Irina Olaru 8th GMO Network Meeting 23 May 2017
Update from EFSA on GMO applications, mandates and
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applications, mandates and other activities Irina Olaru 8 th GMO - - PowerPoint PPT Presentation
Update from EFSA on GMO applications, mandates and other activities Irina Olaru 8 th GMO Network Meeting 23 May 2017 EFSA ACTIVITIES ON GMO Applications under 1829/2003 Under Articles 5 and 17 Renewals under Articles 11 and 23
Irina Olaru 8th GMO Network Meeting 23 May 2017
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Applications under 1829/2003
Under Articles 5 and 17 Renewals under Articles 11 and 23
Guidance documents and explanatory notes External mandates Procurement and grants
EFSA ACTIVITIES ON GMO
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APPLICATIONS Applications under 1829/2003, Art 5 & 17 Completeness check (5) Risk assessment (32) Finalised (80) Withdrawn (24)
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APPLICATIONS
Crop
Maize (21) Soybean (8) Cotton (5) Oilseed rape (3)
APPLICATIONS UNDER 1829/2003, ART 5 & 17 – CC + RA PHASE (37)
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APPLICATIONS
Level of stacking
Singles (13) 2-event stacks (6) 3-event stacks (6) 4-event stacks (7) 5-event stacks (3) 6-event stacks (2)
M (2) S (2) C (1) O (1) M (1) S (3) C (2) M (6) S (1)
M (3) M (2)
APPLICATIONS UNDER 1829/2003, ART 5 & 17 – CC + RA PHASE (37)
M (7) S (2) C (2) O (2)
M=maize S=soybean C=cotton O=oilseed rape
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Renewal applications under 1829/2003, Art 11 & 23
Under risk assessment: 6 (OSR GT73; OSR MS8, RF3
and MS8 x RF3; maize GA21; sugar beet H7-1; maize NK603 x MON 810; maize 1507 x NK603)
Finalised: 2 (maize 1507 and maize 59122)
APPLICATIONS
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Guidance documents under development or recently finalised
Low Level Presence GD – item 4.4 of the agenda Allergenicity GD – item 5.1 of the agenda
Explanatory notes
Literature review – item 4.3 of the agenda Next Generation Sequencing – item 5.2 of the agenda
GUIDANCE DOCUMENTS AND EXPLANATORY NOTES
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MON810 PMEM annual reports – item 6.2 of the agenda Additional information on maize Bt11 x MIR162 x MIR604 x
GA21 (Application 66) – finalised March 2017
Additional information on maize 5307 (Application 95) –
received in December 2016, on-going
Additional information on maize 3272 (Application 34) –
received in April 2017, on-going EXTERNAL MANDATES
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Impact of teosintes – item 6.3 of the agenda Scientific assistance on Bohn et al., 2016 in relation to the risk
assessment of genetically modified Bt crops
Scientific assistance on the commentary published by Kruse-
Plass et al. (2017), in relation to the risk assessment of the GM Bt Maize crops EXTERNAL MANDATES
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Sequencing mandates
Finalised: 3 (maize GA21, maize MIR604, maize 59122) On-going: 2 (soybean 305423, soybean 40-3-2)
EXTERNAL MANDATES
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Contractor support on:
Literature review of baseline information to support the risk
assessment of RNAi-based GM plants – finalised, item 7.2 of the agenda
Literature review of baseline information on RNAi that could
support the food/feed and environmental risk assessment of RNAi-based GM plants – on-going PROCUREMENT AND GRANTS
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23 May 2017 8th GMO Network Meeting Elisabeth Waigmann
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IR 503/2013 (Annex II, 2.2):
“for stacked GM plants, whose cultivation is associated with the production of GM material containing various subcombinations of events (segregating crops), the application shall include all subcombinations independently of their origin which have not yet been authorised.”
“In such case, the applicant shall provide a scientific rationale
justifying that there is no need to provide experimental data for the concerned subcombinations or, in the absence of such scientific rationale, provide the experimental data”
BACKGROUND
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‘subcombinations’ = lower stacks containing combinations of up to N-1 of the events present in the high stack
Subcombinations can be obtained in two ways: By segregation in the progeny of the high stack through targeted breeding programs, by conventional
crossing BACKGROUND
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F1 AxBxCxD (high stack) Harvested F2 kernels will contain:
AxBxD; AxCxD; BxCxD
AxC; AxD; BxC; BxD; CxD
Segregation will
Subcombinations obtained by segregation from the high stack BACKGROUND
hemizygous
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Subcombinations obtained through targeted breeding programs
Example subcombination AxBxD: BACKGROUND
AxB D (done by breeding company) F1: AxBxD hemizygous
targeted breeding program x F1: AxBxD hemizygous marketed to farmers
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Define a GMO Panel approach for the risk assessment
programs, as required in IR 503/2013
GMO panel approach will be published as an annex to
the May 2017 plenary meeting minutes, in line with the EFSA goal to provide transparency in the risk assessment process
Covers maize and oilseed rape
GOAL
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Subcombinations obtained by segregation in the progeny of the high stack (e.g. F2 generation in harvested grains/seeds)
present in F2 grain/seed mixture of the high stack not intended to be further propagated are an integral part of the assessment of the high stack
the assessment of sub-combinations occurring by segregation needs no further consideration. RISK ASSESSMENT STRATEGY
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Subcombinations obtained through targeted breeding programs
stacks in themselves which can be bred, produced and
marketed independently of the higher stack The strategy to assess these sub-combinations needs further consideration RISK ASSESSMENT STRATEGY
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The assessment of subcombinations needs to encompass intended and unintended effects, as for any other stack
Intended effects - directly linked to the objective(s) of the
genetic modification(s)
Unintended effects - not directly linked to the objective(s) of
the genetic modification(s). On the basis of current knowledge
unexpected RISK ASSESSMENT STRATEGY
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The challenge:
these subcombinations may not even exist at the moment of
submission of the high stack application,
experimental data to identify intended and unintended
effects might not be available.
it is also possible that some of these subcombinations have
been the object of past applications and assessed by the EFSA GMO Panel RISK ASSESSMENT STRATEGY
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The GMO Panel considers that the assessment of subcombinations
RA of the single events; RA of the high stack; RA of relevant specific subcombinations (if available); specific data/information that may be required on a case-by-
case basis. RISK ASSESSMENT STRATEGY
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Assessment of:
intended and expected unintended effect(s)
linked to the genetic modification
unexpected unintended effect(s) potentially
linked to the genetic modification RISK ASSESSMENT STRATEGY
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Intended and expected unintended effect(s) linked to the genetic modification When the RA has identified effects linked to the single events or the high stack, the risk associated to particular subcombinations can be anticipated. Two scenarios:
a)
An effect linked to specific subcombinations is expected
additional data is requested
additional data needed
b)
No effect linked to specific subcombinations of the events is expected no additional data needed
RISK ASSESSMENT STRATEGY
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Unexpected unintended effect(s) potentially linked to the genetic modification
If an unexpected unintended effect is identified for the high stack and/or any of the single events, it is assessed as an expected unintended effect, and its associated risk in specific subcombinations
If no unexpected unintended effect is identified, the assessment will be performed on the basis of the available information no additional data needed
RISK ASSESSMENT STRATEGY
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The opinion will report (i) the assumptions made to
complete the assessment of subcombinations, (ii) possible remaining uncertainties, as well as (iii) if appropriate, strategies to reduce such uncertainties. Example of implementation of the strategy can be found in the scientific opinion on application 119. RISK ASSESSMENT STRATEGY
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23-24 May 2017 – GMO RA Network MTG – Yann Devos (EFSA GMO Unit)
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Submission types
GMO market registration applications (APs) submitted
under Regulation (EC) No 1829/2003 before and after the Implementing Regulation (EU) No 503/2013 (IR) entered into force [GMO APs]
Annual post-market environmental monitoring reports
EU [annual PMEM reports]
GMO APs for the renewed market authorisation of
authorised GM food/feed under Regulation (EC) No 1829/2003 [renewal APs]
SCOPE OF EXPLANATORY NOTE
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GMO APs submitted after the IR came into force
IR requires a systematic review (SR) covering the 10
years before the submission of the GMO AP
GMO APs submitted before the IR came into
force
Complement GMO APs with relevant findings published
in the scientific literature during the regulatory review process
SCOPE OF EXPLANATORY NOTE
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Annual PMEM reports
European Commission’s authorisations require to
actively screen relevant scientific publications
Renewal APs
EFSA GMO Panel (2015) requires to search all scientific
databases relevant for the three main areas of the risk assessment in a comprehensive and structured manner, in order to retrieve new scientific information relevant to the safety of the GMO for market renewal
SCOPE OF EXPLANATORY NOTE
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Observations
Applicants have undertaken literature searches to
various degrees of rigour
Lack of clarity on how to address the SR requirement
AIM OF EXPLANATORY NOTE
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Aim
To clarify the scope and methodology for literature
searching
To give recommendations on how to conduct, report
systematic/extensive literature searches, and present the results of any scoping reviews
To complement EFSA (2010) on the application of SR
methodology to food/feed safety assessments to support decision making, with GMO-specific guidance
AIM OF EXPLANATORY NOTE
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Applicants
To provide a more rigorous and
standardised/harmonised approach to literature searching
To perform more consistent and sensitive literature
searches, and improve reporting
To minimise biases (such as publication bias)
Risk assessors and regulators
To provide guidance on how to check/appraise
systematic/extensive literature searches
INTENDED USERS OF EXPLANATORY NOTE
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Scoping reviews
GMO APs submitted after the IR came into force
Systematic/extensive
literature searches
GMO APs submitted
before the IR came into force
Annual PMEM reports Renewal APs
STRATEGY OF EXPLANATORY NOTE
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Scoping reviews
GMO APs submitted after the IR came into force
IR requires a SR Not always useful/necessary to perform SR IR allows for derogation Reasoned justification required Outcome of scoping review can determine
whether it is useful to perform SR and for which topics
STRATEGY OF EXPLANATORY NOTE
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Framework consisting of five successive steps
1.
Identifying review questions and clarifying their purpose (Section 3.1)
2.
Searching for/identifying relevant studies (Section 3.2)
3.
Selecting studies (Section 3.3)
4.
Extracting high level data of the relevant studies (Section 3.4 – only applicable to scoping reviews)
5.
Summarising and reporting the data, and considering the implications of findings (Section 3.5)
STRUCTURE OF EXPLANATORY NOTE
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Appendices
A – Categories of information/data requirements B – Search strategy examples (#4) C – Examples of web-based databases that can contain
relevant information supporting the risk assessment of GMOs
D – Requirements for undertaking scoping reviews
applicable to systematic/extensive literature searchers
STRUCTURE OF EXPLANATORY NOTE
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Problem to address should be specified in the form
Link to GMO risk assessment context
Review questions should be broken down into their
key elements to guide the development of search terms and structure the search:
1.
Structured questions (e.g. PICO, PECO)
2.
Information/data requirements outlined in relevant GMO Panel guidance documents, EFSA explanatory notes and IR (see Appendix A)
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1.
Structured questions (e.g. PICO, PECO)
“Does either the GMO and derived food/feed products,
human and animal health and the environment?”
P = population [human/animal health/environment] I/E = intervention/exposure [GMO, derived
food/feed products, intended trait(s)]
C = comparator O = outcome [adverse effects]
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2.
Information/data requirements outlined in relevant GMO Panel GDs, EFSA explanatory notes and IR (see Appendix A)
Examples
Protein expression data
90-day feeding studies in rodents
Laboratory/greenhouse feeding bioassays with representative non-target organisms
…
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Literature searching involves:
1.
Developing a search strategy
2.
Identifying information sources to search
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1.
Developing a search strategy
Approaches to develop searches
Single search strategy
Series of focused search strategies
Search strings (link to key elements of review questions)
See Appendix B
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1.
Developing a search strategy
Language
Time period
Reference study searches
List of reference studies
Results of searches with reference studies
Appraisal (EFSA critical appraisal tool [CAT])
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2.
Identifying sources of scientific literature
Electronic bibliographic databases Mandatory At least two multi-disciplinary databases for
complementarity (e.g. Web of Science Core Collection, Scopus, CAB Abstracts, Medline)
Optional Searching more specialist/subject-specific
databases (e.g. Agricola)
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2.
Identifying sources of scientific literature
Internet searches (limit publication bias) Mandatory Internet pages of relevant key organisations
involved in GMO risk assessment (e.g. FDA, USDA, US EPA)
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2.
Identifying sources of scientific literature
Internet searches (limit publication bias) Optional Scientific literature that is not indexed in
electronic bibliographic databases via general search engines such as Google scholar (check first 200-300 hits)
Web-based databases known to contain
information specifically on effects of GMOs (examples given in Appendix C)
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2.
Identifying sources of scientific literature
Manual searches Mandatory Checking reference list from recent relevant
reviews, methodological publications and scientific opinions
Optional Hand-searching key journals or assessing
journal contents pages
Citation searching
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Determining “relevance”
Set eligibility/inclusion criteria to determine relevance
Table 1 gives examples of eligibility/inclusion
criteria
Reliability of relevant studies is assessed later in the
process
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Process (2 stages)
1.
Rapid assessment based on title-abstract-keywords
2.
Detailed assessment of full-text documents
Quality assurance
Relevant screening performed by more than 1 reviewer Ensure inter-reviewer agreement Resolve disagreement
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Classification of studies retrieved
Relevant studies To summarise and consider those for reliability Non-relevant studies Give reason(s) for exclusion based on
eligibility/inclusion criteria
Unobtainable studies & studies with unclear relevance Describe (unsuccessful) methods used to try to
Give justification of why relevance cannot be
definitively determined
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Data extraction [only for scoping reviews]
Purpose Enable applicants to describe the overall volume,
strength and direction of the studies
Possible variables Authorship, year of publication, source, title of the
study, objective of the study, experimental design, main results, conclusion, protection goal considered, applicable category of information/data requirement, whether adverse effects are reported
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Summarising and reporting the data
Search methods and outcomes Results of study selection process See template tables 2 to 5 Narrative synthesis/summary of relevant studies,
describing their overall volume, strength and direction [only applicable to scoping reviews]
See template tables 6
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Considering implications of the findings
Value of undertaking SR [only applicable to scoping
reviews]
Implications for risk assessment To assess the reliability and implications for the risk
assessment of all relevant studies retrieved after detailed assessment of full-text documents for relevance: ordered by category of information/data requirement(s) (see template Table 7)
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Applicability of the explanatory note
Six months after publication date of the note New submissions submitted after 10 OCT 2017 Except for: Extensive/systematic literature searchers previously
submitted to EFSA that do not comply with minimum quality standards
Updates of extensive/systematic literature
searchers previously submitted to EFSA
TRANSITION PHASE
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EFSA’s completeness checklist
To be completed by applicants To ensure adequate reporting to facilitate appraisal and
reproducibility
How? Appendix to EFSA’s updated submission
guidance on applications for authorisation of GM plants under Regulation (EC) No 1829/2003
Attached to GMO Panel/EFSA questions asking
for updated or revised literature searches
COMPLETENESS CHECKLIST
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Explanatory note may/will be revised:
when experience is gained in its application in view of any amendments to the IR
FUTURE UPDATES OF EXPLANATORY NOTE
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ACKNOWLEDGEMENTS
Thank you for your attention EFSA wishes to thank the following for the support
provided to this scientific output: Elisa Aiassa, Fernando Álvarez, Hermann Broll, Giacomo De Sanctis, Antonio Fernandez Dumont, Andrea Gennaro, Anna Lanzoni, Nikoletta Papadopoulou, Konstantinos Paraskevopoulos and Matthew Ramon, and experts of the GMO Panel standing Working Groups
Environmental Risk Assessment for inspiring discussions that helped to develop the explanatory note to the guidance
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Guidelines on possible derogation of existing requirements for applications of GM food and feed at low levels submitted under Regulation (EC) No 1829/2003
Anna Lanzoni 8th GMO Network Meeting 23 May 2017
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Introduction The mandate on GMO Low Level Presence (LLP) Project plan and schedule Stakeholders engagement EU Member States consultation The draft guidance: key points Q&A
ROADMAP
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Introduction The mandate on GMO Low Level Presence (LLP) Project plan and schedule Stakeholders engagement EU Member States consultation The draft guidance: key points Q&A
ROADMAP
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Mandate from European Commission
Mandate on possible derogation of existing requirements for applications of GM foods and feeds at low levels submitted under regulation (EC) No 1829/2003
Received by EFSA in 2014 Clarification requested to EC Accepted by EFSA in 2015 (EFSA-Q-2015-00432)
THE MANDATE ON GMO LOW LEVEL PRESENCE (LLP)
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PROJECT PLAN AND SCHEDULE LLP
Sept 2017 July 2015 2 May-13 June 2017 (6-week) Sept 2016
1st draft guidance
EU MS consultation Public consultation
2nd draft guidance
GMO Panel Guidance
28 Oct–9 Dec 2016 (6-week) Apr 2017
Josep Casacuberta Adinda De Schrijver Achim Gathmann Mikolaj Gralak Elsa Nielsen Francesco Visioli - Chair Jean-Michel Wal Yann Devos Antonio Fernandez Anna Lanzoni –Task leader Claudia Paoletti Konstantinos Paraskevopoulos Hearing expert: Thomas Frenzel
LLPWG
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Introduction The mandate on GMO Low Level Presence (LLP) Project plan and schedule Stakeholders engagement EU Member States consultation The draft guidance: key points Q&A
ROADMAP
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Two-step approach Dedicated EU Member States Consultation
28 October - 9 December 2016
Public Consultation
STAKEHOLDERS ENGAGEMENT
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The process
EU MS CONSULTATION
EFSA LLP WG Advisory Forum EFSA Focal Points MS Competent Authorities under 1829/2003 EFSA Focal Points
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EU MS CONSULTATION
The tools
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240 comments summarised replies will be provided in a Technical report
with those from Public Consultation
EU MS CONSULTATION
The outcome
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Main comments
Readibility Scientific contents reassurance on the appropriateness on most EFSA proposals relevant scientific points raised Risk management issues EC involvement
Threshold Scope (“large size” fruit/vegetables) Asynchronicity/asimmetry & mutual recognition
EU MS CONSULTATION
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Introduction The mandate on GMO Low Level Presence (LLP) Project plan and schedule Stakeholders engagement EU Member States consultation The draft guidance - key points Q&A
ROADMAP
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Improved instructions for use Not a stand-alone document!
This document is intended to assist applicants … by indicating which technical requirements of Annex II of Regulation (EU) No 503/2013 are necessary and which are not, in this case providing justification, in order to conclude on the safety of a GMO in a LLP application This document supports Regulation (EU) No 503/2013 and it is not intended to serve as a stand-alone guidance DRAFT GUIDANCE – IMPROVED READIBILITY VS V1
See: 3.1 Introduction
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NOT A STAND-ALONE DOCUMENT
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GMO at maximum 0.9% per ingredient point of entry consumer GMO at >0.9% per ingredient : not in the remit of this
guidance
e.g. GM fruits and vegetables constituting either a full
portion or part of a consumed portion, resulting in an exposure of consumers (or animals) higher than 0.9% to that GMO DRAFT GUIDANCE - SCOPE
See: 1.2 Interpretation of the Terms of Reference
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LLP application: covers a request for the authorisation of a
GMO present at a level of maximum 0.9% per ingredient in any food and/or feed, submitted under Regulation (EC) 1829/2003
LLP GMO: the GMO subject of the LLP application LLP Ingredient: the mixture of the LLP GMO and the same
plant species and/or derived product, at the predefined proportion of a maximum of 0.9% and 99.1% respectively DRAFT GUIDANCE - DEFINITIONS
See: 1.2 Interpretation of the Terms of Reference
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Stand-alone dossier Comprehensive characterisation of the
transformation event (intended trait)
Fit-for purpose assessment driven by:
low exposure under acute/chronic scenarios
DRAFT GUIDANCE - SCIENTIFIC DRIVERS
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MAIN “DEROGATIONS” FROM REGULATION (EU) 503/2013 – AT A GLANCE
Molecular characterisation
Singles: only edible parts Stacks: not routinely needed
Not necessary Comparative assessment
Food Feed Assessment
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Environmental Risk Assessment: case-specific varying depending on the biology of the plant
species, the intended trait(s), the potential receiving environments, and interactions among all three IN ADDITION
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Not mandatory on a routine basis Since in LLP situations the level of exposure of consumers
and animals to the LLP GMO is defined to be at a maximum 0.9% per ingredient, not all differences in comparative analysis endpoints between the LLP GMO and the plant (and/or derived product) constituting the remaining part of the ingredient may be relevant
Why? Which difference might be relevant in LLP?
FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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The level of an endogenous compound in a LLP ingredient is
determined by:
the level of such endogenous compound in the LLP GMO
(and/or derived product)
the level of such endogenous compound in the plant (and/or
derived product) constituting the remaining part of the ingredient.
The ratio between these two levels determines the extent to
which the level of the compound of the LLP GMO impacts the overall level of that compound in the LLP ingredient FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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FOCUS ON COMPARATIVE ANALYSIS
LLP ingredient LLP GMO remaining part of the ingredient
+ =
endogenous compound
Case 1 Case 2 Case 3
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FOCUS ON COMPARATIVE ANALYSIS
Level of a compound in LLP GMO/ level
the compound in the ingredient without the LLP GMO Level of the compound in LLP ingredient/ level of the compound in the ingredient without the LLP GMO
0.991 0.001 0.991009 0.01 0.99109 0.1 0.9919 1 1 10 1.081 20 1.171 50 1.441 90 1.801 100 1.891 200 2.791
Table 1: Impact of variations in the levels of an endogenous compound in a LLP GMO on the level
Case 1 Case 2 Case 3
See 3.2.3.3 Comparative analysis
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On the basis of the current knowledge, the GMO Panel is of
the opinion that variations in the level of compound(s) in LLP GMOs are generally not large enough to impact on the nutritional or safety characteristics of the LLP ingredient POSSIBLE EXCEPTIONS
GMOs with output traits developed to improve nutrition GMOs expected to show compositional changes on the basis
FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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Therefore: No comparative assessment on a routine basis Compositional analysis only if:
the intended trait targets the composition of the LLP GMO (output
trait)
a hypothesis for a relevant compositional change can be
formulated based on available information from the hazard identification (e.g. unintended compositional changes anticipated by the precedent analyses)
compounds are de novo produced in the LLP GMO
No comparative analysis of agronomic/phenotypic
characteristics FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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Implementation Targeted compositional analysis No full list of OECD consensus doc compounds Conditions maximising expected change(s), based on
available knowledge
field trials, greenhouse studies Equivalence test not considered necessary
FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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Comparative assessment studies performed under
non-EU regulatory frames: applicability in LLP applications
studies conducted in accordance with Codex (Codex
Alimentarius, 2009) could support the assessment
studies not aligned to requirements of Codex are not
considered appropriate by the GMO Panel. FOCUS ON COMPARATIVE ANALYSIS
See 3.2.3.3 Comparative analysis
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Testing of whole genetically modified food and feed
(Regulation [EU] No 503/2013; Annex II. II, 1.4.4 subsections 1.4.4.1-1.4.4.3)
the GMO Panel considers that a 90-day feeding study is
not needed to corroborate information on the toxicological characteristics of the whole LLP GM food and feed in rodents and/or to reduce the remaining uncertainties, considering the limited exposure to the LLP GMO FOCUS ON TOXICOLOGY
See 3.2.3.4 Toxicology
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The assessment of the allergenicity of food or feed
from the LLP GMO should be conducted in the case changes in the levels of endogenous allergens are expected in the LLP GMO, possibly impacting the allergenicity of the LLP ingredient
In such situations, relevant identified endogenous
allergens should be analysed and the assessment should indicate whether the GMO could impact the allergenicity of the LLP ingredient FOCUS ON ALLERGENICITY
See 3.2.3.5 Allergenicity
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Considering that the scope of LLP applications is
limited to a level of maximum 0.9% of a LLP GMO per ingredient a nutritional assessment is not considered necessary on a routine basis, unless relevant changes in the levels of food and feed constituents from the LLP GMO are expected FOCUS ON NUTRITIONAL ASSESSMENT
See 3.2.3.6 Nutritional assessment
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In the case of multiple LLP applications for LLP GMOs showing
similar traits, the possible cumulative contribution from the various LLP GMOs to the ingredient should be taken into consideration in the risk assessment
the relative contribution to the ingredient of each of these
taken into account to allow an estimation of their total contribution via the addition of the respective trait-related constituent(s)
Case-by-case, on the basis of compositional analysis outcome
CUMULATIVE RISK ASSESSMENT
See 3.2.5.3 Cumulative risk assessment
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(EFSA-Q-2014-00547)
Antonio Fernandez Dumont 8th GMO Network Meeting 23 May 2017
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Allergenicity guidelines
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Allergenicity guidelines
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Allergenicity guidelines
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Allergenicity guidelines
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Allergenicity guidelines
In vitro protein digestibility
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Allergenicity guidelines
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Allergenicity guidelines
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Allergenicity guidelines
Endogenous allergenicity
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Allergenicity guidelines
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Allergenicity guidelines
Acknowledgement: EFSA would like to thank the members of the Allergenicity Working Group: Eigenmann Philippe, Epstein Michelle, Hoffmann- Sommergruber Karin, Koning Frits, Lovik Martinus, Mills Clare, Moreno F. Javier, van Loveren Henk, Wal Jean-Michel; the EFSA trainee Selb Regina and the EFSA staff member Fernandez Dumont Antonio for the scientific discussions and the preparation of the guidance document
Presented by Nikoletta Papadopoulou GMO Unit Parma, 23-24 May 2017
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This presentation represents the state of discussion at the time of the GMO Network meeting, 23-24 May 2017, and does not necessarily reflect the final
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NEXT GENERATION SEQUENCING (NGS)
Library Construction Cluster Amplification Alignment and data analysis (reference genome) Sequencing
Genomics (whole genome sequencing, exome sequencing, de novo and targeted sequencing) Transcriptomics (total RNA and mRNA sequencing, targeted RNA sequencing, small RNA and ncRNA sequencing) Epigenomics (Methylation sequecning, ChIP sequencing, ribosome profiling)
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NGS is used for the molecular characterisation of the GM plant insert, in the context of GMO applications for EU market authorization, and specifically for:
plant genome and its junction sites
NGS IN GMO APPLICATIONS
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To provide recommendations on the information that should be submitted in GMO applications so that EFSA can perform its quality assessment To provide a standardised approach to NGS
AIM OF THE NOTE TO GUIDANCE
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PREPARATION OF THE NOTE TO GUIDANCE
Consultation by the Molecular Characterisation WG experts Experience from assessing applications using NGS Published literature
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I.
Sequence data and quality
II.
Read depth: Whole genome sequencing approach or Sequence capture approach
DESCRIPTION OF QUALITY PARAMETERS FOR RA
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platforms
characterisation of integration sites: longer read lengths are required.
reads (mapped to insert and host genome)
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cover the genome to a specified depth: e.g. by Lander-Waterman algorithm
Coverage =
𝑜𝑣𝑛𝑐𝑓𝑠 𝑝𝑔 𝑠𝑓𝑏𝑒𝑡∗𝑠𝑓𝑏𝑒 𝑚𝑓𝑜𝑢ℎ 𝑓𝑡𝑢𝑗𝑛𝑏𝑢𝑓𝑒 𝑓𝑜𝑝𝑛𝑓 𝑡𝑗𝑨𝑓
(statistical framework for estimating the probability of sequencing junction reads)
sequences
10
The degree of validation of sequence coverage is greatly dependent on:
Examples are provided in the Note to Guidance
11
Read numbers per sequencing run (raw and
calculated/probability formula)
Data on coverage of reference genes (from read
alignment)
Number of reads when trimmed or removed during
analysis
Description of bioinformatics analysis; step-by step Parameters and versions of software used
12
NOTE TO THE GUIDANCE ON NGS- PUBLICATION Publication: June 2017 EFSA webinar: 11th July 2017
13
Simon Moxon Molecular Characterisation (MC) WG Experts GMO Unit Colleagues
ACKNOWLEDGMENTS
Andrea Gennaro and Giacomo De Sanctis 23 May 2017 8th GMO Network ERA break-out session
2
PART 1 The objective of this presentation The importance of site selection The site representativeness in the EFSA 2011 FF
guidance and IR 503/2013
Strategy proposed in the EFSA 2015 agro/pheno
guidance
PART 2 Classification of the cultivation conditions Graphical representations Assessment of representativeness of selected sites Conclusion on site representativeness
OUTLINE
3
To present a strategy to assess the representativeness of the selected sites where the field trials are conducted
OBJECTIVE
4
WHY SITE REPRESENTATIVENESS IS IMPORTANT
Molecular characterisation Agro/Pheno Compositional
Comparative approach is followed to identify intended and unintended differences between GM plant and the conventional counterpart The risk assessment of GM plants starts with hazard identification (as part of problem formulation)
Selected sites Field trials conditions Test materials Intended and unintended changes
5
… WHICH ARE THE IMPLICATIONS OF SITE SELECTION? Seedling – Vegetative phase – Reproductive phase - Harvest
Seeds FIELD TRIAL Seeds
Agronomic and phenotypic characterisation Compositional analysis
This information is used to drawn conclusions on
materials produced under conditions different from those tested to support the specific application
6
EFSA Guidance on RA of food and feed from GM plants and Implementing regulation (EU) 503/2013
Each field trial shall be replicated at a minimum of eight sites
The replication at each site is the number of results obtained for each test material; the replication should never be less than four at any site.
HOW MANY SITES AND REPLICATES
7
EXPERIMENTAL DESIGN: THE MINIMAL REQUIREMENTS 8 sites, 1 GM plant, 1 comparator, 6 reference varieties (3 per site) Randomised Block Design
GM CC Ref Single plant Plot Single row Number of plants/plot is related to the phenotypic characteristics of the crop and to the applied agricultural practices
Block1 Block2 Block3 Block4
8
be representative of the range
where the crop will be grown, thereby reflecting relevant meteorological, soil and agronomic conditions; the choice should be explicitly justified.
THE PRINCIPLES OF SITE SELECTION
reflect the different
meteorological and agronomic conditions under which the crop is to be grown; the choice shall be explicitly justified.
From the EFSA guidance and IR, it is clear the importance of site selection and its justification The different sites selected for the field trials shall
EFSA Guidance on RA of food and feed from GM plants 2011 Implementing regulation (EU) 503/2013
9
Site selection justification in import & processing applications: …field trial sites were selected in areas where the crop is typically cultivated in the USA OR …the selection was based on the representativeness of the region for the crop production and the availability of GLP compliant test sites Site selection and/or the representativeness of the sites selected by the applicants in frequently challenged by MS. It was considered important:
more clarity to applicants on how sites should be selected more transparency in the assessment of site
representativeness SITE SELECTION NOT SUFFICIENTLY JUSTIFIED
10
The agro/pheno guidance provides recommendations on how to select and manage the field trials The principle to be follow is:
The selection should be able to capture enough variability within the set of possible receiving environments in which the test materials can be grown To agro/pheno guidance requests specific information to support the appropriateness of site selection such as:
geographical location
agrometeorological data
soil characteristics
crop management practices
SITE REPRESENTATIVENESS IN THE AGRO/PHENO GD
11
EXAMPLE OF SITE SELECTION
Step I: delineate the boundary within which sites for the trials could be selected (e.g. acreage) Step II: further delineation of boundaries based on additional factors (e.g. maturity group that is related to the tested materials)
12
EXAMPLE OF SITE SELECTION Step III: sites identification, including sites outside optimal growing area 3 examples for a soybean (maturity group III)
Representative Variable Appropriate for the GM line
13
Key factors to evaluate site representativeness of selected sites (requested in agro/pheno GD):
geographical locations
meteorological conditions
soil characteristics
management practises
REPRESENTATIVENESS OF SELECTED SITES
How?
Multi-factors
Transparent
Repeatable
Component of expert judgement What?
Representative of likely REs
Variable
Inside the limits where the GM will be grown
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Sys et al. 1993 Land evaluation part III crop requirements Based on Land suitability classification from FAO (1976)
HOW WE EVALUATE METEO CONDITIONS
Classes: S1 subcat. 0 optimal areas S1 subcat. 1 near optimal areas S2 suboptimal areas S3 marginal areas N1 not suitable but susceptible to correction N2 not suitable
15
HOW WE EVALUATE METEO CONDITIONS
Classes: S1 subcat. 0 optimal areas dark green S1 subcat. 1 near optimal areas light green S2 suboptimal areas yellow S3 marginal areas brown N1 not suitable but susceptible to correction grey N2 not suitable black
100% 0%
16
EXAMPLE OF METEOROLOGICAL CONDITIONS
Representative
Variable
Inside the limits where the GM will be grown
Representative
Variable
Inside the limits where the GM will be grown
17
HOW WE EVALUATE SOIL CONDITIONS
Classes: S1 subcat. 0 optimal areas S1 subcat. 1 near optimal areas S2 suboptimal areas S3 marginal areas N1 not suitable but susceptible to correction N2 not suitable
18
EXAMPLE OF SOIL CONDITIONS
Representative
Variable
Inside the limits where the GM will be grown
Representative
Variable
Inside the limits where the GM will be grown
19
HOW WE EVALUATE CROP MANAGEMENT
Field crops, usual planting and harvesting dates - USDA report, 2010.
Crop management should be representative of the likely REs:
Planting and harvesting timing
Treatments (e.g. herbicide, type and timing)
Fertilization (amount and timing)
Irrigation (amount and timing)
Tillage (type and timing)
Crop history
20
SELECTION OF REPRESENTATIVE SITES
Historical climatic conditions (average over 30 years)
21
REPRESENTATIVE CONDITIONS ON FIELD TRIALS
Meteorological conditions and crop management applied during the year(s) of field trials
22
Site representativeness is fundamental to drawn any
conclusion on comparative assessment of GM plants
Conclusion on site representativeness takes into
account a multi-factors assessment
Graphical tools could facilitate the expert judgements
making decisions transparent and repeatable
Site representativeness requires expert judgments
CONSIDERATION ON SITE REPRESENTATIVENESS 1/2
23
Applicant might select appropriate sites, but end up with
no representative conditions (meteorological and/or crop management during the field trials)
meteorological additional years as foreseen by the
agro/pheno GD
crop management additional field trials with
representative management
Meteorological and soil conditions figures will be published
soon with submission GD CONSIDERATION ON SITE REPRESENTATIVENESS 2/2
24
THANK YOU FOR YOUR ATTENTION
Fernando Álvarez, GMO Unit 8th GMO Network meeting Parma 23 May 2017
2
Bt maize cultivation in the EU
20 40 60 80 100 120 140 160 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015
SP SK RO PO PO GE FR CR
103xha
Total maize area
Slovakia 104 ha Portugal 8 017 ha Czech Republic 997 ha Romania 2.5 ha Spain 107 749 ha
Opt
Bt-176 MON810
Countries in 2015
3
Since 1998
>100 varieties registered
~90% Bt maize in EU
~25% global adoption rate
Highest adoption rate in Ebro valley ''Hot spot area''
Bt maize cultivation in Spain
67% 81% 88%
>10000 >5000-10000 >1000-5000 >100-1000 >0-100
MON810 ha Castañera et al. 2016.PLOS ONE 11(5): e0154200 Source: Avances
4
Lepidopteran pests of maize in the EU
Ostrinia nubilalis (ECB) Sesamia nonagrioides (MCB)
5
Annual PMEM reports maize MON810
according to Annex VII of Directive 2001/18/EC
Scientific Opinions (SOs) on 2009-2015 PMEM reports (EFSA PMEM GD 2006, 2011)
To monitor changes in susceptibility to Cry1Ab for the assessment of the ‘high-dose/refuge’ strategy ‒ EuropaBio harmonised insect resistance management (IRM) plan To identify unanticipated adverse effects caused by the cultivation of maize MON810 ‒ Farmer questionnaires (FQs) ‒ Literature searching & assessment scientific publications
Case-Specific Monitoring (CSM) General Surveillance (GS)
6
Dose-response
Case-specific monitoring
Insect Resistance Management Plan
Diagnostic dose
Maize MON 810
SS SS SS RR RS
Non-Bt maize Non-Bt maize
ECB collection 2004-2013
7
Case-specific monitoring
Insect Resistance Management Plan
by target pests
resistance
Remedial plan in case of failure
Dose-response
Diagnostic dose
Detection ≤3% Frequency R alleles
8
Case-specific monitoring – 2015
appropriate information systems of GMO cultivation
20 40 60 80 100 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 90
Compliance (%)
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Case-specific monitoring – 2015
Larvae (F0) collected from refuges and conventional maize fields
Larvae reared in the lab and bioassays conducted with progeny (F1)
Insufficient # larvae sampled/represented in the bioassays as F1
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Case-specific monitoring – 2015
Larvae (F0) collected from refuges and conventional maize fields
Larvae reared in the lab and bioassays conducted with progeny (F1)
Insufficient # larvae sampled/represented in the bioassays as F1
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Case-specific monitoring – 2015
1 2 3 4 5 6 7 8 9 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 North East Lab ref strain Resistance ratio 5 10 15 20 25 30 35 40 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 North East Lab ref strain Resistance Ratio
MIC50 (95% CI)
7-10 concentrations of purified Cry1Ab and F1 larvae (diet overlay assay)
Estimation MIC50 and MIC90 (with 95% CI) by Probit analysis
Calculation of Resistance Ratios (RR = MICfield population / MIClab ref strain)
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Case-specific monitoring – 2015
Bioassay conducted since 2013 – Standalone from 2016 onwards?
Diagnostic concentration: MIC99 (derived from baseline data)
No resistant individuals identified (~96 larvae tested/area/year)
Actual limit of R allele frequency that could be detected < 3% threshold Recommendation to increase sampling effort
Species Population Season Moulting inhibition (% ± SE)
ECB North East Iberia 2013 100 2015 100 Central Iberia 2013 100 2015 100 MCB North East Iberia 2013 97 ± 2 2015 100
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Case-specific monitoring – 2015
System allowing farmers to report complaints on
product performance
Including unexpected crop damage caused by target pests
300 complaints received during 2015 season None of the related to infestation by ECB/MCB Useful complement to the info provided by the lab
assays
Additional info needed to appraise usefulness:
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General surveillance – 2015
261 farmers surveyed in 2015: 212 from Spain and 49 from Portugal
Similar methodology compared to previous years
Previous EFSA recommendations on sampling and reporting apply
The analysis of the 2015 FQs did not show any unanticipated adverse effects related to maize MON810 plants and their cultivation
2,627 questionnaires have been completed over 10 yrs. (2006-2015)
15
General surveillance – 2015
(Slightly) Revised protocol based on:
Two databases: WoS Core Collection and CABI CAB Abstracts
Similar search strategy as previous years
18 relevant publications identified in 2015:
No new info that would invalidate previous FF and ERA conclusions on maize MON810
Recommendation to follow EFSA’s explanatory note on literature searching (EFSA, 2017)
FF/MC ERA/Risk management
150 73 PMEM 2009-2015
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human and animal health or the environment arising from the cultivation of maize MON 810 during the 2015 growing season
provide evidence that would invalidate previous GMO Panel evaluations on the safety of maize MON 810
Insect resistance monitoring activities – Do not provide sufficient sensitivity for an early detection of potential resistance
Farmer questionnaires – The sampling frame questionnaires does not allow the assessment of the representativeness of the results
EFSA Scientific Opinion Annual PMEM maize MON810 – 2015
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‒ Annual sampling of both corn borers ‒ Three zones of ~10×10 km where adoption rate >60% for 3 years Info on non-GM and maize MON 810 cropping areas at an appropriate scale should be made available by MS
EFSA Scientific Opinion Annual PMEM maize MON810 – 2015
18
years To confirm that no unintended effects caused by the cultivation of maize MON 810 have been observed. To evaluate the farmer questionnaire methodology for the detection of unintended effects
guidance on literature searching (EFSA, 2017)
EFSA Scientific Opinion Annual PMEM maize MON810 – 2015
19
Acknowledgements
23-24 May 2017 – GMO RA Network MTG – Yann Devos (EFSA GMO Unit)
2
3
Teosinte found in maize fields in the EU
Spain Ebro Valley (Aragón) Region of Cataluña (to a lesser extent) Since 2009 France Region of Poitou-Charentes Since 1990
CONTEXT
4
EFSA was requested by EC to assess whether
“on the basis of the elements provided by this letter,
the existing scientific literature and any other relevant information,
new evidence emerges which would change the
conclusions and recommendations of the EFSA opinions
Bt11 and 1507 and GA21”
Timeline
Mid June 2016 September 2016
MANDATE OF THE EUROPEAN COMMISSION (EC)
5
Materials
Documents supplied and translated by the European
Commission (mostly grey literature)
Available relevant scientific literature
Methods
Narrative review of relevant scientific literature (non-
systematic search)
Problem formulation exercise (pathways of harm) Consultation of representatives of the Competent
Authority of Spain
MATERIALS AND METHODS
6
In centres of origin
Teosinte is native to Mexico and Central America Direct wild ancestor of maize Many teosinte species and subspecies are rare and
endangered, requiring conservation actions
Other teosinte species and subspecies are widely
distributed, and occur in agricultural fields, where they are considered non-aggressive weeds
In some regions, teosinte is grown for forage/feed
purposes
PROTECTION GOAL
7
Outside centres of origin
Teosinte is not indigenous, but has become
naturalised/established in some countries
Teosinte does not represent an environmental entity of
concern requiring protection
Instead, it is occasionally cultivated for its forage, or
considered a weed
In infested agricultural fields, teosinte is subject to
control and/or eradication measures
PROTECTION GOAL
8
Problem formulation exercise focusing on possible
pathways to harm
EFSA explored whether plausible pathways to harm
from the cultivation of maize MON810, Bt11, 1507 and GA21 can be hypothesised for situations where GM maize and teosinte would grow sympatrically, focusing
GM plants
APPROACH
9
Effects of vertical gene flow
Hybridisation potential (teosinte to maize >> maize to
teosinte)
Altered persistence/invasiveness of GM maize ×
teosinte hybrids
Cross-pollination of maize by GM maize × teosinte
hybrids
Interactions of GM maize × teosinte hybrids with Other organisms (target and non-target) The abiotic environment and biogeochemical
processes
APPROACH
10
Pathways to harm
For each of the pathways considered, it is unlikely that
environmental harm will be realised
Previous outputs
No information indicating the necessity to revise the
previous ERA conclusions and risk management recommendations for maize MON810, Bt11, 1507 and GA21 made by the GMO Panel
CONCLUSION
11
Previous outputs
EFSA considers that the previous GMO Panel risk
assessment conclusions and risk management recommendations on maize MON810, Bt11, 1507 and GA21 for cultivation remain valid and applicable
To ensure effective long-term management of teosinte
and maize × teosinte hybrids that acquired glyphosate tolerance through vertical gene flow from maize GA21, and avoid exacerbating weed problems, EFSA recommends that integrated weed management reliant
GA21 in association with GLY
CONCLUSION
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Trtikova et al. (2017)
Teosinte in Europe – Searching for the origin of a novel
Authors genotyped Spanish teosinte plants Genetically distinct from teosinte taxa from Mexico
and Nicaragua, and maize
Teosinte × maize hybrids Origin unclear (EU or country of origin) Study under assessment internally
NEW STUDY
13
ACKNOWLEDGEMENTS
Thank you for your attention EFSA wishes to thank Yann Devos for the preparatory
work on this scientific output, and Magdalena Ibáñez Ruiz, Antoine Messéan, Lucía Roda Ghisleri, Jeremy Sweet and Elisabeth Waigmann for the support provided to this scientific output
14
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