Old DNA the foundation for new identification technologies
As anyone who has watched an episode of CSI or Law and Order or almost any other modern police procedural television series will know, when it comes to making a positive identification of the culprit, nothing beats DNA — not even identical twins have identical DNA. We might be able to alter our fingerprints, but we cannot change our unique genetic code.
The science of genomics is equally valuable for identifying pests and pathogens that can endanger our health, safety and economy.
Mistakes can be costly
Accurate identification is essential. Different species of fungi can look remarkably alike and even experts can have difficulty saying which is which. The consequences of misidentification can be significant. Mistaking a harmless species for another that can devastate a crop, for example, could close down Canada's wheat exports at a cost of hundreds-of-millions of dollars.
Building Canada's capacity to deliver the fast, accurate identification of these organisms that DNA can provide is among the key areas of research being supported through the Government of Canada's Genomics Research and Development Initiative (GRDI).
New technologies for accurate identification
With the access to next-generation sequencing technologies provided through GRDI investments, researchers can now sequence DNA from all of the many organisms that may be present in a sample of wheat or water or soil in a matter of hours or even less. These sequences can be fed into a computer which compares them to DNA sequences of known organisms and provides a list of everything that is in the sample — much the way DNA collected at a crime scene is matched against DNA collected from offenders and stored in law enforcement databases.
In either case, as Canadian Food Inspection Agency (CFIA) research scientist Dr. Guillaume Bilodeau points out, without a good database, identification is impossible.
"This is a big part of the work we're doing through the GRDI," says Dr. Bilodeau. "Going through the thousands of specimens of high-risk organisms federal departments have collected over the years, extracting DNA for sequencing and adding these to the database."
It is painstaking work. Many specimens have been in storage for decades and preserved in different ways and DNA must be extracted from one specimen at a time in order to get enough high quality DNA for sequencing.
Consistency key to credibility
"Actually, while it takes time, getting DNA from these older specimens is not usually a problem," says Dr. Bilodeau. "In fact, for any given specimen, there may be several methods available to extract the DNA we need. We want to identify the best method for each type of specimen, whether it is something in the collection or for a sample taken in the field — the method that will provide the most and highest quality DNA for sequencing."
This is the focus of the research project Dr. Bilodeau is leading. "We have to be able to assure our trading partners that our test results and identification procedures are scientifically valid," says Dr. Bilodeau. "We need to be consistent in the methods we use to obtain the DNA sequences for our database."
Collaboration for results
As part of the larger Quarantine and Invasive Species project funded by the GRDI, Dr. Bilodeau has been able to collaborate with researchers in other federal departments and agencies in developing and sharing Standard Operating Protocols (SOPs) for DNA extraction of different types of specimens.
"With researchers in different departments testing different methods simultaneously, and then coming together to compare results, we have been able to share ideas and suggestions and develop our SOPs a lot faster and at less cost," says Dr. Bilodeau.
Filling an information gap
Dr. Mark Laflamme, a research scientist at the Fisheries and Oceans Canada Aquatic Animal Health lab in New Brunswick, says the development and sharing of SOPs demonstrates the importance of the interdepartmental collaboration enabled by the GRDI in other ways. "The test methods themselves do not represent new knowledge, so it's not the kind of thing that would be published in a journal," says Dr. Laflamme. "At the same time, it is information that is crucial to the credibility of our database and our identification process. Without the GRDI, we would have no mechanism to share the information across departments and ensure we are all on the same page."
"It also makes the job easier for everyone," says Dr. Laflamme. "It's easy to get DNA from a specimen, but it's not always easy to get 'good' DNA. Instead of trying several different methods, we can refer to the SOPs and see that for this kind of specimen preserved in this way, this is the method that will produce the best and most consistent result."
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