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Current Activities 2016-2018

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Opening of Discussion [#9128]
Dear Participants,

Welcome to the online discussions of the Network of Laboratories for the Detection and Identification of Living Modified Organisms.

At their last meeting, on Decision CP VIII/16,  the Parties to the Cartagena Protocol on Biosafety requested the Executive Secretary to continue working on the draft training manual, in collaboration with the Network of Laboratories for the Detection and identification of Living Modified organisms, and make a draft version available for consideration at their ninth meeting. Accordingly, an updated version of the draft manual has been prepared by the Secretariat, in collaboration with a small group of experts from the Network, and it is available for review by all participants of the Network.

This discussion will focus on module 3 which provides an introduction to procedures for sample management, including a brief discussion on considerations for laboratory sampling and subsequent sample preparation and homogenization. This is followed by an overview of DNA extraction and purification methods as well as information on DNA quantification methodologies.

Participants are invited to review and provide feedback on the contents for each module during the course of the next 2 weeks. We request that you review the manual from both a technical and editorial perspective focusing on edits and comments that  would provide additional clarity to the manual. In providing your comments, please refer to specific line numbers or highlight the text directly in the Word document containing the module and upload it together with your message.

We look forward to two weeks of constructive and fruitful discussions which will bring us a step closer to the goal of developing and improved version of the manual for the consideration of the COPMOP.

Kindest regards,
Secretariat
posted on 2018-04-02 02:13 UTC by Dina Abdelhakim, SCBD
This is a reply to 9128 RE: Opening of Discussion [#9177]
Dear all participants

I have added in lines 353-355 and 362-363 information about the alternative use of chloroform:octanol and isopropanol when using a CTAB-based method for DNA extraction.

On the other side, I would like to ask if a "Sample collection methods" section should be take into consideration. I have had handled only leaves samples for LMO detection, besides, for another kind of plant genetics studies. Samples taken in the field must be cafefully collected and handled to assure integrity. Keeping leaves out of degradation is managed by keeping samples cold or at room temperature which is sometimes difficult in tropical climates.
We provide tubes with desiccant silica in order to keep samples as dried as possible prior to arrival to the lab. Humidity removal prevents fast sample degradation and also facilitates sample grinding in the lab.
It might be possible that different procedures are set-up by different labs, so that, my recommendation to include a section in the document regarding sample collection.

Thanks and best regards,

Emanuel.
posted on 2018-04-06 00:43 UTC by Mr. Emanuel Araya, Centro Nacional de Innovaciones Biotecnologicas
This is a reply to 9128 RE: Opening of Discussion [#9182]
Dear Forum Participants,

I would like to thank everyone who has shared their comments on this module so far.

As previously indicated, the main objective of this discussion is to review and provide feedback on the contents of module 3 which can be accessed at http://bch.cbd.int/detectionlabs/trainingmanual/module%203_27mar18_posted.docx.

We request that you review the manual from both a technical and editorial perspective focusing on edits and comments that  would provide additional clarity to the manual. In providing your comments, please refer to specific line numbers or highlight the text directly in the Word document containing the module and upload it together with your message.

I hope you will be able to contribute to this discussion in the coming week and share your knowledge with us in order to contribute to the development of a through and comprehensive training manual.

Kindest regards
Dina
posted on 2018-04-09 16:46 UTC by Dina Abdelhakim, SCBD
This is a reply to 9182 RE: Opening of Discussion [#9193]
POSTED ON BEHALF OF Mr. Adugnaw Admas, ETHIOPIA
--------------------------------------------------------------
Dear Colleagues,
Thank you for you invitation to participate in this online LMO detection form.
Accordingly your  invitation to review the document,I have tried to see carefully all module, really it is interesting and also, i apperciate the module organizers for collecting best materials of LMO detection document.
module 3 from line 34-36
my comment
It will be  nice if it includes as examples  different country management experience
From sampling site up to detection and give permissions for crop exporters and imposter  including the application form
Thank You
Adugnaw Admas
Ethiopian Environment and Forest Research Institute
Biological Science Research Division Coordinator
Tell 0918561763
posted on 2018-04-10 12:42 UTC by Ms. Melissa Willey, UNEP/SCBD/Biosafety
This is a reply to 9128 RE: Opening of Discussion Module 3 [#9199]
Thank you for compiling an excellent summary of this area, and the excellent illustrations.  I have made a significant number of edits in tracking mode and comments that provide additional clarity to the manual.  I have attached the document with my tracked suggested changes and related comments to this reply, as compiling each comment with the line to which it refers to would take much longer than the limited two week time frame that has been allowed for review of all of these documents.

Key suggestions:
In many cases, permits are required in order to move LMO’s either because they are not yet approved for general release in the country of receipt, or for phytosanitary reasons.  I have therefore added to the documentation to be checked: ‘5. Any required regulatory permit information (such as phytosanitary or LMO movement permits)’

We must remove any reference to oils, flours or other processed food products as the protocol only concerns LMOs and thus must consist of plants, plant parts, or seeds or grain, and thus processed foods are out of scope.  While we are right to make use of the EU JRC documents, we must be true to the discussions we had at the meeting in Italy where we resolved to make sure the document is globally relevant.

At line 191, I suggested that it may be necessary to subsample large items, like tubers.  I had some experience some years ago sampling sugar beets and the logistics of grinding 1000 sugar beets defies description (I was only sampling a few!).  I also removed a reference to liquids and flours – which are not LMOs.

As module 4 includes proteins, I added a reference to protein in this section also.

I suggest that we add a reference to ISO 17025 as this is a globally recognized laboratory quality standard in the section on QA.  Some of the text here is multiplicative of module 5 and needs to be reviewed in that context and maybe removed.

Throughout this document there are multiple references to GMO (possibly due to use of text from elsewhere).  I have changed them to LMO as the protocol refers to LMO not GMO.

I concur with the previous comment regarding use of Phenol/chloroform and other solvents: given the environmental impact of Phenol/chloroform and that this protocol pertains to the environment, it may not be appropriate to use this type of protocol in this document.

I find that the references in this and other documents are very out of date – often being from 20 years ago.  Statements and assumptions made at that time may no longer be applicable. We should make a concerted effort to use more up to date citations, especially as this field has developed significantly in the last 20 years.
I also added a more recent publication on sampling grain and seed to the citations, along with other suggested citations that can help address the comment by Mr. Emanuel Araya on sampling.
posted on 2018-04-11 15:50 UTC by Dr Raymond Shillito, Bayer CropScience
This is a reply to 9182 RE: Opening of Discussion [#9205]
Hello,
I have reviewed Module 3. Overall the module focuses on seeds and grains with a few leaf tissue examples thrown in. Tissue sampling of leaves, fleshy produce and other possible LMOs needs to be brought out. Specific comments can be found in the attached document with my primary issues listed below.

Lines 48-50
“A description of each sample submitted to the laboratory is provided by the submitter, including information on the type of sample, for example if it is food, feed or seed as well as its weight and composition.”
Comment: Use “raw foods, feeds and produce” to stay within the LMO scope? Fresh leaf tissue, FTA paper/card  is also a possible submission type.

Line 98
“Furthermore, each individual sample that is submitted for a particular case shall be assigned a consecutive item number and/or barcode label.”
Comment: Proper labeling, tracking and management of submitted samples does not require a barcode.

Lines 131-132
“This can be done by weighing the mass of 100 kernels and extrapolating an estimate of the number of seeds present based on the mass of whole sample.”
Comment: Varietal differences and differences in environment make this method our primary method. An average sample size from the provided table is simply a number derived from the possible range of seed sizes unlikely to match what is submitted to the lab.

Starting on line 202
“Once the sample is homogeneous, following grinding and mixing, if required, the test portion is obtained through “grab sampling.”
Grab sampling in the seed industry has been defined as the quickest and cheapest way to get a sample giving the term a negative connotation for many. I would say the “working sample” or “sub-sample” is taken from the homogenized sample.

Thank you,
Doug Miller
Illinois Crop Improvement Association
posted on 2018-04-12 16:56 UTC by Mr Douglas Miller, United States of America
This is a reply to 9205 RE: Module 3 [#9210]
Dear colleagues,

many thanks to the authors for writing this module as a basis for the development of training materials, which is a very good starting point.

Module 3 should provide an introduction to procedures for sample management including a brief discussion on considerations for laboratory sampling and subsequent sample preparation and homogenization. this is followed by an overview of DNA extraction and purification methods as well as information on DNA quantification methodologies.

I want to highlight again the ISO standards existing since more than 10 years and bringing harmonisation to the global apporaches and strategies concerning the procedures for sample management, DNA extraction and purification and as well DNA concentration measurement.

In addition, I want to draw the attention to document of the European Network of GMO Laaboratories (ENGL) providing valuable guidance documents concerning the sample preparation procedures and considerations if kernels (seeds/grais) are sampled and further prepared for LMO analyses.
http://gmo-crl.jrc.ec.europa.eu/ENGL/docs/WG-SPP-Final-Report.pdf
http://gmo-crl.jrc.ec.europa.eu/ENGL/docs/WG-SeedTesting-Report.pdf

My apologies, not providing comments  to specific line numbers. I added comments and changes/additions directly in the Word document containing the module 3, which is hereby upload  together with my message.

I am look forward for a further and fruitful online discussion towards developing and improving the manuals for the consideration of the COPMOP. Please contact me, if further support and expertise is required.

Kind regards and have a nice weekend,
Lutz
posted on 2018-04-13 12:35 UTC by Lutz Grohmann, Federal Office of Consumer Protection and Food Safety
This is a reply to 9210 RE: Module 3 [#9223]
Dear Dr. Grohmann and the BVL
Thank you for your excellent comments and detailed editing of the module 3.

We support your comment that the statement in the introduction at line 23 is too prescriptive; we should find a more generally applicable statement.  It is good that you have also pointed out in line 49 that the details of the sample are important.
Thank you for referencing ISO 6498.  This is an interesting and possibly useful reference in that it pertains to reduction of the sample in the laboratory.  Figure 1 of ISO 6498 is useful in that it suggests multiple sample reduction steps, which can be useful in processing seed and grain.  ISO 6498 Table 3 does not refer to DNA – it might be useful to think of finding another source or reference that does.  There is not time in this round of comments to research this fully.

We agree with Dr. Grohmann and BVL that the shortened version lab rather than laboratory should not be used, and to expand them all to laboratory (this is relevant to this and other modules).

We appreciate the comment in #9210 regarding use of international guidance (line 111) for consideration of sample size. We also support the comments at line 154 (125 in original text) regarding handling large samples, as I myself have had to deal with such samples using multiple grinding and reduction steps.

As stated in my previous submission #9222 I agree that the table 3 needs some further discussion, especially regarding the number of leaf samples.  Test portions of ground seeds and grains can be as large as 1-5g in some commercial laboratories carrying out LMO detection and quantification; such approaches reduce the need for grinding the sample to a fine particle size. This comment also is relevant to the sample size of two 200mg portion referred to in line 197 in the original text.  Indeed for wheat (because of the large genome size), this portion may not be enough, depending on the LOD that is desired.

I appreciate that Dr. Grohmann and the BVL have also stated and support our comment that the literature cited is outdated.

Further a statement on Grab sampling:
As stated by Doug Miller in submission #9205, grab sampling can be a valuable method of sampling if properly used, and is allowed by ISTA rules, and taught during both ISTA, and to my knowledge, UK sampling courses.  It can be used by taking multiple samples by hand from multiple areas of the container, if the hand is able to reach all parts of the container.  In this way it is analogous to probe sampling.  This means of sampling can be used both for primary samples and for subdividing the bulk sample in order to provide the laboratory and retained samples.
posted on 2018-04-15 21:24 UTC by Dr Raymond Shillito, Bayer CropScience