Bringing Collaborative Genomics Solutions
to Life

Our Impact

Genomics — the science of understanding, interpreting and harnessing the DNA code that exists in every living thing– is a rapidly evolving field that is transforming life as we know it. It is making personalized medicine, safer foods, clean biofuels, improved manufacturing processes and environmentally friendly industrial products possible, thereby driving economic growth.

Ontario has a thriving genomics research and innovation community that is unlocking the power of genomics to develop innovative solutions across all key sectors of our growing bioeconomy, with the potential for a wide range of social and economic benefits for all Ontarians. The integration of these cutting-edge innovations into our economy is complex. It requires that we connect people, ideas and organizations from diverse fields to bring together genomics, big data, operations infrastructure, policies and incentives. It also raises important new ethical, economic, legal, and social issues — all of which require extensive investigation through collaboration.

By applying our expertise and building bridges between the research community, end-users of technologies or services and policy makers in Ontario’s business and industrial sectors, Ontario Genomics leads the application of genomics-based solutions across all sectors of our economy — from health, agriculture and agri-foods, to industrial processing, mining, energy, and natural resources — to create healthier lives, a healthier economy, and healthier plant.

Message from the President and CEO

We live in the most interesting of times, where scientific knowledge and data are exploding all around us, and technologies that impact our everyday lives are changing at a pace that is hard to keep up with, a pace that is continually accelerating and that is fueled by global competition. The ability to imagine and develop new ideas and apply them rapidly through multidisciplinary collaboration between researchers, innovators and end-users is not only essential, but it is Ontario’s most crucial competitive advantage. It is the way to drive new knowledge, to translate it into technologies that open global markets and to create successful businesses and jobs in Ontario, for Ontario.

Ontario and Canada have long recognized the value of investing in genomics research and innovation. Because they are found in all living things, understanding and harnessing the genomes holds the promise of shaping a healthier and more prosperous future across all sectors of our economy – health, agriculture and agri-food, forestry, aquaculture, manufacturing, bioproducts, mining, energy and natural resources.

With more than 18 years of focused investments into genomics-based research and innovation, we are now ever closer to transforming life as we know it in very real and significant ways: diagnosing diseases rapidly and noninvasively, improving agricultural yields, providing safer foods, improving manufacturing and processing technologies and addressing environmental challenges.

The power of collaboration to advance our mission underpins everything we do; our success is measured by our ability to support Ontario’s research and business communities to succeed in harnessing and translating genomics innovations to solve real world problems in areas of priority for the province. We do this by proactively applying our expertise to help scientists find paths to the marketplace for their discoveries, assisting genomics-based start-up companies with advice, funding and networking, and by connecting people, ideas and organizations to create public-private partnership programs through our industry-pull model that enable all partners to leverage their funding.

The Ontario Genomics team works with scores of multi-disciplinary academic and industry project teams from across the province and beyond, and I am constantly inspired by both their ingenuity and drive to make our world a better place. By developing and applying cutting-edge genomics innovations to solve real world problems, not only are they passionate about saving lives and improving health and safety, but they are also building new companies, strengthening established ones, advancing industries, attracting domestic and foreign investment, and creating new high tech jobs in Ontario.

It has been a riveting first 6 months for me at Ontario Genomics. I am so proud to have the opportunity to work with such an accomplished team, to have met so many of our partners and collaborators and to drive some stellar initiatives over this short period of time. For example, Ontario Genomics, together with our partners, was proud to host Canada’s first national Engineering Biology conference last March. 2018 Canada Synbio drew over 320 people together from across Canada and around the world for two days of learning and collaboration with a full day conference followed by a second day of workshops. This inaugural conference was aimed at harnessing the collective knowledge, experience and creativity of stakeholders from all segments of the bio-economy to advance Canada’s position as a global leader in the field of Engineering Biology. Please see our Synbio Event page for conference highlights and the workshop report. We will further build upon this momentum at our second annual conference in March 2019. Stay tuned!

We look forward to ongoing collaborations with all of our stakeholders and even greater community engagement to surface and advance the best of the new opportunities that are continually emerging. It is through the power of these collaborative partnerships that we will accelerate the benefits of genomics and exponentially bolster Ontario’s collective strengths.

On a more personal note, I’d like to take this opportunity to thank all of the people who have helped me during my transition into this new role as President and CEO of Ontario Genomics. In particular, I would like to recognize and extend special thanks to our outgoing Chairman, Brian Underdown, for his many years of valuable service and guidance to Ontario Genomics. Brian will be dearly missed.

I have sincerely enjoyed getting to meet and know everyone, and I look forward to continuing to work with everyone towards a better Ontario through genomics-based solutions. The best is yet to come.

Message from the Board Chair

When I first joined Ontario Genomics 14 years ago, the world was largely focused on trying to map the human genome — to decipher and understand the genetic information encoded in our DNA. Since then, the field of genomics has exploded. While genomics is still a relatively young science, the technological capacity we now have to read this code of life is unprecedented and it’s advancing at breakneck speed. Genomics is transforming life as we know it. The insights from genomics research are fueling innovations in health, agriculture and agri-food, forestry, aquaculture, manufacturing, bioproducts, mining, energy and natural resources — presenting enormous opportunities to drive economic growth and improve the quality of life for people in Ontario, Canada and around the world.

Ontario Genomics was founded in 2000 to fuel research and innovation, and translate genomics-based discoveries into commercially viable applications aimed at addressing real world problems. Since then, we have raised over $1.2 billion for genomics research, enabling us to fund over 200 projects in partnership with universities, hospitals, government, non-profits and industry, and directly supporting more than 7,900 jobs. These projects have been the catalyst for great success, and have resulted in accelerating the advancement of many companies along the development continuum — from research to industry-driven application and commercialization — securing millions of dollars in follow-on funding, creating hundreds of private sector jobs and generating millions of dollars in new revenue.

For example:

• Northern Biologics, which is a spinout company from one of our projects, has since raised $82M in venture capital to help patients use their own immune system to fight cancer; and
• Dr. Kym Boycott, at the Children's Hospital of Eastern Ontario Research Institute, has discovered 112 new rare diseases and is using DNA sequencing to end the diagnostic journey for children suffering from rare disease; and
• Dr. Trevor Charles, at the Centre for Bioengineering & Biotechnology at the University of Waterloo, is using specialized bacteria to convert methane, a potent greenhouse gas, into biodegradable plastics and fibers, which will have a significant impact on climate change.

These are just a few of many great examples, but Ontario Genomics’ ambitions for the future are even more audacious. The world’s growing bio-economy is projected to be worth $1 trillion globally by 2030. Canada is a relatively small player on this global stage, but we have a unique model that links a national organization, Genome Canada, with regional centers across the country. This model provides us with the ability to collaborate and to leverage our individual strengths for an enormous collective impact.

Collaboration is the key to success, and there is a strong Ontario Advantage. Our province has one of the best educated talent pools in the world and is home to more than 50% of our nation’s researchers. We have a very rich life-sciences ecosystem and the largest active private sector in the country. By leveraging these advantages, and collaborating on outcomes-focused solutions with all of our stakeholders – researchers, industry, policy-makers, and funders - we are attracting greater international investment to strengthen our bio-economy and equip our industries to be more productive, sustainable and competitive globally.

It has been my great privilege to serve Ontario Genomics as Chair of the Board of Directors. I would like to extend my sincere thanks to all of the hard-working management and staff, our many stakeholders and partners, as well as my fellow board members for their unrelenting efforts and achievements in bringing the benefits of genomics innovations to life. I am confident that the best is yet to come.

Genomics for Agriculture & Agri-Food: Ontario’s Strategic Opportunity

Ontario’s agriculture and agri-food sector is uniquely diverse and critically important to all of us — as individuals and as a society. At over $37B, it accounts for approximately one third of the total GDP generated by the sector in Canada.

Ontario’s agriculture and agri-food sector is strong and growing. However, the demands and challenges the sector is faced with are also growing. In the context of enhancing a sustainable, and socially and environmentally responsible industry, genomics-based innovations and technologies provide significant opportunities for farmers, producers and consumers in multiple ways. For example, genomics can:

• enhance crop and livestock production and protection
• maintain healthier soils
• provide tastier and more nutritious foods and beverages
• mitigate and adapt to the impacts of climate change
• preserve and enhance biodiversity
• support global food security
• help Ontario’s bioeconomy flourish

Last fall, Ontario Genomics engaged Synthesis Agri-Food Network and Nature Niche Scientific Consulting to identify key areas of opportunity for Ontario’s agriculture and agri-food sector through the application of new technologies.

We held interviews with both regional and global experts, and group discussions with Ontario stakeholders – including 100 representatives from industry, academia, associations, not-for-profits and the provincial and federal governments.

These extensive stakeholder consultations together with a thorough review of the sector provided the basis for a Genomics Strategy Report for Ontario’s Agriculture & Agri-Food Sector, and a set of recommendations to ensure the continued sustainability and accelerated growth of Ontario’s agriculture and agri-food sector over the next decade.

For more information, please visit the Ontario Genomics Agriculture & Agri-Food Sector Strategy microsite at http://www.ontariogenomics.ca/Ag-Sector-Strategy/.

Partnering to Advance Precision Medicine in Ontario

Precision medicine is a rapidly evolving field that is changing the landscape for health care. It can improve both patient care and the cost efficiency of our health care system.

Ontario Genomics has been an active agent in advancing precision medicine in Ontario. This occurs both through its role in helping to catalyze, develop and manage the Ontario-based research projects in precision medicine, such as the four projects awarded a total of $42M in the 2017 Genome Canada Genomics and Precision Health competition, and through Ontario Genomics’ provincial strategic initiatives such as the Ontario Personalized Medicine Network, and the Call for an Ontario Health Data Ecosystem.

The overriding questions at this point in time are, what is next and how do we best get there.

In order to answer these questions and help policymakers and other stakeholders prepare for a new era of health care with the most up-to-date information, Ontario Genomics has partnered with the Laboratories and Genetics Branch of the Ontario Ministry of Health and Long-Term Care to conduct a sector scan of precision medicine in the province.

This scan will help identify Ontario’s strengths, key contributors, possible gaps and precision medicine technologies that are having or have the greatest potential to have significant impact in the province — both from the perspective of improved health and economic impact. This scan will also outline how Ontario compares to international leaders in the development and adoption of precision medicine, and what can we learn from these leaders.

Ontario Genomics has been working in close partnership with the Ministry on the development of this important provincial initiative. This project will be conducted in two phases, with the first phase to be conducted in 2018-19.

For more information Ontario Genomics’ precision medicine initiatives, please visit www.OntarioGenomics.ca

Building Our Engineering Biology Community

In March 2018, Ontario Genomics hosted and led Canada SynBio 2018, Canada’s first national conference focused on Engineering Biology in partnership with ISED Canada, the Genome Canada Enterprise, the Ontario Ministry of Economic Development, Job Creation and Trade (formerly the Ministry of Innovation, Research and Science and the Ministry of Economic Development and Growth), NSERC, MaRS Discovery District, Autodesk, and our generous sponsors. Over 350 people packed the MaRS Discovery District auditorium for the event.

Conference Highlights

The first day was open to the public and run ‘conference style’ with a series of keynotes and panelists exploring the intersection of Engineering Biology and next generation genomics with AI, manufacturing, and human health and other sectors.

The second day was a facilitated workshop aimed at creating a shared vision for synthetic biology in Canada, as well as identifying opportunities and challenges specific to Canada.

The purpose of the workshop day was to understand opportunities and challenges for Engineering Biology in Canada and to identify specific opportunities and a path forward. Topics included levering Canada’s existing strengths in areas like regenerative medicine, agriculture and Industrial Bioprocessing, building on international efforts like the Genome Project Write, and equally critical, regulation and public engagement.

The results of the workshop have been published in a discussion paper highlighted below. We invite the community to reach out to us to discuss their ideas for this exciting area and to continue to embody the spirit of collaboration that was present through the two days. Most importantly, we invite everyone to join in this effort to move Canadian Engineering Biology beyond talk into action.

For more information including keynote speakers’ and panelists’ bios, Canada SynBio 2018 presentations, and upcoming Engineering Biology events, please visit www.OntarioGenomics.ca

Health

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Synbio

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Care4Rare: Diagnosing rare genetic diseases in children

There are more than 7,000 rare genetic diseases, many of which haven’t been identified yet. For more than one million Canadians and their families, these diseases can have a devastating impact.

Care4Rare will more than double our ability to diagnose unsolved rare disease and bring these capabilities to hospitals across Ontario and Canada, while building the infrastructure and tools for worldwide data sharing.

Led by Dr. Kym Boycott at the Children’s Hospital of Eastern Ontario Research Institute in Ottawa, Care4Rare is a pan-Canadian collaborative team of clinicians, bioinformaticians, and researchers focused on improving the care of people living with rare disease in Canada and around the world. Building on the outcomes of two earlier projects supported by Ontario Genomics (FORGE Canada 2010 and Enhanced Care for Rare Diseases 2012), this initiative includes 21 academic sites across the country and is recognized internationally as a pioneer in the field of genomics and personalized medicine.

Care4Rare’s work is speeding up the diagnostic process, preventing years of diagnostic testing and visits to multiple specialists that patients and their families would otherwise have to endure. Providing a timely diagnosis improves the care and wellbeing of patients and their families and reduces unnecessary healthcare spending.

Cool facts about Care4Rare’s innovations:

• Care4Rare is increasing the connectivity between clinicians and scientists to translate genetic findings into understanding disease mechanisms and finding new treatments for patients with rare diseases;
• Individuals with rare diseases and their families are now connected with others around the globe through RareConnect – an online platform that provides a supportive and safe environment to ask questions, share experience, and interact with others with a similar condition. There are currently over 31, 000 members and over 150 disease – specific communities, including a community for individuals without a diagnosis;
• The time it takes to diagnose rare disease can be reduced to weeks versus years;
• Treatments can be as straightforward as supplementing a single amino acid that is readily available and inexpensive.

For more information, please visit http://care4rare.ca/.

Precision medicine for pediatric inflammatory bowel disease (IBD)

Canada has one of the highest rates of IBD in the world, a disease that causes significant suffering and serious health issues due to chronic gut inflammation.

In partnership with Toronto-based startup Biotagenics, Ontario researchers are developing simple and quick tests to determine optimal personalized treatment plans for IBD patients using next generation genomics.

Inflammatory bowel disease inflames the lining of the gastrointestinal tract and disrupts the body’s ability to digest food, absorb nutrition and eliminate waste in a healthy manner. With more than 10,000 new cases diagnosed each year in Canada and an estimated total of over 250,000 patients nationally (including more than 5,900 children), IBD costs the Canadian economy approximately $2.8 billion per year. Most alarming, the number of Canadian children with IBD has doubled since 1995.

Treating IBD can be unpredictable. If treatments are not sufficiently aggressive they may not be of help. On the other hand, if treatments are too aggressive, there is a risk of doing more harm than good. There is no cure for this lifelong condition and its cause remains unknown, although it seems to be tied to an imbalance of key beneficial and deleterious intestinal microbes.

Building upon the outcomes of an earlier 2012 Large-Scale Applied Research Project, Ontario researchers are developing precision medicine for IBD patients. Led by Dr. Alain Stintzi at the University of Ottawa and Dr. David Mack at the Children’s Hospital of Eastern Ontario, in collaboration with spinout company, Biotagenics, researchers are using genomics to characterize, identify and quantify the microbes that change in IBD patients during treatment. They are using this information to design simple and quick tests to reveal the optimal personalized treatment based on each patient’s characteristics in order to keep people with IBD healthy. These tests will help clinicians use the right drug at the right time for the right patient.

Cool facts:

• The project team is unraveling the mechanisms underlying IBD development.
• As part of this work, researchers have developed an industry leading end-to-end platform that provides sophisticated analysis of the impact of diet on intestinal bacteria – providing important information on personalized dietary changes needed to keep people with IBD healthy.
• They are also identifying new targets for future drug development that have the potential to restore the long-term biological interaction and healthy balance between intestinal microbes in order to modify and manage the course of disease.

The work being done by this project team will set the stage for future clinical trials aimed at restoring IBD patients’ microbes to a healthy state. It will reduce long-term disability and enable patients to reach deep and long-lasting remission, thereby improving quality of life and enabling significant cost savings for individuals and our healthcare system.

For more information about Biotagenic’s progress, please visit http://www.biotagenics.com/.

Increasing yield in canola using genomic solutions

The canola industry accounts for nearly a third of the gross production value of all Canadian crops, generating $1.48 billion and nearly 16,000 jobs in Ontario. The industry has set a goal of increasing canola yield by 53 per cent in the next 10 years to meet increasing global demand. New technologies are needed to meet this goal. Ontario researchers are collaborating with Benson Hill Biosystems to address this challenge and produce game-changing varieties of canola.

Led by Dr. Peter Pauls, Dr. Michael Emes and Dr. Ian Tetlow at the University of Guelph, the research team has identified genes that increase yield in model plants and other crops that are being incorporated into canola. These new traits are expected to significantly enhance crop productivity by increasing photosynthetic capacity, metabolic efficiency and stress tolerance, without negatively impacting seed quality. This research team is working with Benson Hill Biosystems (BHB), a crop improvement company, to develop higher-yielding plants with increased photosynthetic efficiency, enhanced nutritional profiles and healthier oil content. These innovations will significantly increase crop yields, increase carbon capture, and reduce greenhouse gas emissions.

The results of this project will enable commercialization of the improved plants through licensing or collaborative development agreements. Increasing the yield of the canola crop benefits growers and others across the value chain, boosting industry revenues by $3-$4 billion per year.

Cool Facts

• As one of the healthiest sources of fatty acids, canola could be the key to satisfying increased consumer demand for lower trans fats in foods.
• Benson Hill Biosystems has established a Canadian subsidiary, Saturn Agrosciences, for this game-changing canola project, resulting in newly created jobs for Ontarians including the general manager position held by Dr. Lomas Tulsieram.
• Based in Guelph, Ontario, Saturn Agrosciences has a single focus: to create healthier, more sustainable varieties of canola.
• Benson Hill’s and Saturn Agrosciences’ approach lies in CropOS™, a machine learning platform and suite of genomics tools that helps researchers identify and optimize genes to develop better crops. This innovative platform enables them to bring improved crops to market faster.

Improving disease resistance in greenhouse vegetables

Canada’s greenhouse vegetable industry generates more than $1 billion from retail sales and exports. It is an extremely competitive market, and plant diseases are an enormous burden on growers, causing up to 20 per cent crop loss. There is a strong demand for genomics-based technologies to mitigate these losses.

Led by Dr. David Guttman, a team at the University of Toronto have discovered a previously uncharacterized family of genes that allow plants to show broad-range disease resistance against bacteria and fungi, which is extremely difficult for pathogens to overcome. This team is working with the Vineland Research and Innovation Centre and its reverse genetics platform (developed with earlier Genome Canada funding) to optimize these Broad Range Resistance genes for uptake by growers. Their innovative solutions will protect crops against multiple pathogens, reduce losses and increase yield. The result will be new varieties of vegetables that give Canadian growers a competitive advantage.

Vineland will take this gene technology from its translation through to the commercial release of new plant varieties with improved disease resistance, within five years of the end of this project. Annual benefits of approximately $26 million will start to accrue to the Canadian greenhouse industry within the same timeframe.

The enhanced competitiveness of Canadian growers will lead to sustained growth, expansion of operations and further job creation.

Cool facts about Vineland Research and Innovation Centre:

• Located in Ontario’s Niagara Region, Vineland is a world-class research centre dedicated to enhancing Canadian growers’ commercial success through results-oriented innovation.
• Vineland’s platform technology used to develop new tomato and pepper varieties with traits such as disease resistance and enhanced flavour has attracted the attention of major seed companies and researchers from around the world.
• To-date, Vineland has undertaken six contracts with other plant breeding organizations to use this technology. These contracts have established important research collaborations and have already generated new revenue for Vineland.
• Vineland plans to re-invest its licensing revenue from the new vegetable varieties into further research, driving innovation, global competiveness, job creation and additional benefits throughout the entire horticultural sector.

Competitive dairy production

Demand for aged cheddar is increasing, requiring Canadian producers to increase their manufacturing capacity in order to remain globally competitive. To achieve this goal, researchers at the University of Guelph are implementing genomics-based tools to improve manufacturing processes and controls, significantly increasing production capacity of high quality aged cheese, and generating higher revenues for dairy farmers.

Trade deals — such as CETA — make it more urgent for Canadian dairy producers to gain efficiency and protect their market share.

Led by Dr. Gisele LaPointe, a team at the University of Guelph has partnered with Parmalat Canada to better understand the microbiota of cheese and increase its manufacturing capacity. The microbial components of cheese play a key role in its physical, chemical and organoleptic properties, such as taste, sight, smell, and texture. By validating and implementing genomic-based tools, this project will improve manufacturing processes and controls to overcome current bottlenecks and significantly increase the production capacity of high-quality, competitive aged cheddar cheese.

With over 120 years of brand heritage in the Canadian dairy industry, Parmalat Canada is committed to the health and wellness of Canadians and markets a variety of high-quality food products that help them keep balance in their lives. Parmalat Canada produces milk and dairy products, fruit juices, cultured products, cheese products and table spreads, employing more than 3,000 people, with five operating facilities in Ontario and eleven more across the country.

This project will bring the Canadian knowledge base related to cheese making processes into a new era. With increased production of high quality cheese, Parmalat will contribute even more to the Canadian economy. At the same time, our dairy farmers will benefit significantly from the increased demand for and utilization of Canadian milk and increased revenues for dairy farmers estimated at approximately $28 million a year.

Cool facts:

• Cheddar is the most popular cheese around the world.
• Parmalat Canada’s commitment to quality and innovation has helped them become one of the largest food group companies in Canada, and the largest dairy company in Ontario.
• Parmalat is the top producer of premium-quality, award-winning aged cheddar (winner of the 2016 world cheese championship – see http://baldersoncheese.ca/about-us/awards/).

Renewable chemicals

The cosmetic, flavour and fragrance industries are dominated by petrochemical-derived ingredients largely due to reliability and cost of supply. These ingredients rely on finite resources, such as petroleum, and the processes used to manufacture them are a significant source of pollution.

Ontario start-up, Ardra Inc., has developed a synthetic biology platform enabling the economical replacement of these petrochemicals with a steady supply of environmentally friendly, natural ingredients to produce a large portfolio of high-value products.

Many industries currently rely on petrochemical-derived ingredients because natural ingredients have fluctuating and high prices along with seasonal variations. By using genomics technologies, many petroleum-derived products could be replaced by less expensive and better-performing biobased products based on renewable materials grown in forests and agricultural fields.

Ardra is a specialty chemicals company focused on the production of natural ingredients for the cosmetics, flavour and fragrance industries. Their synthetic biology platform is used to produce petroleum-free, high-purity chemicals that are made from completely renewable resources. By using renewable feedstock, such as under-utilized agricultural or forestry biomass, and engineered microbes, Ardra’s processes allow for low cost production and a steady supply of natural ingredients at a constant price.  Additionally, their processes provide a more environmentally friendly alternative because biomass does not contribute to carbon dioxide in the atmosphere the way fossil fuels do.

Ardra’s development pipeline has two ingredients: 1) natural butylene glycol used in cosmetics, and 2) green leaf volatiles used in flavours and fragrances. The investment from Ontario Genomics will enable Ardra to further develop their innovative product pipeline.

Cool Facts:

• Increasing consumer awareness about the harmful effects of petroleum-based ingredients in cosmetics products is resulting in greater demand for petroleum-free cosmetics products. Natural petroleum-free ingredients is now the fastest growing segment of the cosmetics industry.
• Ardra (an Ontario startup spun out of BioZone at the University of Toronto’s Department of Chemical Engineering) caters to this high-growth, consumer-driven market by producing natural ingredients for use in cosmetic products as well as flavor and fragrance formulations. Their technology builds on outcomes from the BEEM project previously funded by Genome Canada.
• Ardra’s first product is the ingredient butylene glycol. This ingredient is used in a broad range of industrial applications such as foods, polymers, and pharmaceuticals. However, the main application of butylene glycol (over 55% worldwide) is in cosmetic products as an additive to reduce the loss of moisture.
• Petroleum-based butylene glycol has impurities that cause odour on storage as well as skin sensitization problems. Ardra’s natural butylene glycol provides a green alternative free from impurities causing odour or skin sensitization issues, which has been certified by the Natural Products Association, Health Canada, and USDA for use to make certified natural cosmetics formulations.
• Ardra’s second product is natural leaf-aldehyde, an ingredient used in many fruit flavour formulations including apple and peach, as well as in perfumery as a fresh, green note.

To learn more about Ardra’s technology and innovative product pipeline, please visit http://www.ardrabio.com/.

Reducing Sulphur Contamination in Mining Wastewaters

Sulfur-contaminated wastewater is the largest global mining-related environmental liability, with a legacy cost of trillions of dollars. Ontario researchers are applying genomics technologies to develop innovative monitoring, management and treatment tools. These innovations will safeguard the quality in receiving waters, better monitor, manage and reduce toxicity, and generate new tools to support cost-benefit decision-making.

The Canadian mining sector is a cross-country presence, with mines in every province and territory contributing more than $57 billion to the economy (3 per cent of Canada’s GDP) and employing over 375,000 people. As pressures on Canada’s freshwater water supplies grow, the sector as a whole, is seeking to develop the most sustainable approaches to mining possible. Mining wastewaters contain sulphur compounds, which can cause acidification and toxicity in receiving waters if not properly managed. Currently the industry lacks effective monitoring tools and innovative biological solutions to better controls these contaminants.

Dr. Lesley A. Warren of the University of Toronto, along with Dr. Jillian Banfield of University of California, Berkeley, is leading a project that will apply genomics, geochemistry and modeling to mining wastewaters to develop innovative biological monitoring, management and treatment tools. The integration of genomics will provide understanding of bacterial opportunities in these wastewaters for new flexible management and treatment options to safeguard the quality of wastewater.

Cool Facts:

• This project — the first of its kind in Canada and possibly the world — involves three mining and two environmental consulting companies, provincial and national sector industry associations and government.
• Project collaborators are focused on ensuring the project’s findings are applied to lowering costs, decreasing risk of environmental damage, reducing liabilities for the industry and developing better safeguards for Canada’s vital freshwater supplies.
• The project includes a research component to develop a Risk and Options Assessment for Decision-making. This process will enable translation of the team’s scientific knowledge into a nested set of decisions to help guide mining operational practices, corporate strategic planning and policy development.

Using Genomics to Create Biopolymers from Tree Biomass

In a world that is requiring increasingly biological-based solutions to meet a growing need for sustainable materials, tree biomass remains one of the most abundant resources on earth. Ontario researchers are applying genomics technologies to create materials from underutilized tree biomass to replace those made from fossil fuels used in everyday products — such as resins, adhesives and food packaging. These innovations will create higher value bioproducts, reduce our carbon footprint, and develop new tools for effluent treatment and energy recovery.

While there is general appreciation of the potential of microbial enzymes in expanding the range of products made from tree biomass, to date, biotechnology development has focused largely on the deconstruction of renewable biomass into sugars that can then be converted through fermentation to biofuels.

Drs. Emma Master of the University of Toronto and Harry Brumer of UBC are leading a team looking in the other direction. Their project, SYNBIOMICS, is distinguished from other projects by focusing on biocatalysts that upgrade (rather than degrade) tree biomass to create and replace materials made from fossil fuels used in everyday products, from adhesives to packaging. By upgrading biomass, Synbiomics aims to leverage the unique qualities of Canadian bioresources, which can open new opportunities for the Canadian forestry sector.

The project will also foster small and medium-sized enterprises that will work together synergistically with nearby pulp mills, creating lasting knowledge-based economic opportunities for Canada’s forestry sector and breathing new life into rural communities across Ontario.

Cool facts:

• As part of this project, the research team is coordinating an iterative bioproducts development cycle with end-users to ensure sustainability.
• The team is also developing economic ecosystem models for small and medium enterprises in the forestry sector.
• Additionally, the project includes a research component to develop predictive tools for effluent treatment and energy recovery, thereby reducing both economic and environmental burdens for Ontario.

For more information about the SYNBIOMICS projects, please visit http://www.synbiomics.ca/.

The Centre for Applied Genomics

The Centre for Applied Genomics (TCAG) is dedicated to conducting and promoting groundbreaking research in genomics, including service and training support. Each year TCAG supports research performed by more than 800 different scientific investigators from academic, government, non-governmental organization and private sector research labs around the world. TCAG’s impact reaches far beyond human health, supporting research in the areas of food safety, the environment, fisheries and oceans, conservation biology, agriculture and agri-food, and many other disciplines.

TCAG is located on a full floor of the Research Institute of The Hospital for Sick Children (SickKids), in the Peter Gilgan Centre for Research and Learning in downtown Toronto, and is affiliated with the McLaughlin Centre and the University of Toronto. It contains core facilities, including Informatics, Biostatistics, Sequencing, Microarrays, Genotyping, Cytogenomics and Biobanking, that collectively form a full-service, end-to-end genomics pipeline that can accommodate projects from the very small to the very large.

Data are generated on a fee-for-service, cost-recovery basis, and belong to the client. TCAG data handling and analysis activities take advantage of the SickKids High Performance Computing Facility (HPF) and HPC4Health Compute Canada node, as well as cloud-based resources. There have been many milestones in TCAG’s history, some of which are highlighted in the cool facts below.

Cool facts:

• The centre is a founding member of Canada’s Genomics Enterprise (CGEn), a national genomics platform that is one of the Major Science Initiatives funded by the Canada Foundation for Innovation (CFI) as a national platform critical to Canada’s research success.  Since 2006, TCAG has provided services to over 2,200 laboratories: 85% from Canada including all ten Canadian Provinces; 45 countries; 331 academic institutions (universities, teaching hospitals and colleges); 157 companies (58% Canadian), and 49 government or NGO institutions. Dozens of trainees (students, fellows, visiting scientists, clinician-scientists, etc.) have trained within the facility.
• TCAG is the first genome centre in Canada to install and operate Illumina HiSeq X whole genome sequencers; these are run alongside Illumina NovaSeq and other HiSeq instruments, and many other technologies.
• TCAG developed the Ontario Population Genomics Platform repository that contains over 2,500 cell lines, DNA and demographic data from healthy controls, and has comprehensively genotyped over 850 of these. These data and population control DNA samples are available as a public resource. Under the leadership of current Director Stephen Scherer, and in collaboration with Google, Verily, BioTeam and DNAstack, TCAG leads the Autism Speaks “MSSNG” project, generating whole genome sequences from 10,000 members of families with autistic children. Over 8,000 genomes have been completed to date, with analysis of the first 5,200 reported in Nature Neuroscience. The capacity and capabilities built for MSSNG have resulted in many benefits to TCAG clients. One recent example is the development of an improved pipeline for whole-genome copy number variation analysis.
• The centre also developed and hosts the Database of Genomic Variants (DGV). Last year, the DGV website was visited over 230,000 times by users from 88 different countries and is cited in over 350 publications every year.
• TCAG has leveraged a total of over $223 million in funding over the past 20 years, including over $93 million in billed, cost-recovery services contributing to research studies in Canada and around the world. Major funding partners include CFI, the Ontario, Genome Canada, CIHR, the SickKids Foundation, and the McLaughlin Centre of the University of Toronto.

To learn more about TCAG, please visit http://tcag.ca/.

Network Biology Collaborative Centre

The Network Biology Collaborative Centre (NBCC) is a national platform that helps scientists by providing a suite of resources for functional genomics and proteomics to support the discovery and validation of targets and disease mechanisms. They allow users to map dynamic physical interactions between proteins and understand the impact on a myriad of cell behaviours when specific genes and their protein products are removed or silenced. This information is critical for understanding the basis for disease and developing new therapeutics.

Located at the Lunenfeld-Tanenbaum Research Institute (LTRI) in Mount Sinai Hospital, Toronto, the NBCC was formed from the amalgamation of two flagship LTRI facilities: The Proteomics Facility for mass spectrometry-based analysis of protein function and the SMART High-Throughput and High-Content Screening laboratory for functional genomics studies. The NBCC subsequently expanded with new offerings in single cell biology that include high spatio-temporal resolution imaging (led by Dr. Laurence Pelletier), transcriptional profiling, and next-generation sequencing. The Centre is a member of the Genome Canada Genomics Innovation Network.

The mandate of the Centre is to assist Canadian and International scientists in their investigation of complex biological networks related to human health and disease by providing access to advanced instrumentation, proven workflows, and world-class expertise in functional proteomics and genomics. As a national platform, the NBCC works with users from across Canada and Internationally on projects ranging from small to large-scale on a fee-for-service basis. Hand-on training at the Centre is offered to interested users who wish to learn more about NBCC’s technologies.

Cool facts:

• The NBCC’s Modular Assay and Robotic Technology (SMART) Facility, was one of the first high-throughput screening centres established in Canada. SMART uses robotic platforms and automated cell imagers to characterize and/or manipulate genes to identify those of particular importance for disease initiation and progression.
• Dr. Jeff Wrana, who co-directs the NBCC with Dr. Anne-Claude Gingras is a Senior Investigator at the Lunenfeld-Tanenbaum Research Institute (LTRI) and was awarded the McLaughlin Medal by the Royal Society of Canada (RSC) in September 2018 in recognition of his pivotal contributions to our understanding of biology, human diseases, and its treatment. Dr. Wrana has made a prolonged series of major discoveries in developmental biology and cancer, and he established the high throughput, robotics facility which, together with the proteomics facility, formed the Network Biology Collaboration Centre (NBCC).
• Under Dr. Wrana’s direction, more than 70 graduate students and post-doctoral fellows have been trained, and high school students have been provided with real life science experiences in his lab.
• The NBCC has published over 200 publications since 2011, resulting from collaborations with >175 Principal Investigators across Canada and internationally, and the Centre been cited in over 2,300 publications.
• The Centre is supported by funding from the Canada Foundation for Innovation (CFI), The Ontario Ministry of Economic Development, Job Creation and Trade, Genome Canada through Ontario Genomics, Canadian Institutes of Health Research (CIHR), Terry Fox Research Institute and the Lunenfeld-Tanenbaum Research Institute.
• In June 2017, Repare Therapeutics announced it had raised $68M in Series A funding led by Versant Ventures. This company was co-founded by Dr. Daniel Durocher at LTRI, based on a CRISPR-enabled platform that was developed in collaboration with the NBCC.

For more information about NBCC, please visit https://nbcc.lunenfeld.ca/.

The Centre for Phenogenomics

TCP is a world-class facility owned and operated by The Hospital for Sick Children and Mount Sinai Hospital. It opened in 2007 and has transformed strategic investments by the Hospitals, the Canada Foundation for Innovation (CFI), and Genome Canada into a unique national resource to provide critical tools (mouse and more recently rat models) and services that enables biomedical research of the highest caliber across the country. State-of-the-art infrastructure and technologies are combined at TCP to support excellent research and help companies succeed. TCP was designated a national research facility by the CFI in November 2014, and a Genomics Innovation Network Node by Genome Canada in April 2015. TCP is also a founding member of the International Mouse Phenotyping Consortium which was recognized as a distributed global infrastructure by the G7’s Ministers of Science in 2017.

TCP’s facility is uniquely programmed to design, produce, manage, analyze, and distribute mouse models to enable hypothesis-driven discovery, purpose-drive translational studies, and preclinical bioavailability, safety, and effect evaluation for therapeutic discovery. Quality assurance of processes and quality control of data and products is a priority at TCP. The Model Production Core provides services for embryonic stem (ES) cell- and Cas9 RNA-guided nuclease (Cas9 RGN) genome editing-derived mouse and rat production, genetic quality control, and colony management to deliver experimental cohorts. TCP is licensed to provide Cas9 RGN to academic and industry researchers so the customer is able to use the model. The Clinical Phenotyping Core provides services for comprehensive or customized user-focused analysis of gene function, mutant gene dysfunction, or validation of drug target and evaluation of treatment effect across diverse areas of biology, disease, or therapeutics in mice. This Core uses non- or minimally invasive phenotyping tests to identify abnormalities. The Pathology Core provides services for necropsy, gross pathology, histology, immunohistochemistry, semi- and quantitative image analysis, and histopathology to correlate genetic or compound-associated changes with tissue structure and disease. The Cryopreservation & Recovery Core provides state-of-the-art embryo, ES cell, and sperm services, and global acquisition and distribution so customers can get the models they need and access secure and convenient storage and distribution of their rodent models. All data generated from each of the Cores belongs to the customer.

Recently, TCP expanded to establish the Infection & Inflammation Core directed by Dr. Silvia Vidal at McGill University. Dr. Vidal is globally recognized as an expert in the genetics of susceptibility and resistance to infection. A purpose-built Biosafety Level 2 and Biosafety Level 3 facility, this Core extends TC P’s services to enable genome-wide assessment of genes and variants associated with resistance or susceptibility to infectious disease. Colonization with bacterial, viral, fungal, or parasitic agents is available to model host response to infection and explore preventative or therapeutic proof-of-principle. Antigen-induced inflammatory disease models are also available to users to assess host response to in vivo immunological challenges such as neuro- or intestinal inflammation.

TCP is supported by its multidisciplinary Informatics Team that provides web-enabled access for users (on-line requests, service descriptions, service fees, guidelines, reports) and the informatics software, databases, infrastructure, and interfaces necessary to support TCP’s operation. A Senior Biostatistician was recently recruited to provide study design and statistical analysis services using available software tools and approaches or developing bespoke methods if needed by the customer.

TCP’s mission is to help you with your research whenever we can add value. The facility’s Services Coordinator provides pre-sales support, information flow, project coordination, timely and complete access to data, and post-delivery follow-up to users. To find out more, go to TCP, or email services@phenogenomic.ca.

Canadian Data Integration Centre

Major advances in genomics and informatics over the past several years have resulted in individual research projects producing enormous amounts of data. In particular, genomic data from large population and clinical cohorts, coupled with extensive health and lifestyle data, have the potential to generate critical biological insights into human health and novel determinants of disease. These technological developments have emerged as a new challenge for researchers because advances in genomics will be made (or limited) by bioinformatics analytical capacity and the ability to store and analyze data in new and more sophisticated ways.

The Canadian Data Integration Centre was established to help translate the biological research insights into tangible improvements for patients with cancer and chronic disease. Genome Canada recently renewed its commitment to the Canadian Data Integration Centre (CDIC), with a $6.4 million investment to establish a Genome Canada’s Genome Technology Platforms. Housed at the Ontario Institute for Cancer Research (OICR), the CDIC offers opportunities for cutting-edge pan-disease health research and big data analytical approaches.

As Canada’s first public site to offer third generation bioinformatics and genomics tools to support both functional and clinical genomics, the CDIC has emerged as a tried-and-tested solution for challenges faced in the application and management of advanced sequencing technologies, pathology and biospecimen handling, genomics, and data integration. This is evidenced by the platform supporting large-scale health and research initiatives such as the International Cancer Genome Consortium and Canada’s largest population cohort and precision health program, the Canadian Partnership for Tomorrow Project.

The CDIC is led by Dr. Philip Awadalla (Director of the CDIC and CPTP), and co-investigators Lincoln Stein, Jared Simpson, Vincent Ferretti and John Bartlett, bringing together a team of international experts on the collection, harmonization and publication of genomic and phenomic data. Together, they are able to provide the full breadth of support for projects ranging from the initial design, collection and analysis of complex data, through to the development of integrated data portals to facilitate data sharing and the translation of research findings into tangible health outcomes. The CDIC provides client-oriented access services that are customizable to diverse research areas, such as genomics, epigenetics and population level studies, in addition to supporting biopharmaceutical initiatives in biomarkers discovery, drug development and repurposing. Having supported some of the world’s largest programs in data analysis and hosting, including the NCI Cancer Genomic Data Commons and the Pan-Cancer Analysis of Whole Genomes Consortium, the platform has been established as an international leader in genomics, informatics, and translational research.

To date, the CDIC has attracted more than $87 million in grants and generated $14 million in service revenue through providing bespoke support for local and international projects. This has culminated in numerous high-impact publications in Nature, Science and Nature family journals, including a recent study featured in Nature Communications, and highlighted in the Globe and Mail, showing that environmental exposures are more determinant of respiratory health outcomes than inherited genetics.

The investment through Ontario Genomics will support the expansion of the CDIC’s services to include the genomic infrastructure supported by OICR’s Genome Technologies and Diagnostics teams. The informatics and bio-computing core at the CDIC is currently the largest academic cancer informatics program in Canada, offering real-time, long-read PromethION direct sequencing technology, Chromium 10X single cell library preparation and is proudly home to the first operational NovaSeq in Ontario. This allows the CDIC to equip researchers and industry clients alike with state-of-the-art software and analytical tools to interrogate the underlying causes of complex diseases. As CDIC researchers help to facilitate a new era of Canadian-led genomics and informatics research projects, they will develop novel technologies and methodologies for long-read sequencing, facilitate the development and clinical roll-out of therapeutic biomarkers and streamline the translation of research innovations to the clinical context. With this renewed commitment from Genome Canada, the CDIC looks forward to supporting national and international efforts to better combat cancer, chronic and infectious disease.

Our Team — Our Board

The primary mandate of Ontario Genomics’ Board of Directors is to provide strategic insight and operational governance. The Board comprises leaders from Ontario’s life science sector, including not for profit research and education institutions, biotechnology enterprises, financial entities, public policy centres, and government. Their time and expertise are essential to our ongoing success and future direction, and we are grateful for their many contributions.

Board of Directors

(for fiscal year ended March 31, 2018)

• Brian Underdown, Chair, 2011-2018
• Maurice Bitran, CEO, Ontario Science Centre
• Stephen Cummings, CEO and General Managing Partner, Rizolve Partners
• Jack Gauldie, Vice-President, Research, St. Joseph’s Healthcare Hamilton
• Shana Kelley, Professor, Pharmaceutical Sciences, Chemistry, Biochemistry, and Biomedical Engineering at the University of Toronto
• John Kelly, Chief Executive Officer, KeliRo Company
• Jay A. Lefton, Partner, Fasken Martineau DuMoulin LLP
• Alex MacKenzie, Senior Scientist, CHEO Research Institute and Professor of Pediatrics, Faculty of Medicine, University of Ottawa
• Benjamin Rovinski, Managing Director, Lumira Capital
• Deb Stark, Former Deputy Minister of the Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)
• Cal Stiller, Chair and CEO, Stilco
• Scott Tanner, Former CEO, DVS Sciences Inc.
• Alan Winter, B.C.'s Innovation Commissioner and former Director, Geoscience BC

Observers

(for fiscal year ended March 31, 2018)

• Marc LePage, President and CEO, Genome Canada
• Katherine Kelly Gatten, Director Science and Research, Ontario Ministry of Economic Development, Jobs and Trade
• Christopher Hamden, Director Finance and Administration, Innovation, Science and Economic Development Canada

Our Team — What We Do

Ontario Genomics connects scientists, ideas and partner organizations for collaborative investment opportunities in genomics-based applied research, translation and application. We do this by:

• Helping scientists find paths to the marketplace for their discoveries
• Helping genomics-based start-up companies with advice, funding and networking
• Helping established companies with genomics-based solutions to increase competitiveness and market share
• Enabling all partners to leverage their funding

Since 2000, Ontario Genomics has led genomics innovation in Ontario across key sectors of the province’s economy. Managing a cumulative portfolio of over $1.2 billion in more than 200 genomics projects, we have helped to create over 8,500 jobs in Ontario while addressing challenges in key sectors across the province.

For more information about the current Ontario Genomics team, please visit: http://www.ontariogenomics.ca/about-us/staff/