Advances in genomics technologies create opportunities—and some challenges

To quote Agriculture and Agri-Food Canada Research Scientist Dr. André Lévesque, the possibilities have become almost infinite. Dr. Lévesque is talking about the latest developments in the science of genomics—a still-new and revolutionary branch of science that is undergoing a revolution of its own.

Genetic code

Genetic code

"The changes in the amount of information we can obtain and how quickly and inexpensively we can do it are just incredible," says Dr. Lévesque. "The first full sequencing of a human genome was completed in 2000—a global effort that took more than 10 years and cost over $3 billion. Today, with next-generation sequencing (NGS) technologies, we can sequence a human genome for less than a thousand dollars."

Understanding and exploiting the opportunities presented by advances in genomics is the major focus of the Government of Canada's Genomics Research and Development Initiative (GRDI)—and the opportunities are many, from faster identification and tracking of contaminants in our food and water to new and more effective treatments for cancer.

Agricultural trade

Protecting our agriculture industry is just one example. Canada is the sixth-largest exporter of agricultural and agri-food products in the world, with annual exports of some $40 billion a year.Footnote 1

"To maintain access to global markets we need to show that our exports are free of the damaging pests and pathogens that are listed as quarantine species in international agreements," says Dr. Lévesque. "We also need to protect Canadian agriculture from pests and pathogens that may arrive from other countries."

Accurate testing essential

With NGS, testing for the presence of pests and pathogens is both faster and more accurate. "A lot of these organisms are very similar to one another," explains Dr. Lévesque. "With conventional testing, there is the risk that something harmless will be misidentified as a quarantine species—a mistake that could lead to another country closing its border to Canadian exports of a commodity at a cost of many millions of dollars."

Albert Tenuta, a field crop plant pathologist with the Ontario Ministry of Agriculture and Food, says NGS technology is protecting the industry in other ways. "We have worked with AAFC and other provinces to set up monitoring stations across the country to collect samples of pests and pathogens that move through the air," says Mr. Tenuta. "With NGS, we can identify what we collect very quickly, and provide growers with real-time warning of threats so they can take steps to manage a pest or pathogen before it becomes established."

Filling the gaps

There are challenges. "Other countries are using various kinds of genetic testing on agricultural commodities from Canada," says Dr. Lévesque. "Not everyone has the same testing capacity nor are they using the same methods so there is a risk of disagreement and potentially costly errors. That is why we continue to explore new international collaborations to share information and methods."

A key problem is gaps in reference data. "It is not enough to have the DNA of a species," explains Dr. Lévesque. "To make an identification, you have to have something to compare your sample to. That means building up a database of DNA sequences from a whole range of organisms."

With the support of the GRDI, Government of Canada science departments are working together to collect and sequence DNA from the tens-of-thousands of specimens in their collections. "As we go along in processing environmental samples with NGS technologies, we are also identifying gaps in the database so we can work with partners in Canada and other countries to fill those gaps," says Dr. Lévesque. "Unfortunately, NGS can't help yet in filling these gaps s. Because these specimens are no longer living and have been stored in different ways over the past 100 years or so, they have to be sequenced one at a time with more traditional technologies."

Making it work

As the database grows, it presents another challenge: how to manage all the information. "We are talking about petabytes of information," says Dr. Lévesque. "A petabyte is a million gigabytes—enough to fill 20,000 iPads."

To address this challenge, GRDI-funded researchers are developing Canada's bioinformatics capacity and identifying the computing tools and power and network infrastructure needed to manage and share massive amounts of data quickly and efficiently.

Positive impacts

While there are challenges, Dr. Lévesque says they are far outweighed by the opportunities. "It is difficult to overstate the real and potential positive impacts of next-generation sequencing technologies," says Dr. Lévesque. "Breeding better crops, protecting Canada from invasive species, assuring access to global markets for our agricultural commodities—NGS is already playing a key role in all of these and more. Research supported by the GRDI is helping to ensure we can put these technologies to work for the health, safety and economic well-being of Canadians."

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