Genomics Blog

March 1, 2016 1:43 PM
Genomics on the Hill - A Snapshot of Genomics Research in Canada

On February 22nd Genome Canada hosted Genomics on the Hill which showcased Canada's Genomics Enterprise research in front of 200 guests which included 73 federal MPs, Ministers, and Senators.  This post comes to us courtesy of Brian Jobse who has a PhD in Medical Sciences from McMaster University and was able to attend the event, talk to the researchers, and hear what the attendees had to say.

Where are we going as a society? Where will the next big advance come from? How will we overcome some of the challenges we face?

If you’re like me, you wonder about these questions continually in this age of rapid technological and social development. Some of these questions seem daunting and it’s easy to get lost in the complexities of the many tangents the possible answers can take, but it’s obvious that one organization is already making strides to help move us forward, and has been doing so for the past fifteen years. That organization is Genome Canada and, as a guest and independent observer at Genomics on the Hill this February, I’m feeling better informed and actually hopeful about where we’re headed. At this event only 12 projects were highlighted, really just the tip of the iceberg, to demonstrate the potential, power and promise of genomics research and application. Below I’ve briefly summarized each of these projects, many of which were in turn summarized to me by the some of the talent involved in implementing these wide-reaching avenues of discovery. So, in no particular order…

Application of Genomics to Innovation in the Lentil Economy – Genome Prairie

Project Leaders: Kirstin Bett and Albert Vandenberg, University of Saskatchewan
Lentils – a useful, nutritious, easy-cooking no brainer – right? Just grow them and let people eat! Well not so fast. While we have the land in Canada to help feed the world, it’s not exactly the land to which lentils are accustomed. As such, it’s incredibly useful for both the economy and for global food security if we can better adapt these incredible pulse crops to our conditions. There are many, many varieties of lentil but only a few that have been stabilized to our climate, so the research focuses on understanding what genes play a role in this, and learning how to select for plants that can handle being Canadian.

Commercial Application of Genomics to Maximize Genetic Improvement of Farmed Atlantic Salmon on the East Coast of Canada – Genome Atlantic & Ontario Genomics

Project Leaders: Elizabeth Boulding, University of Guelph, and Jake Elliot, Cooke Aquaculture and Kelly Cove Salmon Ltd.
Don’t let the name scare you off, and don’t immediately jump to the thought of genetically modified organisms! Selective breeding of animals is something Darwin understood, and this project just takes it to the next level. By looking at a plethora of genetic markers, we can start to select for salmon that are naturally more resistant to disease and parasites. This means less waste and, with luck, a stronger maritime economy, something we can all get behind.

Protecting Canada’s Forests against Invasive Alien Species by Next Generation Biosurveillance – Genome British Columbia & Génome Québec

Project Leaders: Richard Hamelin, University of British Columbia, and Roger Lévesque, Université Laval
I know, this one sounds like the next epic summer blockbuster, but it’s actually an important topic of discussion: how do we stop invasive species from causing irreversible damage to ecosystems and the economy? While invasive species are nothing new in biology, the potential for accidental introduction has increased due to globalization. It takes time for ecosystems to recover, sometimes a very long time, so at this stage in the game biosurveillance is definitely a step in the right direction. By finding better ways to detect invasive alien species, namely through genetic sampling, we can learn about common routes of transmission and, importantly, identify a potential threat in days instead of months so that a response can be effected. Coming soon to a globalized world near you.

A Metagenomic Approach to Evaluate the Impact of Cheesemaking Technologies and Ripening Conditions on the Microbial Ecosystem of Premium Washed Rind Cheeses – Génome Québec

Project Leaders: Steve Labrie, Université Laval, and Manon Duquenne, Agropur Cooperative
Cheese making is a complex process. Throughout history, whenever a microbial culture is involved in food production it’s as much an art as it is a science. This project seeks to take the science a few large steps further than it’s ever gone before by creating genomic profiles of the cheese rind, in both health and disease, to better understand the microenvironment and ultimately rectify precarious situations (for the cheese). If we can understand the cheese, maybe, just maybe, we can teach the cheese to be better, stronger, and cheesier. But in the meantime we can limit losses, improve shelf life, and even create new cheeses! This is an unprecedented line of study, and Canadians may soon be responsible for an enlightenment in cheese making.

PACE-‘Omics: Personalized, Accessible, Cost-Effective Applications of ‘Omics Technologies – Genome Alberta

Project Leaders: Christopher McCabe and Tania Bubela, University of Alberta
Personalized medicine is (hopefully) our future. Knowing what drugs or therapies will work, or more importantly won’t work, before using them could save money for our budget-intensive healthcare system and has the potential to improve quality of life for many Canadians. It wasn’t so long ago that the human genome was sequenced and work has only truly just begun on unlocking the secrets therein. The ‘black sheep’ of this group of projects, as it is not itself directly assessing a genome, is the absolutely necessary development of guidelines, regulations, and tools for evaluating emerging technologies and techniques in personalized medicine. If we want Canada to be a leader in healthcare, this is an avenue of thought and policy-making we can’t afford miss.

Increasing Feed Efficiency and Reducing Methane Emissions through Genomics: A New Promising Goal for the Canadian Dairy Industry – Genome Alberta

Project Leaders: Filippo Miglior, Canadian Dairy Network, and Paul Stothard, University of Alberta
We have a lot of cows in Canada, and we’re probably going to get a lot more as demand for cows milk increases through the world. There are two issues this project seeks to resolve through selective breeding of dairy cattle. On one side, cows are feed-intensive animals, which is not only expensive but requires production of that feed on large swathes of land. On the other, they produce relatively large quantities of methane, an incredibly powerful greenhouse gas that we really shouldn’t be adding to the atmosphere in great volumes. Using genomics based approaches to select for good dairy producing cattle that require less feed and that produce less methane will benefit the dairy industry and help to mitigate the ecological footprint.

Exploiting the Full Potential of Next Generation DNA sequencing for crop improvement – Genome Atlantic

Project Leader: Sean Myles, Dalhousie University
It's all well and good to sequence a genome; a task that at one time seemed impossible, but knowing what to do with the information found therein is another problem all together. And when we start talking about plants the situation can get murky, as the genomes are as wide and varied as the varieties of plants themselves. In the effort to breed crops that require fewer chemicals or pesticides, that are more disease resistant, and that produce greater yields it will be incredibly advantageous to have software tools that help to guide us through the genetic diversity of plants and allow users to select for the strains that best suit their needs. Even putting aside the potential for software of this nature to impact other fields of genomics research, we stand to gain a great deal by starting to make genomic integration accessible to researchers and innovators.

Autism Spectrum Disorders: Genome to Outcomes – Ontario Genomics

Project Leaders: Stephen Scherer, SickKids Hospital, and Peter Szatmari, University of Toronto
When we think of epidemics it's usually a virus or other communicable disease that springs to mind, but in autism we are clearly witnessing an epidemic that we currently have little to no understanding of or explanation for. It is therefore imperative to get as much information as possible about this rampantly expanding spectrum of disorders so that we can make earlier diagnoses, provide personalized care to those affected, reduce the cost to our health care system, and perhaps provide an explanation to what is causing this particular set of brain developments to become so common in our population. With some autism specific DNA anomalies already identified through Genome Canada and CIHR funded research, the next step is to sequence and analyze the genomes of a large sample of autistic individuals. This project represents Canada's contribution to a ground breaking international initiative to do exactly that, so that we can start to get answers and make a positive impact on the lives of those with this condition.

Personalized Risk Stratification for Prevention and Early Detection of Breast Cancer – Génome Québec

Project Leaders: Jacques Simard, Université Laval, and Bartha Maria Knoppers, McGill University
We all know someone who has fought cancer, and at present our greatest hope is always that we catch it early so that we stand the best chance of treating the disease while it is still relatively less aggressive. Breast cancer is one cancer that we can honestly hope to always catch early on, but the current paradigm of using mammography in older individuals has significant gaps that need to be addressed. By learning more about the genetic polymorphisms that lead to breast cancer we can do a better job of distinguishing those that are likely to develop the disease in their lifetimes. Being able to identify those most at risk of developing breast cancer, no matter their age, could lead to better screening, diagnosis, and treatment for those at risk. If knowledge is power, then this one is putting power back into the hands of our loved ones.

Stratifying and Targeting Pediatric MedulloBlastoma through Genomics – Genome British Columbia and Ontario Genomics

Project Leaders: Michael Taylor and David Malkin, University of Toronto, and Marco Marra, BC Cancer Agency
Cancer is a disease linked with growth and proliferation of cells, and so, unfortunately, cancer is bound to affect some of us at that time in our lives when we're growing the most, during childhood. Currently, our only response to childhood brain cancer is to treat it as aggressively as possible in hopes of saving a young life, but often this leads to over-treatment of children with good prognoses; the problem being that aggressive chemotherapy and radiation treatments in those developing minds can cause complications and quality of life issues. On the flip side, those with poor prognoses could potentially be spared the painful treatments. Investigating childhood brain cancers on a genetic level will eventually allow for more accurate treatment, proactive diagnosis, and better information for the families to make some of the hardest decisions they will ever face.

Towards a Sustainable Fishery for Nunavummiut – Ontario Genomics

Project Leaders: Virginia Walker, Stephen Loughheed, and Peter Van Coeverden de Groot, Queen’s University, and Stephan Schott, Carleton University
We have to admit our shortcomings, lest we continue the same behaviour into the future, and our treatment of our world's fisheries is a definite shortcoming. As the Arctic sea ice melts, we have one last opportunity to fish responsibly, and to let the economic benefits of this unspoilt bastion fall predominantly on those peoples that have lived in the ecosystem for generation upon generation. To know how to fish responsibly we need to know exactly what we're fishing and how we're affecting the stocks; along with the traditional knowledge found in Nunavut, genomics can play a huge role in helping to ensure that we actually know what we're dealing with and what impact we're having on the ecosystem so that we avoid the over-fishing we've been so good at in the past. This also happens to be an opportunity to gain an unprecedented amount of scientific knowledge in an area largely untouched by human hands. For the peoples of Nunavut, who need better food security, and for the Arctic ecosystem itself, this project is a necessary step in a more mature direction.

Improving Mining Sustainability through Metagenomics – Ontario Genomics

Project Leader: Lesley Warren, University of Toronto
Mining is huge in Canada, with mining activities in every province and territory, and the industry will only get bigger as warming temperatures open up previously inaccessible areas. Unfortunately, along with the advantages of having mineral wealth at our fingertips are the consequences of needing large amounts of water to concentrate the metals of interest. This water is left contaminated by sulphur-containing waste rock that then needs to be stored, potentially next door to or within sensitive ecosystems. Thus, development of sustainable wastewater management and degradation of harmful compounds is absolutely key to our future as a mining-intensive country. Currently, this is an area that has been disregarded from a biological standpoint. Bacteria play a major role in the consumption of the hazardous materials in the tailing ponds, but almost nothing is known about the ecosystems, that are doing such valuable work for us, contained within these ponds. As such, this project seeks to use genomics to study the waste water environment and ecosystem, and to provide indicators of microbial health and productivity, vastly increasing our ability to monitor, manage, and intervene in these almost primordial, alien worlds we create.

Again, these amazing projects only represent a selection of the work in genomics taking place across the country. In speaking to many of the project leaders I came not only to a better understanding of where their respective projects were heading, but to a better understanding of where we’re headed as a country. You may have noticed, throughout this piece, my use of ‘we’ instead of ‘they’ in describing the work.
While I have no affiliation with Genome Canada or any of the researchers, I couldn’t help but embrace the ideas presented to me as a Canadian citizen, trained scientist, and policy wonk. At this stage in our development as a nation, and as a species, it is imperative that we continue exploring the very essence of life in all of its forms. Embracing genomics is not only good for our economy, but for the environment, our health, and the scientific endeavour.