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Past Discussions 2013

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Opening of the Discussion: Access to DNA sequence information and reference material [#5390]
Dear Participants of the Laboratory Network,

Welcome to the second round of discussion of the Network of Laboratories for LMO Detection & Identification. The topic that will be focused on for the next two weeks is regarding “Access to DNA sequence information and reference material”.

In the page of the discussion (http://bch.cbd.int/onlineconferences/portal_detection/discussions.shtml#access), we have provided a brief overview of some challenges related to this topic, such as obtaining reliable reference materials, the stability of the products, the use of different sample matrices of the reference material versus the sample, amongst others. We have also listed a few guiding questions (below) to help initiate the discussion. However please feel free to bring up other related issues that you would like to discuss.

1. What experiences do laboratories have in accessing such materials?
2. How have laboratories been coping thus far with the challenges related to the availability and access to reference materials?
3. Would the creation of a single portal for collecting information about reference materials available worldwide be valuable?
4. How can countries with less experience in the detection of LMOs gain access to reference materials?
5. What recommendations for solutions do you propose to improve accessibility to reference materials?

We are looking forward to a fruitful discussion!
Best Regards,
The Secretariat
posted on 2013-06-16 05:07 UTC by Dina Abdelhakim, SCBD
This is a reply to 5390 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5393]
Hallo everyone,

Access to Reference Materials is quite a challenge to us as lab in Kenya being that the only place we have been sourcing our reference materials is JRC. The problem we have been facing is delay to get the RM in time and also the cost of getting and delivery into Kenya is quiet high. This makes it beyond reach of most Labs to acquire such material due to cost implication or just lack of information of where to find such materials for analysis of GMOs. It would be very useful to have access such information at the Biosafety Clearing House web page for countries to be able to know where they can get such materials and even access the list of the ones that are available in the market.
posted on 2013-06-22 09:36 UTC by Ms Lilian Okiro, Kenya Plant Health Inspectorate Service
This is a reply to 5393 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5394]
Dear Ms Okiro
I agree that reference material often can be a challenge to get. The GM traits authorized in Europa can be bought. Normally from Institute of reference materials and measurements, (IRMM: Http://irmm.jrc.ec.europa.eu/reference_materials_catalogue/Pages/index.aspx) or from American Oil Chemist’s society (AOCS: https://secure.aocs.org/refsamp/refsamp.pdf). Some of the IRMM reference materials are available from Sigma as well.
The IRMM reference materials you can normally get in different concentrations. The AOCS reference materials can be frustrating to work with because they normally are 100 % poorly grinded flour or purified DNA of low concentration. We have in the European network of GMO laboratories ENGL many examples on DNA reference material from AOCS of bad quality or with expired certificates.
Some of the other GM traits can be obtained from JRC as plasmids. They are normally not used for quantification, but used as positive control.
posted on 2013-06-24 08:14 UTC by Ph.D. Lotte Hougs, Danish Veterinary and Food Administration
This is a reply to 5390 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5395]
Dear Network Colleagues,

Any analytical analysis is as reliable as the type and quality of controls in use. This allows maintaining clarity and correct interpretations of results. Like Ms. Okiro and Dr. Hougs correctly indicate, I believe access to suitable reference materials is a strong limitation that many laboratories share worldwide, not to mention the difficulties encountered to get hold of certified standards (CRM) important particularly when quantitative outputs are part of a decision. Mexican laboratories are not the exception and normally rely on reference materials that are requested to IRMM/AOCS directly or by means of commercial providers; this can represent additional costs and occasionally important constraints regarding the concentrations that can be used. Time from  request of CRMs to the actual import of the standard (at least in our region) is variable, so some times this can represent a long wait for the lab if it does not foresee its availability in advance or faces an emergent need. According to our regulation, detection methods and reference materials shall be provided to the Biosafety Authorities before any permit can be issued. So collaborations amongst labs can apply when possible, facilitating their duties and response times, provided there is a RM available for the event under scrutiny.

Facing the growing need for this kind of resources, our official labs have sought alternatives in order to prepare Certified Reference Materials locally. We’ve been fortunate enough to count with the assistance of the National Metrology laboratories and the participation of the Reference laboratories from the three main National authorities. The process has proved useful for growing local expertise and building up technical capacity, and has helped identify operational necessities that for a single lab were hard to establish, such as: assessing the homogeneity and stability of the materials or measuring uncertainty, besides the know-how experience.  For such purposes, collaborative assays have been tested over the past years involving the laboratories from the National Network (RNLD-OGM) with good results and in agreement to international standards [Please refer to our previous post [#5365] @ Overview of existing networks for LMO detection and identification]. This experience has opened the possibility to use these schemes discretionally according to local needs. However, limitations are mainly present in terms of financial resources to perform the certification analyses and the availability of sufficient raw material.

Certainly a guide at BCH would be of great value, specially if it might include information on all available CRM sources and perhaps could mention the approval status of the events at the different countries in order to harmonize analytical capacities if necessary (e.g. regulatory compliance, international trade or LLP).  

Look forward to hear the comments of our other colleagues on how to approach this very important issue.

Best Regards,

Natalhie.
posted on 2013-06-25 02:32 UTC by Dr. Natalhie Campos-Reales, National Commission on Biosafety and GMOs (CIBIOGEM)
This is a reply to 5395 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5398]
POSTED ON BEHALF OF GURINDER RANDHAWA
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The reliable detection and quantification of GMOs mainly depends on the calibrators employed such as Certified Reference material (CRM) or plasmid reference molecules. However, accessing reference material still remains a problem for the developing countries. IRMM is no doubt the best source of reference materials but unfortunately the CRMs for Indian GM events are not available with them. Joint Research Centre (JRC) has a good collection of plasmid reference materials, they also provided us some of the plasmid reference materials for GM Maize events during participation in proficiency testing to use as positive controls. They also do not have plasmids for Indian GM events. Getting reference material, on the other hand, from AOCS is a very difficult procedure as they require advance payment which is not possible in the Govt. set up where normally payments are made after satisfactory receipt of the material. Another problem, as also pointed out by Dr. Hougs, is that sometimes the quality of material from AOCS is not very good for quantification purposes. Also the procedure involved in import of the reference material needs to be simplified, as sometimes the gap between the time of request of reference material and actual time of delivery gets longer delaying the GMO testing in the laboratories on routine basis.

Creation of a single portal for collecting information about reference material and access to reference material along with details of flanking sequences of GM events would be of great help as some of the GM detection laboratories are not in position to purchase these CRMs from the authorized suppliers.

Another alternative could be to develop a mechanism of signing a Material Transfer Agreement (MTA) with the developer of reference material for research purposes, irrespective of any country.

To cope up with this challenge, it would be highly beneficial if an independent international agency can bring out universal guidelines for producing CRMs/ plasmid reference material to ensure their quality in the way it is being done in Mexico as discussed by Dr. Natalhie in the previous post.
posted on 2013-06-25 13:33 UTC by Dina Abdelhakim, SCBD
This is a reply to 5398 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5400]
Dear Secretariat and members of the Network,

I would like to thank the Secretariat for organizing this very important discussion. And also thank the previous posts. It has been quite enlightening to read about other experiences.

Dr. Natalhie has made good contribution about the limitations regarding the access to CRM. I would like to emphasize some of the common constrains also experienced by our lab. In summary, we have been facing additional costs, concentrations limitations, and long time of delivery too. Even general products for detection, such as antibodies, can be also a problem. For example, anti-cry1ab (0.5 mg polyclonal from rabbit) from a commercial company (from the US) costs in the US about 800USD, in Norway about 980 USD and in Brazil 2000 USD.  Most, if not all, of these materials are imported and take around 30 up to 60 days to arrive. Taken into account that the minimum salary in Brazil is about 300 USD, these values can be quite expensive.

Access DNA sequence information is also another limiting aspect of the detection methodologies in general. As said before, here in Brazil, all insert sequence plus junction regions are CBI. Therefore, in order to be able to detect, one has to use the methodology proposed by the company, commercially available products or get sequence information elsewhere. Public databases, such as http://gmdd.shgmo.org/, help us a lot but still it is not the ideal situation. For example, we now need the sequence of the NK603 event and it is not available in the database website. In the end, we have to ask for this kind of information to our partners in Europe.

To rely on methodologies proposed by the company is not the ideal situation either. Although competent authorities do have the permit to get this kind of information, researchers working in the academia or accredited labs, for example, do not.  And for many reasons, we need to design and develop our own methodology for detection. For example, our lab is now switching to Minor Grove Binding real-time PCR probes.  I cannot find a certified or validated methodology anywhere. There are also situations where you want to amplify a specific region of the insert which available primers and probes are not located.

Certainly, the creation of a single portal at BCH would be of great value. My suggestion is that, as proposed by others, it includes information on all available CRM sources. Literature linked to these materials would be also great. It was interesting to see that some of the participants also mentioned the fact that some CRM do not work properly. I have myself experienced that with commercial Elisa kits that are somewhat certified.  In addition to that, some endogenous controls do not work on maize landrace material. Therefore, I suggest that some space could be made available in this portal for user comments on each CRM.

The questions about how could countries with less experience in the detection of LMOs gain access to reference materials and what recommendations do we propose to improve accessibility to reference materials is even harder to answer. As you might know, Brazil is the second largest adopter of the GM technology but still faces big challenges in detection methodologies. As said by Dr. Natalhie, to prepare CRM and develop methodologies locally seems to be the most suited action.

Best regards,

Sarah.
posted on 2013-06-25 18:03 UTC by Ms. Sarah Agapito-Tenfen, Brazil
This is a reply to 5390 RE: Opening of the Discussion: Access to DNA sequence information and reference material [#5403]
POSTED ON BEHALF OF LAURA ESTHER TOVAR
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On behalf of the National Reference Center for Detection of Genetically Modified Organisms (CNRDOGM), Ministry of Agriculture of Mexico (SAGARPA)

It is a pleasure for us to share the experiences we have had in the National Reference Center for Detection of Genetically Modified Organisms (CNRDOGM) belonging to the Ministry of Agriculture of Mexico (SAGARPA). As you mentionated, the reference materials are essential for our tests, but access is limited. Our laboratory in collaboration with the National Metrology Center (CENAM) have obtained certified materials for different genetic modifications in corn, soybeans and wheat. These materials have been certified and successfully used, allowing quantification of GMOs with precision and confidence. Unfortunately the original matrix which was used to generate this certificates materials is limited and difficult to access by this reason, we have tried to find other alternatives, such as the production of plasmids containing the specific genetic modification and the endogenous gene, these plasmids have been developed under an agreement with the Autonomous University of Mexico (UNAM), so we believe that the generation and use of plasmids as reference materials is an option to the existing problems in the access the reference materials. We believe it is necessary to unite efforts between different laboratories and institutions to ensure collaborations that make us overcome the different challenges, finally we thank these spaces where we can  exchange views and share our experiences
posted on 2013-07-01 23:00 UTC by Dina Abdelhakim, SCBD