Rising superstar in fish nutrition: Dr. Stefanie Colombo

Dr. Stefanie Colombo is on a roll.  A talented researcher focused on alleviating some of the environmental and nutritional issues stalking fish farm operations in Atlantic Canada and elsewhere, Dr. Colombo is hard at work developing novel solutions for environmentally sustainable, economically viable farmed seafood.

Her specialty is improving aquatic nutrition for farmed fish through nutrigenomics, a growing source of practical solutions for aquaculture.  In just five years she has transformed from a 2015 PhD candidate into an established scientist, a Tier II Canada Research Chair at Dalhousie University with her own Aquaculture Nutrition Lab at the Truro Agricultural Campus, a $1.5 million research program and more than 30 research papers to her credit. Her work also is getting international attention.

Last fall, the transplanted Brantford, Ont. native made headlines as one of the main authors of a research paper that warned if global warming goes unabated and the world’s population keeps growing, in 80 years’ time, 96 per cent of humanity could be starved of Docosahexaenoic acid (DHA). The nutrient is one the most abundant fatty acids in the human brain and is considered vital for neuroprotection, cell survival and inflammation control. The human body produces insufficient DHA on its own and relies on seafood and dietary supplements to supply the rest.  Meanwhile, the availability of DHA in seafood, based on their mathematical modelling, could be severely reduced by global warming.

In an age when women scientists can struggle to advance, Dr. Colombo’s rise has been close to meteoric.  In addition to her research skills, her luck and timing have been excellent. “I chose a field that I felt passionate about, but that’s also a field where research is needed for our future food security and our environment,” she explains.

As an undergrad, Dr. Colombo started out in marine and freshwater biology, veering to fish nutrition in graduate school and then to nutrigenomics for her PhD. Altogether, she says, “it’s given me quite a tool box to work with in approaching new challenges in aquaculture.” 

Her motivation, though, actually stems from an enduring enthusiasm for deep sea diving that began in childhood. It opened the wonders of the aquatic world and became a profound and enduring source of inspiration and, in the age of climate change, a source of concern.

Describing the sport’s influence on her, she said, “it has had everything to do with shaping my career. That passion has been the driver of my career and in many ways, some of the most important decisions I’ve made in my life. It’s why I do what I do.”

Hooked first on snorkeling at age six, she says, “as soon as I was able to dive at 12 years old, I got certified and I’ve been diving ever since.” Now rated a divemaster, Dr. Colombo has explored waters off Nova Scotia, Vancouver Island, Mexico, the Bahamas, the Philippines, and Hawaii – or more precisely and memorably, Maui, the place where she first caught the diving bug.

Her underwater adventures led her to become a strong advocate for aquaculture, which by 2030 is predicted to supply more than 60 per cent the world’s seafood. Dr. Colombo’s appreciation for the industry and its challenges was reinforced as a hatchery technician with Scotian Halibut Ltd., Clarks Harbour, a job she took after her undergraduate degree. Since then, she has given support to the industry outside the lab, as president of the Aquaculture Association of Canada and now as Scientific Advisor to the Aquaculture Association of Nova Scotia.  

In her view, the big advantage of fish farming lies in its ability to supply seafood without depleting ocean life, now under increasing duress from climate change. Unsurprisingly, the mission she has set for her lab is “to improve sustainable production in aquaculture by making scientific discoveries toward growing healthy, nutritious fish with the ultimate goal of food security and ocean conservation.”

Well aware that the aquaculture industry is often a flashpoint in public policy debates because of perceived environmental concerns, Dr. Colombo sees her work as part of the solution. She acknowledges, “I’m not doing research on public trust, but my research is working to alleviate some of the environmental concerns: using algae-based products instead of wild fish, improving utilization of the diet so there’s less waste, better understanding of fish metabolism for more efficient production so we use less resources, ensuring nutritional and product quality of farmed salmon.” And she says getting the word out is also “a very important piece – informing the public about efforts in these areas and providing fact-based science to dispel misconceptions.”

As a PhD candidate, she was involved in the $6.1 million camelina oil project supported by Genome Atlantic and ACOA. That research facilitated the Canada Food Inspection Agency’s approval of the oil produced by the oilseed, camelina sativa, for use in fish feed for Canadian farmed salmon and trout. It is hoped, the product will help reduce reliance on traditional fishmeal made from wild fish, for which growing demand will soon overwhelm supply.

Much of her research, in fact, has been driven by the ongoing search to replace wild fish and  wild fish oil with cheaper and suitably nutritious plant-based alternatives.

Recently Dr. Colombo’s lab has been investigating the “nutritionally perfect fit “of algae – or more correctly microalgae ­– to fill that bill. Microalgae can also supply the necessary Omega-3 needed by the fish and demanded by consumers. Genomic breeding techniques, she said, could develop Atlantic salmon that grow with improved commercial efficiency on this kind of plant-based diet.

While the camelina project marked her first formal training in genomic-related research, her introduction came earlier at Scotian Halibut Ltd. The company had an ongoing collaboration with the National Research Council and she was a co-author on two studies, under a project named Pleurogene, funded by Genome Canada in partnership with Genome Spain.

“I was really excited and proud to be part of those studies at that time,” she recalls. “The experience was really formative in my career.” It looked at the effect of partially replacing fish meal with soybeans in the diet of juvenile Atlantic halibut.

Genomics has evolved alongside her career. “I have learned so much in the past 5-6 years; I’m still learning! Every time I learn something new, it opens a new door or possibility to address a problem, with a new approach or direction that I hadn’t thought of before. I would say my overall research goal hasn’t changed much, but my approach has evolved by becoming more sophisticated and streamlined since my PhD. I owe a lot of my genomics knowledge to Dr. Matthew Rise at Memorial University, who has been a mentor since my PhD research. We continue to collaborate on genomics-related projects.”

On the board now is a follow up to her work warning of the impending global depletion of DHA, an important component in wild fish meal and oil aquafeeds. To do that, she plans a lab trial to test theories from two previous studies and examine the impact of reduced DHA with warming temperatures and reduced oxygen levels in coldwater fish and their ability to synthesize new DHA.

According to current projections, she says, “in 80 years, we will need to supply about twice as much fish oil in aquafeeds to get the same amount of DHA we currently get in farmed fish.” With human brain development reliant on DHA and with humanity largely dependent on seafood to obtain an adequate supply of this nutrient, she says, “Aquaculture has a huge opportunity to solve both problems.

She explains, “While we estimated that climate change will reduce DHA from wild fish, we can control the diet for farmed fish. This means we can continue to supply DHA through farmed seafood to the growing human population. Also, there are many new sources of DHA that are on the horizon that will significantly reduce the use of fish meal and oil – like microalgae, microbial, and other single-celled products – and provide DHA to farmed fish.”

Evident by her enthusiasm, projects and passion have been a winning combination for Dr. Colombo, but it’s really the latter element that drives her success: “I love what I do and always keep trying and won’t give up,” she says.

Employment Opportunity [one-year term]

Sector Innovation Associate [one-year term]

The Sector Innovation Associate is responsible for opportunity generation and actively supporting the Business Development Strategy for Genome Atlantic. Aimed at maintaining the organization’s robust pipeline of end-user-driven future opportunities, this position helps lead the development of assigned proposals with guidance from the Director, Innovation Programs and also supports the CEO, as needed.

Focused on identifying and cultivating key opportunities in our 7 target sectors, this role involves attending key events, supporting and enhancing existing relationships, as well as developing new partnerships. This role serves as the Sector Lead for the Health, Environment and Mining sectors while supporting lead development in other sectors, as needed. 

The Sector Innovation Associate contributes to a small, energetic and talented team, and supports meaningful connections between private sector needs and academic research expertise. This opportunity is ideal for a driven and highly organized, natural connection-builder known for delivering excellence in a fast-paced environment. If you’re a self-aware, “glass-half-full” team player with a great sense of humour, you’ll feel right at home on our team!

Key Qualifications

  • A graduate-level science degree in a relevant discipline or an undergraduate science degree with an MBA or a comparable combination of science and business training in academia.
  • A minimum of 7 years of dedicated business development/innovation experience within the Bioscience sector, in roles of progressing responsibility.
  • Deep understanding of genomic applications for key sectors driving the economy of Atlantic Canada with specific experience in one or more sectors, particularly ocean technology, considered an asset.
  • Well-developed and proven leadership skills to help mobilize end-users (from the private and public sectors) and academic experts to address strategic opportunities of importance to Atlantic Canada. 
  • Natural matchmaker with a proven track record of identifying and developing high-value opportunities capable of enabling significant socio-economic benefits.
  • Hands-on experience with the development of large-scale, multi-million-dollar proposals linking private sector needs with academic expertise. 
  • Vision and experience to assess/coordinate the review of the strengths and weaknesses of new opportunities (including the science, GE3LS and socio-economic impact elements) and in turn advise on proposal strategy.
  • Excellent written, verbal and interpersonal communications skills.
  • Prior experience overseeing direct reports and contractors preferred.
  • Experience working with government agencies and funding partners.

This position requires schedule flexibility, including availability some nights and weekends to accommodate travel, address time-sensitive matters and adapt to meetings in different time-zones, as required.

This position is based out of our Halifax, NS office and may require travel throughout Atlantic Canada on occasion.   Given the current COVID-19 conditions, Genome Atlantic acknowledges that some flexibility will be required to accommodate the successful applicant, and as such are willing to consider a remote working situation in other parts of the country.

How to Apply

Kindly forward your cover letter and resume (as one document) with the heading “Sector Innovation Associate” in the subject line of your email to ktweel@genomeatlantic.ca. Please entitle all attachments to include your first and last name. Your cover letter should articulate why you believe you are a fit for this position, key career accomplishments relevant to this opportunity, and how you see yourself contributing to our team dynamic. 

Closing date for this posting is Monday, November 16th, 2020.

Individual accommodations due to a disability are available upon request for candidates taking part in all aspects of the selection process. All qualified applicants will receive consideration for employment without regard to age, race, religion, ethnicity, gender, disability, citizenship status, marital status, actual or perceived sexual orientation. 

Genome Atlantic is committed to creating an inclusive environment and building a team that represents a variety of backgrounds, perspectives, and skills. We value diversity and recognize that experience comes in many forms and skills are transferable. Please view this description as a general overview, but not a mandatory comprehensive list. If you feel passionate about our efforts and believe that you have the skills to contribute and lead in this role, apply!  

We thank all interested parties; however, only those applicants under consideration will be contacted.

About Genome Atlantic

Genomics is a powerful combination of genetics, biology and computer science. It provides us with the unprecedented ability to better understand all living things, leading to a host of opportunities across a variety of sectors. Genome Atlantic is a not-for-profit corporation with a mission to develop and lead a program of genomics R&D that delivers tangible economic, social and environmental benefits to Atlantic Canada. 

We connect ideas and people across public and private sectors to find new uses for genomics, invest in large-scale science and technology to fuel innovation, and translate discoveries into solutions across key sectors of national importance. Key sectors include health, agriculture and agri-food, forestry, fisheries and aquaculture, the environment, energy, and mining. Together with our many partners, we have enabled over $120 million in strategic R&D since our inception in 2000.

New genomics research investments to tackle health challenges and a resilient recovery for Canada

$16 M in federal funding to support new genomics research in health, agriculture and the environment

Genome Canada Press Release – October 26, 2020

As Canada addresses ongoing challenges posed by the COVID-19 pandemic and charts a course for economic recovery, harnessing the game-changing potential of genomics can deliver homegrown solutions and help protect and improve Canadian lives.

Read More

Check out our article on the rare disease research project announced today as part of this federal funding support.

“Genomics is the future, and the future is hope.”

A conversation with leading Canadian oncologist Dr. Janessa Laskin

Vancouver, BC – 03 July 2019 – Dr. Janessa Laskin – Medical Oncologist and Senior Scientist BC Cancer. (Photo: Chuck Russell)

Personalized OncoGenomics, probing an individual’s genome for bespoke cancer treatment, is a reality for a select group of patients with incurable cancer in British Columbia. The project, known as POG, now in its seventh year and offered through BC Cancer, has vaulted its clinical leader, Dr. Janessa Laskin, into the forefront of international discussion on the future of this revolutionary approach to cancer.

A medical oncologist at BC Cancer, Vancouver, Dr. Laskin has drawn at least four conclusions from her ground-breaking work with POG, a novel collaborative research project between clinical oncologists and the Michael Smith Genome Sciences Centre in Vancouver:

• Cancer is a disease of the genome

• Genomic technology can help us better understand cancer biology, behaviour and response to therapy

• Genome/transcriptome data can be used to identify novel treatment strategies

• Such comprehensive data can make a difference in clinical care for the individual and this knowledge can be translated to help patients on a global scale

POG is the only project of its kind to accept adult and pediatric patients with all types of advanced cancer for evaluation in such extensive detail. As of August 2019, 1,068 patients have been enrolled in the study since the program’s launch. Whole-genome and RNA sequencing is done on biopsied cancer cells taken from every patient, generating enormous amounts of data which are then subjected to thorough analysis and discussion by researchers and clinicians. Their combined effort is focused on generating hypotheses about what might be driving a particular person’s cancer to grow uncontrollably and to exploit those vulnerabilities with drug treatments. Of the cases completed, over 80 per cent of the time the genomic/transcriptomic data generated potentially clinically actionable drug targets that could often be aligned to actual treatments for the individual patient.

POG considers cancer a disease of genetic mutations with drivers that are individual to the persons affected. Using a patient’s analyzed genomic and transcriptomic (RNA) data, POG can search for drug treatments – some of which may be off label or approved for other diseases – with potential to contain or neutralize the drivers.

Conventionally, cancer has been approached as a disease differentiated by its site of origin and it has been treated according to standards, based on what has helped others affected in the same way. In some respects, it has been a one-size-fits-all approach.

“Unfortunately,” Dr. Laskin has acknowledged, “we know that this strategy can only help some patients, which means that many people endure potentially toxic and ineffective treatments. POG is about trying to identify the right treatment for the right person at the right time; we are still in the discovery phase but POG has had its share of fascinating success stories as well as disappointments, as outlined in a 2017 episode of The Nature of Things, broadcast by CBC.”

Yet even at this early trial stage, the concept behind POG is considered promising enough that many observers in the cancer field expect it to eventually provide more options to patients, for whom the traditional approach has been unsuccessful, and to present scientists and clinicians with new, fruitful lines of inquiry for more effective cancer treatments.

Dr. Laskin stopped at Genome Atlantic on a visit sponsored by Sanofi-Genzyme, Genome Atlantic, Integrated Microbiome, Illumina and Dalhousie University. She was in Halifax to speak to the local medical and research cancer community about POG.  To mark the visit, we asked her five questions:

Do you find oncologists and cancer researchers open to the idea that cancer is a disease of the genome or do they need convincing?

At this point I think there is a general agreement that the unregulated cell growth that defines cancer is driven by something wrong at the genome or transcriptome level. We have clear examples of success when we are able to identify and target these specific abnormalities and many of these are now integrated into the standard of care for testing and treating certain types of cancers. Lung cancer with EGFR mutations, melanoma with BRAF mutations would be examples of this integration of genomic technology directly into mainstream care. However, it is also clear to clinicians and researchers that this is still a wide-open space and there are many aspects that are as yet unclear and many of these likely lie in the space around the genome such as epigenetics, proteomics, and so on.

It has been found that chemotherapy changes the genome. Is this conclusion an obstacle or an opportunity for improved cancer based on the POG approach?

We have a lot to learn about the untreated cancer genome, so the changes after chemo- or radiation therapy pose an additional important challenge. We have demonstrated many of these changes over time with serial biopsies and analyses; this is one of the most interesting aspects of the research aspect of POG. In the future I am hopeful that we can learn how to harness the power of this sort of knowledge; by understanding how a cancer might evolve in the face of a specific treatment perhaps we can guide it in a direction that would allow a treatment we could anticipate and therefore take advantage of.

Apart from cases of remission, how does POG know if it has improved the condition of its patients, given that all the participants have been diagnosed with terminal cancer.  In other words, how does POG evaluate success?

This is an important question that everyone in the “precision” medicine field is grappling with; if you are treating each individual how do you know they would not have done just as well with a standard or different therapy? There have been many approaches to this in clinical trials, comparing how a person did on the previous treatment is the most common method. For POG we have been more focused on development of a process to create meaningful analyses and testable hypotheses so we have not yet focused on this sort of clinical value.

We do have some early data with matching cohorts of patients who have not had treatment informed by POG and we do find that patients treated based on POG information do at least as well if not better; but these are early days and the study was not designed to answer that specific question. It is definitely something we are motivated to address, and we work closely with our Health Economics team to try to measure and understand the value of this sort of data. And “value” can mean many things, not just financial but also the utility of having more information and a biological rationale to choose treatments.

We do think that in time finding the right treatment for each person will be more effective care, though it may not be less expensive. If people are living longer, they will need to be on treatment for longer.

The POG project has been running for seven years now. Has the program provided enough proof of concept yet, to be considered worthy for adoption into the health care system?  If not, what stands in the way?

POG has been an innovation and discovery project, we would not envision that POG as it currently exists would be the right answer for every person with cancer. It is clear that more information is helpful for treatment planning and to understand cancer biology and evolution. Once we have sequenced tens or hundreds of thousands of these individual cases, I think we will have a much better idea of what sort of patient requires each level of testing. And as we acquire this experience, the technology will change, and we need to adapt along with it.

Much as you might not have envisioned a smart phone when you bought your first cell phone, your needs changed as the technology evolved. For now, funding is a significant issue, we need to amass enough data to understand the best way to include genomic technology into care.

What is next for the POG project?

We have a number of exciting projects on the go. We are about to launch a trial using POG data to identify markers for immunotherapy. This is an area of great need because there are no reliable markers for these drugs currently, and they are costly and often toxic. We have been doing some innovative work in pancreas cancers, understanding that there are some niche populations in this devastating cancer that can be selected out by POG-like analysis.

Our next goal is to work close with the Marathon of Hope Cancer program in collaboration with the Terry Fox Research Institute, to bring cancer genomics to all Canadians. We have a novel program to generate information more rapidly for clinical use while selecting some genomes for more in-depth analysis. We are committed to collaborations and data sharing, and we hope to bring our experience into the field, to pave the way for other researchers and clinicians.

Genomics is the future, and the future is hope.

Recipe for successful industry-academic partnerships

Drs. Matthew Rise (Memorial University) and Richard Taylor checking out aquaculture pens.

Years of experience in the aquaculture industry have taught Dr. Richard Taylor that successful co-ventures with academic researchers begin with the industry partner’s ability to lead the project.

“Having the industry scientist lead is essential so that they can communicate the results to management and keep a commitment, based on what management expects and needs,” he explained.

Dr. Taylor knows first-hand about the ins and outs of that relationship as the former Principal Scientist, Method Development, first at EWOS, the main aquafeed supplier to the farmed salmon industry worldwide, and then at Cargill, the multi-sector food and agricultural giant that scooped up EWOS in 2016. He retired from Cargill in February this year.

A second collaborative must-have, he says, are realistic goals for the university scientists.

“To develop a new salmon health feed in three years, for example, can be an extreme challenge for an academic team,” said Dr. Taylor. On the other hand, he said, “To develop high throughput gene expression in three years should be one of their core areas of expertise.” He also points out, that task is more likely to generate a published research paper that advances the scientific-academic enterprise.

Dr. Taylor co-led two highly successful multi-million-dollar Genome Canada projects, supported by Genome Atlantic, under the Genomics Applications Partnership Program or GAPP, in collaboration with Cargill Animal Nutrition. (The first GAPP project actually started in 2014 under EWOS, before its acquisition by Cargill.)

Those projects teamed him first with co-leader, Dr. Matthew Rise, and with Dr. Chris Parrish, both in the Department of Ocean Studies, Memorial University.  The collaboration with Memorial University scientists continued, leading to a second project, which also added Dr. Mark Fast, Professor of Fish Health and Immunology, at the University of Prince Edward Island.

The results pinpointed salmon genes – or biomarkers – related to salmon growth and immune response, and the means to improve Cargill’s clinical diets.

The first study showed the way for more effective impact assessments of new feed ingredients on farmed salmon, while the second project offered a means to better fortify the fish against single infections and co-infections, a constant industry concern.

The partnership came about by chance. Dr. Taylor was then working in Norway, the site of EWOS’s – now Cargill’s – salmon research centre. The company wanted to collaborate more with EWOS Canada and by happy accident he met Dr. Rise at a genomics conference and later contacted him about a biomarker project that became the first GAPP initiative.

It spiralled into a second project, focusing on co-infections in salmon, and brought in Dr. Fast, well known to EWOS’s health team. Scientific conferences, says Dr. Taylor, are great venues for industry to spot needed scientific expertise and potential partners. Cargill – as did EWOS – regularly attends and presents at conferences and supports publication of research in scientific journals.

“The strategy of EWOS was to use external collaboration to develop new technology and that was the goal of the GAPP projects,” said Dr. Taylor. “We started by buying instruments; in the case of the GAPP biomarker project we bought a gene multiplexing instrument before applying for the project and it was the first one purchased in Norway. The benefit was not to develop new feeds but to develop new technology that would allow us to reach that objective.”

Dr. Taylor said, “I feel that this worked very well for all partners because the EWOS CEO had a clear mandate which was to use state-of-the-art technology at EWOS Innovation, so we knew precisely what we could and could not do – we knew which deliverables and milestones would be approved by EWOS.”

For the academic research community, EWOS was an attractive partner because it could supply samples academic partners couldn’t easily obtain.

“In this case,” said Dr. Taylor, the samples were from “large and precise salmon feeding trials, of which we did about 70 per year. We could also do pathogen challenge trials which are very valuable to academic partners.” And further, he said “we had a long history of academic collaboration so we knew what worked.”

He said, “I think that, in general, this is a good model for success,” adding “Canada has excellent universities in the field of aquaculture and maintaining their expertise should be the goal of GAPP projects.”

Drs. Fast and Rise agree their partnership with Dr. Taylor was very successful. “Definitely my experience with Richard has encouraged more work with the company he worked for, but also with the industry as a whole, “said Dr. Fast. He was impressed by Dr. Taylor’s “excellent scientific mind,” which encouraged “basic research beyond the work which can directly impact his company or industry over the short term.”

Dr. Rise called Taylor “a creative and dynamic scientist, and an excellent communicator.” He termed the relationship “extremely important” in advancing his own research program over the last five-six years. Not only did it yield important publications in aquaculture nutrigenomics and immunogenomics, but he said it gave his undergraduate and graduate students as well as his postdoctoral fellows the chance to work closely with an aquafeed industry leader and to apply their genomic and other research expertise to real-world problems.

Despite potential benefits, Dr. Taylor says a key stumbling block to cementing more widespread industry-academic partnerships is often Intellectual property rights. Those issues, he said, will usually preclude collaborative ventures on straight product development.

Dr. Taylor praised Genome Atlantic’s role as facilitator for the two GAPP projects in which he was involved. “This was my first experience with a GAPP proposal and they provided unlimited hours to aid the writing and to edit all the drafts. “When the proposal was green-lighted, Genome Atlantic supplied a half-time project manager, Cara Kirkpatrick, whom he described as “magnificent,” to do the administration. “If we had not had this extensive aid from Genome Atlantic in the first GAPP we would not have applied for the second GAPP.”

The aquaculture feed industry’s main concern in working with academic partnerships, says Dr. Taylor, is fear of losing control over research findings with commercial implications, creating a reluctance to provide extra funding outside their large internal R&D operations – Cargill maintains two state-of-the-art research centres in Norway and Chile – to accelerate the development of fish feed. However, the limited number and highly regulated environment of fish feed ingredients makes feed development a constant challenge.

Whether salmon aquaculture research is done alone or in collaboration, he says, genomics is now central to solving the pressing problems in the sector worldwide: climate change, environment, and disease.

“There are thousands of salmon biomarkers published and hundreds validated in publications. Some land animals can be phenotyped using antibodies or clinical chemistry, but for salmon the only resources available are genomic. We have determined in our GAPP projects that the genomics tools allow predictive phenotyping at a reasonable cost.”

By predictive phenotyping he means the expectation of observable or biochemical characteristics of salmon – growth, size, disease susceptibility etc. – based on their genetic and environmental influences.

Shortly before his retirement, Dr. Taylor helped secure one additional funding opportunity enabling Cargill to co-sponsor a post-doctoral fellowship via a Mitacs Accelerate grant.  This work will employ, and expand on, several of the genomic tools developed in previous collaborations to delineate markers of environmental stressors on farmed salmon and will ultimately allow Cargill to better promote fish health in an uncertain environment.    

Dr. Taylor retains a soft spot for Atlantic Canada and his former academic scientific partners here. Reached by email during the covid-19 pandemic at his secluded home in Wilkes County, N.C., two hours from Charlotte, Dr. Taylor says, “being isolated now and not having been in a restaurant for a while, I must say that we always had very good meals and conversation when I traveled to Atlantic Canada, and I certainly miss that.”


FastTRAC-ing better white spruce

JDI used genomics data to select and remove from this orchard the poorest growing white spruce trees. This photo from February 2019 shows the freshly cut stumps. Photo credit: JD Irving Ltd.

JD Irving Ltd., also known as JDI, the Canadian forestry company based in New Brunswick, is leaping ahead with genomic selection, a technology that promises so much efficiency, it could eventually eclipse conventional tree breeding practices.

Josh Sherrill, JDI’s genetics and forest productivity leader, said the company’s participation in a recent research project, dubbed FastTRAC, for Fast Tests for Rating and Amelioration of Confers, with a focus on Norway and white spruce, “allowed JDI to move to the front of the pack and gain experiences with genomic selection that many industry players around the world have not benefited from.”

At the company’s six-hectare, second generation white spruce seed orchard in Parkindale, N.B., JDI has been using genomic predictions, based on diagnostic tools developed during FastTRAC, to cull what Mr. Sherrill described as “the least desirable parents” for new white spruce. “By using genomics, we were able to do this several years earlier than we normally do,” he said. The estimated time saving was eight years, compared to traditional methods that require more tree growth before field test data can be collected and analyzed.

Indeed, with genomic profiles, the genetic value of a tree can be estimated while it is still a seedling, reducing the need for field evaluation. By contrast, conventional breeding practices can require growers to wait up to 20 years before some economically and environmentally important traits can be assessed in the field. FastTRAC showed genomic selection, which can predict the breeding value of a candidate tree for many traits of interest using its genomic profile, will reduce the timeline for the selection of enhanced reforestation stock by 20 to 25 years in spruces.

Moreover, genomic predictions have enabled JDI to more reliably select trees with the best traits for industrial use and employ them more often for breeding.

“Both these applications will result in increased growth and other quality traits in the seedlings we plant,” Mr. Sherrill said. “These applications are intended to grow our wood supply for our sawmills and pulp mills. That means more jobs and economic development throughout the supply chain from the forests to the consumer.”

While genomics is not new, it is a relative newcomer to the world of forestry and to conifers in particular. “JDI had followed developments in the research and only recently, through development of genomic selection methods, has the technology advanced to the point where it could be evaluated for an applied industrial tree improvement program,“ explained Greg Adams, a forestry consultant with a long association with JDI. Essentially, he said it was the advanced state of genomic selection that piqued JDI’s interest in the project.

For more than 30 years, before entering the consultancy business, Mr. Adams ran JDI’s tree improvement program. He also represented JDI on the FastTRAC team, a research partnership that included the Canada Research Chair in Forest and Environmental Genomics at Laval University; Forest Products Innovations, the world’s largest private non-profit forest research centre;  the New Brunswick Tree Improvement Council, the Canadian Wood Fibre Centre; the Quebec Ministry of Forestry of Forests, Wildlife and Parks; and Natural Resources Canada. Funding came from Genome Canada and Génome Québec, through the Genomic Applications Partnership Program (GAPP). The province of New Brunswick was also a contributor, while  Genome Atlantic provided support and assisted with co-funding.

 “This effort was certainly among the first in North America to apply genomic selection in applied tree improvement programs,“ said Mr. Adams.

 “Tree growth rate and stem quality are important traits in selection programs and are easily assessed in field tests,” he said. “Other traits, such as wood properties and pest resistance, are more difficult and expensive to assess but also important for long-term value. Genomic selection offers significant potential to address these difficult-to-assess traits.”

“The FastTRAC project was highly successful,” said Mr. Adams.  Originally, the plan was to test genomic selection results against available data as a proof-of concept. The results proved so encouraging, the research effort expanded to include the New Brunswick Tree Improvement Council’s entire second-generation white spruce population. “This provided growth and wood quality predictions used in orchard management and brought increasing efficiency of breeding to the next cycle,” said Mr. Adams. “Further to this, genotyping from the FastTRAC project has also been used to build genomic selection models related to spruce budworm resistance.” The genotyping process examines DNA for variants tied to the unique traits of an organism.

As an industry participant, JDI helped shape the project’s goals to have practical application for the forestry business. The company also supplied some financial backing, and most importantly, provided access to several decades worth of genetic data. “The field data is essential to any program hoping to integrate molecular genetics into applied tree improvement, Mr. Adams stressed.

Back at JDI’s white spruce seed orchard, where Mr. Sherrill oversees the application of the genomic tools for genomic selection developed by FastTRAC, he said, “We implemented quickly but have proceeded carefully. In the seed orchard, we could have removed more parents but we were conservative. As we gain confidence in genomic selection, we will rely more heavily on it and make increasingly bolder decisions.”

He said, “Currently we are working on validation of the FastTRAC models using field data. This will help us to adjust our level of reliance over time and make improvement to the methodologies.”

The results of the first FastTRAC project are “quite encouraging,” he said, and “the usefulness of the information means that breeding programs will be different going forward. The new normal for breeding will be genomics-informed, and as we build confidence there is the potential for breeding to be genomics-led.”

In the meantime, a follow up proposal, FastTRAC 2, is shaping up to focus on genomic selection for red and black spruce, conifers that JDI also plant and count on for raw material. The two species are the most planted in eastern Canada.

Due to the success of the first FastTRAC, the new proposal has attracted greater investment from New Brunswick and Nova Scotia tree improvement participants. FastTRAC 2 proposes to create genomics technologies that can stock future tree plantations with seedlings capable of withstanding the effects of climate change and minimizing the impact on Atlantic Canada’s forestry sector.

Taking the long view of genetic selection, Mr. Sherrill says that “beyond creating predictive models for additional species, we expect there will be opportunities to refine and build on existing methods and practices. For instance, our rich genetic marker data could be used to better understand genetic diversity and help us optimally manage our breeding populations.”

The FastTRAC team was named the 2019 recipient (Collaboration category) of the prestigious Canadian Forest Service Merit Award. Congratulations to the team on this recognition! 



Regional genomics projects get funding for COVID-19

Halifax, NS – Two teams of Dalhousie University scientists are receiving more than $300,000 in funding for genomics research into critical areas in the battle against COVID-19.  Drs. David Kelvin and Alyson Kelvin (also IWK Health Centre) are pursuing biomarkers for COVID-19 that could predict disease severity; while Drs. Nikhil Thomas, John Archibald and Morgan Langille will pilot an innovative protocol for large-scale surveillance testing.  Both projects are supported by Genome Atlantic with $250,000 in funding from Genome Canada’s COVID-19 Regional Genomics Initiative, with an additional $60,000 provided by Research Nova Scotia to the Thomas project. This new Genome Canada money augments existing funding to the Kelvin project in their search for biomarkers, including funding from Research Nova Scotia provided earlier this year.

Genomics plays an important role in COVID-19 research, from detecting infections and understanding how the virus mutates, to tracking these mutations and developing vaccines and treatments.  Through the COVID-19 Regional Genomics Initiative, Genome Canada and regional Genome Centres across the country are responding to the urgent need for further research.

Drs. David and Alyson Kelvin are at the forefront of an international effort to find biomarkers associated with mild, severe and critically ill patients.  This funding will enable the expansion of current work to include a set of patient samples collected during the outbreak at Northwood long-term care facility. Collaborators include Drs. Melissa Andrew, Ken Rockwood, Sam Suriel, Lisa Barrett, and Barry Clarke (Dalhousie/Nova Scotia Health Authority); Mark Cameron and Cheryl Cameron (United States); and Jesus Bermejo Martin and Salvador Reno Garcia (Spain). This international team will develop and contribute to rapid and reliable patient assessment tools, protocols and Point of Care Devices which utilize biomarkers identified from their work. These tools could help doctors triage patients and inform treatment protocols in a variety of settings including emergency rooms, hospitals, long-term care facilities and ICUs.

The Chief Medical Officer of Canada has identified an urgent need to ramp up COVID-19 testing capacity to support the re-opening of the economy.  While standard diagnostic testing is primarily used for people who are symptomatic or a close contact of a COVID-positive individual, the model piloted by the Thomas-Archibald-Langille team is a surveillance tool that could quickly identify early trends in transmission in high risk settings like long-term care or in workplaces where physical distancing is impossible such as fishing vessels or food processing facilities. Individuals who test positive would then be sent to hospital for a diagnostic test. This new model represents a simple, quick and relatively cheap way to identify hidden chains of transmission in at-risk populations.  

“Canadian scientists are at the forefront of the global race to fight COVID-19. Genome Atlantic is proud to support local scientists who are helping lead the charge, and we thank our funding partners Genome Canada and Research Nova Scotia for enabling this important research,” says Genome Atlantic President and CEO Dr. Steve Armstrong.


Interview

Dr. Nikhil Thomas

Dr. Nikhil Thomas talked with freelance broadcaster Don Hill about the work aimed a ramping up testing to curb COVID-19 or other future disease outbreaks.


Part 1: On the Trail of COVID-1

Part 2: The Race for a Vaccine

-30-

Genome Atlantic is a not-for-profit corporation with a mission to help Atlantic Canada reap the economic and social benefits of genomics technologies.  Since its inception in 2000, the corporation has worked with a range of private and public-sector partners to enable more than $120 million in new genomics R&D. To learn more, visit www.genomeatlantic.ca

Contact:  Charmaine Gaudet, Director of External Relations, 902-488-7837/cgaudet@genomeatlantic.ca


Genome Canada leads $40 million genomics initiative to address COVID-19 pandemic

Thursday, April 23, 2020

New Canadian network will undertake viral and host genome sequencing to improve patient outcomes

Following an announcement in Ottawa by Prime Minister Justin Trudeau, Genome Canada launched today the Canadian COVID Genomics Network (CanCOGeN), a newly formed initiative backed by $40 million in federal funding. Led by Genome Canada, in partnership with the six regional Genome Centres, national and provincial public health labs, genome sequencing centres through CGEn, hospitals, universities and the private sector, CanCOGeN will coordinate and scale up existing genomics-based COVID-19 research in Canada and internationally in order to accelerate public impact. This initiative is part of a $1 billion package of measures announced by the Prime Minister today to support new countermeasures to fight the virus.

CanCOGeN will undertake two related genomics projects to help us understand how the virus works, how it is evolving, and why people experience such different health outcomes. CanCOGeN will sequence the genomes of up to 10,000 patients and 150,000 viral samples and will build a bank of “virus to patient” data that will inform decision-making by public health authorities and support the development of therapies and vaccines. Of critical importance, CanCOGeN will establish and manage a framework for cross-Canada safe data sharing, coordination and analysis.

Data will be shared with national and international collaborators to enable additional research, including Canadian vaccine development efforts. This will ultimately help respond to the current COVID-19 emergency as well as build capacity to respond and manage future outbreaks of this virus, or other pandemics. The initiative will be supported by an Advisory Committee to ensure strategic coordination with other Canadian and international COVID-19 health and medical research efforts.

“Genome Canada and the six regional Genome Centres are on a mission to meet the COVID-19 challenge head-on. We will do that by generating accessible and readily usable genomics data to inform public health decisions that impact Canadians,” said Dr. Rob Annan, President and CEO of Genome Canada. “A multi-pronged coordinated national approach to harnessing robust genomic solutions and convening partners across sectors and borders will ultimately lead to better patient outcomes.”

Canada is a world leader in genomics-based research in the healthcare sector, contributing significantly to the responsible application of biosciences to advance human health. CanCOGeN is an open and collaborative initiative that will allow for the gathering of scientific data required in the short-term and for the development of tools needed in the long-term to better protect Canadians’ health in the face of similar outbreaks in the future.

Quotes

“Since the beginning of the COVID-19 pandemic, we have been working closely with Canada’s health experts and researchers, who are some of the most skilled and brightest in the world. We are making sure that Canada remains at the forefront of scientific research to help us make smart and effective decisions on the path to recovery.”

—The Right Honourable Justin Trudeau, Prime Minister of Canada


“The Government of Canada is committed to protecting the health and safety of Canadians. We are all in this together: Canada is benefiting from the impressive and innovative power of Canadian researchers in our coordinated national approach to fight COVID-19. Together, we are rapidly scaling-up our research capacity to harness genomic sequencing data to inform public health interventions and to advance a vaccine against COVID-19 to protect our population and end the crisis.”

The Honourable Navdeep Bains, Minister of Innovation, Science, and Industry


“Genome Canada and the six regional Genome Centres are on a mission to meet the COVID-19 challenge head-on. We will do that by generating accessible and readily usable genomics data to inform public health decisions that impact Canadians. A multi-pronged coordinated national approach to harnessing robust genomic solutions and convening partners across sectors and borders will ultimately lead to better patient outcomes.”

– Dr. Rob Annan, President and CEO of Genome Canada

[Genome Canada, in partnership with the six regional Genome Centres, will lead the newly formed Canadian COVID Genomics Network (CanCOGeN).]


“This investment by the Government of Canada will harness the power of world class genomics infrastructure in Canada to explore the genetic architecture of the human genome and to inform our understanding of the variable clinical response to COVID-19, bringing us closer to enabling personalized risk prediction and precision therapeutic strategies.”

– Dr. Naveed Aziz, Chief Administrative & Chief Scientific Officer, CGEn

[CGEn will lead the COVID-19 host genome sequencing initiative, with support from Genome Canada, Canada Foundation for Innovation’s Major Science Initiatives and others, through its nodes in Toronto, Montreal and Vancouver.]


“The national Viral Genome Sequencing Initiative within the Canadian COVID Genomics Network (CanCOGeN) is tremendously important in that we are significantly building out our sequencing capacity in real time to rapidly respond to this Canadian and global health crisis. With expertise coming in from researchers, sequencing centers, clinicians, health care facilities and industry across the country, we will be streamlining guidelines, protocols and data quality control towards building a robust Canadian genomics network that strengthens the Canadian response now and for future outbreaks.”

– Dr. Terrance Snutch, Professor, Michael Smith Laboratories and Director, Translational Neuroscience, Djavad Mowafaghian Centre for Brain Health, University of British Columbia

[Dr. Snutch and his team at UBC’s Michael Smith Laboratories will lead the COVID-19 genome sequencing component of the viral genomics initiative and coordinate with leaders and sequencing sites in each province.]


“The Public Health Agency of Canada’s National Microbiology Laboratory welcomes the opportunity that the CanCOGen presents to coordinate large-scale SARS-CoV-2 sequencing efforts, facilitate genomic capacity building more regionally, promote best practices for data management and analysis, and disseminate data, sequencing results, and research outcomes to partners and stakeholders. Studying the genome of the virus and collectively developing tools to analyze the traits of the virus across Canada will provide critical information for our public health response.”

Dr. Matthew Gilmour, Scientific Director General, Public Health Agency of Canada

[The National Microbiology Lab will coordinate the public health laboratories’ response and host the data analytic core for the viral genomics initiative, which will ensure rapid sharing of the sequence data.]


Quick Facts

  • On March 6, 2020, Genome Canada announced participation in a federal investment of $27 million to fund coronavirus research. This commitment was since increased by the Government of Canada to $54.2 million, with 99 COVID-related projects now funded.
  • On March 11, 2020, the federal government announced a $1-billion package to help Canadians cope with the COVID-19 outbreak, which included $275 million for coronavirus research and medical countermeasures, and $50 million to ensure adequate supplies of personal protective equipment for provinces and territories, as well as to address federal needs.
  • On March 26, 2020, Génome Québec launched COVID-19 – A New Initiative from the Québec Research Sector -the Québec COVID Biobank and Genome British Columbia launched a call for Rapid Response Funding for COVID-19 Projects.
  • On April 2, 2020, Genome Canada launched additional rapid response funding for COVID-19 research in the six regional Genome Centres across the country. That $1.5 million in funding aims to leverage other funding and support genomics-informed solutions to COVID-19 at local, provincial and national levels through collaborations between academia, industry, not-for-profit and public sectors.
  • Since 2000, the Government of Canada has made $1.5 billion in targeted investments for genomics research through Genome Canada.
  • The global genomics market is expected to reach US$27.6 billion in the next six years.

Social Media

Genome Canada news is on social media @GenomeCanada: Twitter, Facebook, LinkedIn

Contact

Nicola Katz
Director, Communications
Genome Canada
Cell: 613-297-0267
nkatz@genomecanada.ca

Genome Canada is a not-for-profit organization that acts as a catalyst for developing and applying genomics and genomic-based technologies, to create economic and social benefits for Canadians. Genome Canada connects ideas and people across public and private sectors to find new uses for genomics, invests in large-scale science and technology to fuel innovation, and translates discoveries into applications and solutions across key sectors of national importance, including health, agriculture, forestry, fisheries & aquaculture, energy, mining, and the environment.

COVID-19 REGIONAL RAPID RESPONSE PROGRAM FOR ATLANTIC CANADA

Genome Atlantic is inviting proposals for genomics enabled project concepts from Atlantic Canadian stakeholders to address specific, short term needs which will allow the region to better respond to the pandemic. A total envelope of $250,000 in funds is available within Atlantic Canada. Registrations are being accepted until April 10th.

Genome Atlantic remains operational to support our clients, partners & community

Genome Atlantic is closely monitoring the developing situation around COVID-19 and we are taking every step to reduce the risk of transmission while ensuring that we remain fully operational.

Our top priority is the safety of our staff, clients, partners and their families, and therefore, all travel has been cancelled, our employees are working from home, and we are either postponing face-to-face meetings or replacing them with virtual options – in strict compliance with guidelines issued by our federal and provincial governments.

At the same time, we remain fully operational and all members of our team can be reached at any time as per our usual emails and numbers below:  

Steve Armstrong, President & CEO – sarmstrong@genomeatlantic.ca / 902-456-9256 (C)

Nil d’Entremont, Chief Financial Officer – ndentremont@genomeatlantic.ca / 902-430-0020 (C)

Charmaine Gaudet, Director of External Relations – cgaudet@genomeatlantic.ca / 902-488-7837 (C)

Kristin Tweel, Director, Sector Innovation – ktweel@genomeatlantic.ca / 483-8398 (C)

Britta Fiander, Director, Innovation Programs – bfiander@genomeatlantic.ca / 902-802-7281 (C)

Richard Donald, Associate – rdonald@genomeatlantic.ca / 902-220-2300 (C)

Cara Kirkpatrick, Program Officer – cara.kirkpatrick@dal.ca / 902-957-0030

For general inquiries email info@genomeatlantic.ca.

We thank you for your flexibility and patience and we wish you and your families continuing good health.