as being GMO, it is compliant.

 

You need to decide if the confirmation of the presence of GA21 is sufficient for your laboratory, or if you want to confirm all possible candidates.


 


 

 

 

 

 

 

 

5.0                          Input and Feedback


 


5.1 Input and Feedback

On its homepage EUginius offers two links that allow you to give feedback or to provide input on interesting GMOs.

5.1.1 Suggest New GMO

 

Clicking Suggest new GMO opens your local e-mailing software (e.g. Microsoft Office Outlook) with numerous filled-in fields. This is the standard layout for suggesting GMOs (see right).

The To... field should say database@euginius.eu with Suggested new GMO for EUGINIUS as subject.

Below this, we would like you to provide the name of the GMO you would like to see added to EUginius, your name, e-mail address, your affiliation and a source of information.

It greatly benefits EUginius staff if you provide as much information as you have available.

 

5.1.2 Give Feedback

 

Clicking Give feedback opens your local e-mailing software (e.g. Microsoft Office Outlook) with numerous filled-in fields. This is the standard layout for giving feedback on EUginius (see right).

The To... field should say databasemanager@euginius.eu with Feedback on EUGINIUS as subject.

Below this, we would like you to provide your name, e-mail address, your affiliation and your comment/feedback for the EUginius staff.

It greatly benefits EUginius staff if you provide as much information as you have available.

 

 

 

 


 


 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

6.0                          Terms and Conditions of Use



6.1 Terms of Use

The most recent terms of use can be found in EUginius’ footer under Terms of use.

6.2 Conditions of Use For Registered Users

EUginius is a web-based database application providing information on genetically modified organisms. It was jointly developed by the German Federal Office of Consumer Protection and Food Safety (BVL; Berlin) and the Dutch Wageningen Food Safety Research (WFSR; Wageningen UR).

EUginius also consists of an access-restricted section. Access to this section is restricted to authorised users of institutions that signed a membership agreement. Permission to use data obtained from EUginius shall be granted subject to the following terms and conditions:

1.       Authorised users shall receive a username and password with which they can gain access to the secure/protected area of EUginius. This user authorisation is personalised and may not be used by anyone other than the owner.

 

2.       A written request for access shall be submitted to BVL through the applicant’s employer.

 

3.       Authorised users are obliged to keep their password and username secret in order to avoid risk of abuse by third parties. If the authorised user becomes aware of any abuse of his/her access data, he/she shall be obliged to inform BVL without delay.

 

4.       Authorised users are obliged to ensure that the contact details they have stored in the EUginius system are kept up to date at all times. Notwithstanding this, all access authorisations will be reviewed on a yearly basis.

 

5.       All data stored in the EUginius system for which this access authorisation is required shall be used for official purposes only. Any entry, recording or preservation of the data and any form of publishing or transfer to third parties is not permitted.

 

6.       The authorised user shall be liable for any abuse attributable to him/her. In cases of abuse BVL is entitled to block that user’s access immediately.

 

7.       For technical reasons, the username and its email address will be transferred to servers of the BVL and to a server of its cooperation partner (WFSR – Wageningen UR) in the Netherlands for storage once a day during data update. The authorised user hereby agrees to this.

 

8.       All data stored in the EUginius system by authorised users shall be treated confidentially by BVL and by BVL’s cooperation partner in the Netherlands and shall not be transferred to third parties.

Data protection information: Your personal data are processed for access management purposes and are being stored for ten years. The Controller for personal data processed is the Federal Office of Consumer Protection and Food Safety, Bundesallee 551, 38116 Braunschweig, Tel: +49 (0)30 18444 99999, email: poststelle@bvl.bund.de. If the conditions are met, you may – possibly under certain conditions – exercise your rights according to Art. 7 par. 3, Art. 15 - Art. 18, Art. 20 - Art. 21 and Art. 77 of the GDPR.  You can find further information here:

https://www.bvl.bund.de/EN/Service/Datenschutz/datenschutz_node.html