Genomic Applications Partnership Program (GAPP)

The Genomic Applications Partnership Program (GAPP) funds translational research and development projects that address real-world challenges and opportunities as identified by industry, government, not-for-profits, and other “receptors” of genomics knowledge and technology.

Launched on June 03, 2013, Genome Canada’s GAPP program aims to fund projects that have a clear and defined partnership between Academia and User partners (receptors) to promote the application of genomics-derived solutions that address key sector challenges or opportunities and which will have socioeconomic benefit to Canada.

Funded Ontario GAPP Projects

Round 10
On February 4, 2019, The Honourable Kirsty Duncan, Minister of Science and Sport, announced the funding recipients from Genome Canada’s GAPP Round 10 competition. Ontario Genomics led three (3) of the four (4) awarded projects – driving $2.9 million of federal funding into the province and an additional $5.8 million in investments by industry, the Ontario government and other funding partners, for a total of $8.7 million. This investment will support translational research and development projects that address real-world challenges and opportunities as identified by industry, government, not-for-profits, and other organizations of genomics knowledge and technology.

Round 9

Round 8

Round 7

Round 6

Round 5

Round 3

Round 2

Round 1

GAPP Project Descriptions:

Assessing Freshwater Health Through Community Based Environmental DNA Metabarcoding

Project Leaders: Elizabeth Hendriks World Wildlife Fund Canada (WWF-Canada); Laura Maclean, Environment and Climate Change Canada; Mehrdad Hajibabaei, University of Guelph
Genome Centre: Ontario Genomics
Total Project Funding: $2.6 million

With a growing economy, increasing population, and climate change, Canada faces increased pressures on its precious resource: freshwater (20% of the world’s freshwater). Current methods for monitoring the health of our watersheds remain slow, laborious, expensive and imprecise. Canada’s geographic diversity and low population density makes monitoring networks a challenge to maintain. We need more efficient, comprehensive monitoring tools to inform governments, communities and industries about the true consequences of economic development on freshwater quality, to support rapid and effective protection of vulnerable ecosystems.

The WWF- Canada and Environment and Climate Change Canada (ECCC) are working with Dr. Mehrdad Hajibabaei of the University of Guelph to validate and implement a new technique called environmental DNA metabarcoding, which uses bulk environmental samples for identification of species through species specific genomic sequences (DNA ‘barcodes’) using high-throughput sequencing technologies. The project will generate biodiversity data for freshwater benthic macroinvertebrates, the small animals that live at the bottom of streams, rivers. The technique will be used to analyze bulk samples collected by community-based monitoring efforts across a wide range of Canadian watersheds. Sampling by community groups will be coordinated by WWF-Canada and its partner organizations such as Living Lakes Canada.

Implementation at this scale will be a world first, supporting the wider adoption of these technologies within existing environmental monitoring and assessment applications, including ECCC’s Canadian Aquatic Biomonitoring Network (CABIN) which engages over 1,400 users, including federal, provincial and territorial government agencies, First Nations, academia, industry, NGOs and environmental consulting firms.

Many of these organizations already use biomonitoring to understand and manage the impacts of resource projects such as mines, hydro dams and energy projects. By providing access to this new genomics-based technique, and by demonstrating its reliability in assessing river health, we can broaden the reach and impact of existing community-based monitoring programs, ultimately leading to better informed decisions.

Translating High Immune Response (HIR™) Genomics to Improve Beef Cattle Health and Welfare

Project Leaders: Michael Lohuis, The Semex Alliance and Bonnie Mallard, University of Guelph
Genome Centre: Ontario Genomics with Mitacs partnership
Total Project Funding: $1.6 million

High Immune Response (HIR™) is a patented test developed by Dr. Bonnie Mallard and colleagues of the University of Guelph that identifies animals with naturally superior immunity. First used successfully in dairy cattle, the test is now being adapted to fight Bovine Respiratory Disease (BRD), the costliest disease of beef cattle raised on feedlots. BRD results in the death of some 53,000 beef cattle in Canada each year, an economic loss of more than $100 million. In North America as a whole, the estimated annual cost of BRD as high as $1 billion dollars/year.

Dr. Mallard is working with the Semex Alliance and through them, the Canadian Angus Association (CAA) and the American Angus Association (AAA), to develop an HIR™ genomics test for beef cattle. The application of the test could result in a significant (20-50 per cent) reduction in deaths among calves from birth to weaning age and reduce the need for antibiotics throughout the lifetime of beef cattle. All Angus bulls marketed in Canada and the United States will have access to the HIR™-genomic test, allowing beef producers to select bulls for breeding purposes better equipped to improve animal health and welfare.

The new test will demonstrate the leadership provided by Semex, the CAA and the AAA in beef cattle genomics. Integration of the HIR™ technology and selective breeding for enhanced immunity in the North American Angus population is expected to cumulatively increase BRD resistance of beef cattle over multiple generations, which if fully applied, could ultimately reduce the costs of BRD in North America by $500 million per year, $65 million of which will be in Canada. Reduced use of antibiotics will provide further benefits to consumers and retailers.

Devices for Detection and Identification of Surface Microbial Contamination in High-Risk Facilities

Project Leaders: Mark McInnes, Charlotte Products Ltd., and Shana Kelley, University of Toronto
Genome Centre: Ontario Genomics
Total Project Funding: $4.5 million

Healthcare-associated infections (HAIs) are the 4th leading cause of death in Canada, predicted to move up to second place by 2050. Attention to cleanliness and disinfection of surfaces plays a large role in reducing HAIs. However, historically it has been difficult to measure cleaning effectiveness and meaningfully improve practices. There is a clear need for a system that can identify disease-causing bacteria and viruses on surfaces.

Charlotte Products Ltd. (CPL), a family-owned Canadian company, has developed an environmental monitoring system and optical sensor technology, called Optisolve Pathfinder®™, to complement its innovative, award-winning cleaning products. Dr. Shana Kelley is working with the company to further enhance the OptiSolve offering to allow for recognition and identification of specific pathogen species.

Dr. Kelley and her team will combine novel nanomaterials with a genomics-based approach to allow for precise identification of pathogens that cause HAIs. The resulting technology, Optisolve Insight, will allow hospitals long-term care facilities, and more to rapidly detect and identify infectious agents, such as MRSA, C. difficile, and influenza, with the resultant benefits of proactive prevention and quick interventions.

The service and technology will significantly reduce HAIs while enabling environmental services and IPAC managers and to avoid taking a “worst-case scenario” approach to infection outbreaks, which can include bed closures and cancellation of procedures. The result will be improved health of patients, residents, staff, and visitors as well as healthcare savings. This first-to-market technology will contribute to economic growth and employment for highly qualified personnel.

Broad-range disease resistance in greenhouse vegetables

Project leaders: Michael Pautler, Vineland Research and Innovation Centre, David Guttman, University of Toronto
Genome Center: Ontario Genomics
Total Funding: $2 Million

Canada’s greenhouse vegetable industry generates more than $1 billion from retail sales and exports. Its top three crops are tomatoes, peppers and cucumbers, produced mainly in Ontario, British Columbia and Quebec. In an extremely competitive environment, 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.

Drs. David Guttman, Darrell Desveaux, and Adam Mott of 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. Further, it is extremely difficult for pathogens to overcome the resistance linked to these genes. Now Dr. Guttman and team are working with the Vineland Research and Innovation Centre and its reverse genetics platform (developed with earlier Genome Canada funding) to further develop these Broad Range Resistance genes, as they are known, to protect 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 around $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. Additional benefits will be seen as Vineland re-invests its licensing revenue from the new vegetable varieties into further research, driving innovation throughout the entire horticultural sector.

Applying the Adapsyn genomics platform to the identification, isolation and characterization of immune modulators from the human microbiome

Project leaders: Andrew Haigh, Adapsyn Bioscience Inc., Michael Surette and Nathan Magarvey, McMaster University
Genome Center: Ontario Genomics
Total Funding: $6 Million
Mitacs partnership

Adapsyn Bioscience has a proprietary platform whereby it applies patented algorithms, proprietary artificial intelligence, and machine learning to genomic and metabolomic data from microbes to identify and characterize novel natural products that can then be developed as novel therapeutics. The company is working with McMaster University and Dr. Michael Surette and his team to systematically mine the human microbiome – the collection of microbes that colonize the body – for compounds that can be used to treat human disease.

The microbiome contains approximately 100 times as many genes as the human genome, and has been shown to produce antibiotics, vitamins, fatty acids, neurotransmitters such as serotonin, histamine and acetylcholine, and immunomodulators. As a result, the microbiome has the potential to affect the nervous system, suppress pathogen growth, and modulate the immune response to invading pathogens. Dysregulation of the microbiome has been implicated in inflammatory bowel disease, cancer, and neurological conditions, and can affect how people respond to immunotherapies.

Dr. Surette and Adapsyn Bioscience are focusing on the microbes responsible for immunological effects of the microbiome. Their work will lead to personalized medicine based on the composition of the microbiome and new treatments for inflammatory diseases and cancer. Adapsyn has secured financing to ensure future development of the results of this project. The project will also contribute to future partnership opportunities, thus ensuring that the economic benefits of commercialization remain in Canada.

Pre-emergence surveillance for reportable influenza viruses at the human-animal interface

Project leaders: Mohammed Qadir, Fusion Genomics, Samira Mubareka, University of Toronto
Genome Center: Ontario Genomics
Total Funding: $791K

It’s hard to tell when a virus risks becoming an epidemic – but it’s important for risk management, public health and biosecurity. Most companies working in the area, however, focus on diagnostics rather than pre-emergence surveillance. This project’s goal is to fill that gap.

Current methods for surveillance, especially before a virus emerges as a danger, are neither timely nor efficient, and a better tool is needed. Next-generation DNA sequencing provides genomic data that can offer insight into the origin, diversity and transmission potential of viruses found in animals, such as avian or swine flu, particularly the likelihood of their making the jump into humans. But there are obstacles to this sequencing being adopting into mainstream surveillance, including pathogen enrichment, sample quantity and computational resources.

Fusion Genomics Corp. is working with the University of Toronto’s Dr. Samira Mubareka to further develop its genomic technology, ONETest™ EnviroScreen, which already includes assays for detecting avian influenza, to detect swine flu as well. The result will be a highly sensitive, informative and scalable technology for infectious disease surveillance that harnesses the power of next-generation sequencing. Its ability to provide surveillance in animals before the emergence of an influenza virus will drive a paradigm shift in transmission dynamics, outbreak predictions and vaccine design and production.

The main market for this innovation will be government agencies and institutes charged with pathogen surveillance. Fusion will work with such organizations to validate the technology and bring them on board as early adopters. Further expansion of its use will happen both nationally and internationally. Use of the technology will enable early outbreak warnings and damage-mitigation efforts. It will also reduce losses among poultry and swine producers and support the growth of a Canadian biotech start-up.

Validation of TAC receptors for use against liquid and solid tumours

Project leaders: Christopher Helsen, Triumvira Immunologics, Inc. (receptor); Jonathan Bramson, McMaster University (academic)
Genome Center: Ontario Genomics
Total Funding: $2.3 Million

Immunotherapies show tremendous potential to unleash the immune system to attack cancers. However, while some patients benefit, others do not respond and, even when it is successful, immunotherapy treatments can carry with them severe, and sometimes fatal, toxicities. The most promising of these immunotherapies are based on T-cells, cells of the immune system, particularly CAR-T cells, which are showing significant efficacy in treating terminal cancers, but which can also often result in significant life-threatening toxicities.

Dr. Jonathan Bramson, of McMaster University, is working with Triumvira, a young Canadian biotech company, to further develop the company’s platform for engineering T cells, the T-Cell Antigen Coupler (TAC). The platform has already demonstrated equivalent or superior efficacy and much greater safety compared to other CAR-T cell platforms. Currently, however, the TAC platform is limited primarily by access to novel binding domains. Genome Canada funding will be used to validate TAC receptors carrying novel binding domains developed in the Bramson lab and at the Centre for Commercialization of Antibodies and Biologics. Triumvira will then commercialize those domains that are successful by working with commercial pharmaceutical companies.

The primary economic benefit to Canada in the short term will be new jobs and the attraction of investment capital. Within three-to-five years of the project’s completion, human clinical trials will be underway, providing hope to patients with cancer who otherwise have no treatment options.

Leveraging Leukocytes as Endogenous Biosensors to Create Novel Diagnostics for Preterm Birth

Project leaders: Liu Xin, BGI-Research (receptor); Stephen Lye, Lunenfeld-Tanenbaum Research Institute (academic)
Genome Center: Ontario Genomics
Total Funding: $4.6 Million

Two hundred million women around the world become pregnant each year. Of those, 13 million will give birth preterm, one million of their babies will die and millions more will experience serious, life-long medical and developmental disorders as a result. In Canada, the annual cost associated with preterm births is estimated to be $600 million.

BGI and Dr. Stephen Lye of the Lunenfeld-Tanenbaum Research Institute, part of Sinai Health System, have agreed to collaborate in the development of preterm birth diagnostics and screening solutions.

BGI is the largest genomic organization in the world and is committed to reducing the rate of major disease by offering accurate and affordable genetic tests and molecular diagnostics services. Dr. Lye has identified gene expression signatures in maternal white blood cells that can predict which women who experience too-early symptoms of labor will go on to experience preterm birth of their infants.

BGI and Dr. Lye will work together to enhance the diagnostic capability of these gene expression signatures and aim to develop a simple genomic test to identify risks and prevent preterm births. The test aims to reduce rates of preterm birth by enabling intervention with women at risk, potentially saving the healthcare system $200 million per year and reducing the burden on neonatal ICUs.

BGI intends to continue its research collaboration with the Sinai Health System and expand its R&D activities in Canada, which will generate downstream investment and create jobs for highly qualified personnel.

Genomics Driven Engineering of Hosts for Bio-Nylon

Project leaders: Kit Lau, BioAmber (receptor); Radhakrishnan Mahadevan, University of Toronto (academic)
Genome Center: Ontario Genomics
Total Funding: $5.7 Million

Currently, nylon is made from petroleum. While the process works well, it is not as environmentally friendly as many would like. There is strong demand for nylon produced using man-made chemicals derived from sugar, which requires less energy and results in fewer greenhouse gas emissions.

BioAmber, an industrial biotechnology company located in Sarnia, Ontario, is successfully manufacturing succinic acid (used in producing polymers, resins and solvents) from sugar streams, which materially decreases the carbon footprint. These same principles could be used to develop a process for the manufacture of adipic acid, used in producing nylon.

A genomics-driven bioengineering approach has been developed by the University of Toronto’s team at BioZone led by Dr. Radhakrishnan Mahadevan to convert sugars into value-added industrial chemicals such as adipic acid. Adipic acid alone has a market of 2.2 million tonnes; chemicals that can be derived from it have similarly large markets. As an industrial biotechnology company, BioAmber is positioned to apply the results from this research program to the development of next generation chemicals.

The results of its work will benefit Canada’s economy by growing the biorefining industry and creating new manufacturing jobs, while protecting the environment through reduced greenhouse gas emissions and pollution.

Increasing Yield in Canola Using Genomic Solutions

Project leaders: Matthew Crisp, Benjamin Gray, Benson Hill Biosystems (receptor); Peter Pauls, University of Guelph (academic)
Genome Center: Ontario Genomics
Total Funding: $3.4 Million

The world’s population is growing and so is demand for the crops to feed it, among them canola. The canola industry in Canada accounts for nearly a third of the gross production value of all Canadian crops, generating $19.3 billion and nearly 250,000 jobs across Canada. The industry has set a goal of increasing yield by 53 per cent in the next 10 years. Traditional breeding techniques are not sufficient to meet this goal; new technologies are needed.

Dr. Peter Pauls and collaborators at the University of Guelph have identified the genetic links of traits that can be incorporated into canola. The new traits are expected to significantly enhance crop productivity by increasing photosynthetic capacity, without negatively impacting seed quality. The researchers are working with Benson Hill Biosystems (BHB), an innovative crop genetics firm, combining their strengths to produce game-changing varieties of canola for producers across Canada.

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, growing industry revenues by $3-$4 billion per year. BHB will also establish a Canadian subsidiary, CanolaCo, for this project that will result in newly created jobs for Canadians.

Translating OMICS for competitive dairy products

Project leaders: Maria Pepe, Parmalat Canada (receptor); Gisele LaPointe, University of Guelph (academic)
Genome Center: Ontario Genomics
Total Funding: $1.3 Million

Aged cheddar is a classic of cheese boards, pairing with everything from apple pie to zinfandel. Parmalat Canada is the number one producer of premium-quality aged cheddar that has been winning many cheese contests including the 2016 world cheese championship. Demand for aged cheddar is projected to steadily increase in the future, requiring Parmalat to increase its manufacturing capacity. Trade deals (such as CETA) make it more urgent for Parmalat Canada to gain efficiency and protect its market share.

To achieve this goal, Parmalat Canada is working with Dr. Gisele LaPointe of the University of Guelph, a well-known scientist in the field, to validate and implement metagenomic, metaproteomic and metabolomics tools modified to meet the technical requirements of cheese production. The 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 16 operating facilities 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 of about $28 million a year.

Application of genomic selection in turkeys for health, welfare, efficiency and production traits

Project leaders: Dr. Ben Wood, Hybrid Turkeys, a Hendrix Genetics Company (receptor); Dr. Christine Baes, University of Guelph (academic)
Genome Center: Ontario Genomics
Total Funding: $6 Million

Dr. Christine Baes of the University of Guelph and Ben Wood of Hybrid Turkeys will be collaborating to adapt and apply genomic tools developed in other livestock species to improve the health, welfare and productivity of Canadian turkeys. Hybrid Turkeys’ parent company, Hendrix Genetics, has already implemented genomic selection in layer chickens and pigs and it will now adapt and apply the technology to achieve improvements in feed efficiency, bodyweight, yield, egg production and livability in commercial turkeys. This will lead to estimated economic gains for the Canadian turkey industry of $39 million over the next five years. The project will also have environmental benefits due to improved feed efficiency and reduced manure and greenhouse gas production.

Hybrid Turkeys is part of Hendrix Genetics, a multi-species breeding company with primary activities in layers, turkeys, pigs, aquaculture, and traditional poultry. Its R&D headquarters is located in Kitchener, Ontario. By applying advanced genomic selection, Canada’s role as a supplier of turkey genetics to the world will be secured. By more accurately estimating the genetic potential of selection candidates, the rate of genetic gain can be increased from 15 per cent to 60 per cent, depending on the trait chosen. These improvements will provide value across the production chain, from breeders and farmers to turkey processors and, ultimately, to consumers.

Standardization of molecular diagnostic testing for non-small cell lung cancer

Academia-User Partnership: David Stewart, The Ottawa Hospital and the University of Ottawa; Craig Ivany, Eastern Ontario Regional Laboratory Association Administrative
Start Date: October 1, 2016
End Date: September 30, 2019
Total Project Funding: $2 Million

Non-small cell lung cancer is the most common type of lung cancer, accounting for 85 per cent of cases. Specific genetic mutations in a patient’s tumour can determine which drug will work best for that patient. As new targetable genetic mutations become known, it is more important than ever to be able to carry out genetic analysis of patient samples. Dr. David Stewart, from The Ottawa Hospital and the University of Ottawa, is working with the Eastern Ontario Regional Laboratory Association (EORLA) to develop an assay that can accurately detect important genetic mutations in the very small biopsy samples that can be obtained safely from most patients with advanced lung cancer. The assays will test for multiple genetic variations at once, for a more timely result than is possible with current sequential testing strategies. Patients will benefit from the rapid availability of information that will permit them to receive the most appropriate treatment. The financial benefits are also significant. If this new assay is implemented across the country, it could result in savings of $35.9 million in testing costs and $151.4 million overall due to the elimination of ineffective treatments. The project team will assemble a national advisory board to drive national translation of its technology so that these savings can be realized.

Clinical development and translation of genomics-driven paediatric cancer diagnostics using NanoString

Academia-User Partnership: Cynthia Hawkins and John Racher, The Hospital for Sick Children (SickKids); Barney Saunders, NanoString Technologies Administrative
Start Date: October 1, 2016
End Date: September 30, 2019
Total Project Funding: $1.9 Million

Over the past decade, there have been many high-impact, genomics-driven cancer discoveries. The overriding challenge, however, lies in making the transition from the laboratory to the clinic – literally, bench to bedside. Toronto’s SickKids is a leader in the discovery and implementation of clinical diagnostics for children’s health. NanoString Technologies is a leader in providing tools to individual labs to enable laboratory-developed tests. Now, their individual strengths are being brought together to develop additional tools for diagnosing cancer in children that will deliver key information in a targeted, cost-effective and timely way. Led at Sick Kids by Dr. Cynthia Hawkins and Mr. John Racher, in partnership with NanoString Technologies, their initial work will focus on low-grade glioma (brain tumours), leukemia and soft-tissue sarcoma, for which no comprehensive tests currently exist. Further along, the tests can be expanded to adult cancers as well. Within three-to-five years, their work will result in marketable diagnostic tests for pediatric cancer. This will improve survival times and quality of life for children with cancer, reduce healthcare costs and generate licensing revenue, which will be shared between the partners. This is a market with high demand and low competition, underscoring the importance of this product.

A genetic toolbox for tomato flavour differentiation

Academia-User Partnership: Dr. Charles Goulet, Université Laval; Dr. David Liscombe, Vineland Research and Innovation Centre
Start Date: April 1, 2016
End Date: March 31, 2019
Total Project Funding: $1.8 Million

Tomatoes, it is said, are the quintessence of summer in a bite. They are also responsible for more than half a billion dollars in annual farm gate sales and are Canada’s biggest fresh vegetable export. Canadian growers are facing competition due to lower production costs in other regions, leading to difficulties maintaining their market share. Canadian producers need to innovate in order to offer a differentiated product that will give them a competitive edge.

Generally, plant breeding programs focus on production traits, such as yield or disease resistance. Vineland Research and Innovation Centre (Vineland) is working with Dr. Charles Goulet of Université Laval to ensure new tomato varieties possess these traits, in addition to something more important to the consumer – flavour. Flavour is a complex trait, reflecting sugar, acid and aroma, as well as texture. Because aroma is defined by more than 30 volatile chemicals and dozens of genes, genomics can greatly facilitate breeding with much greater precision than ever before. This project will use variation in aroma-related genes to develop new tomatoes with differentiated flavour. The resulting plant lines will be used to breed tasty tomatoes at Vineland, and will be made available to other tomato breeders. The first varieties should be commercially available within three years of the project’s completion.

The development of locally-adapted, flavourful tomato cultivars will give Canadian greenhouse producers a clear advantage in a competitive consumer market, with total direct economic benefits estimated at more than $30 million per year.

Scale-up of bioaugmentation cultures and development of delivery strategies and monitoring tools for anaerobic benzene and alkylbenzene bioremediation

Academia-User Partnership: Elizabeth A. Edwards, University of Toronto; Sandra Dworatzek, SiREM, Mitacs partnership
Start Date: April 1, 2016
End Date: March 31, 2019
Total Project Funding: $950,000

BTEX compounds – benzene, toluene, ethylbenzene and xylenes – are natural components of crude oil and petroleum and are used in the synthesis of a wide range of useful materials and chemicals. They are also toxic, and benzene in particular is a known human carcinogen. As a result of extraction, transportation and refining processes, as well as accidental spills and leaks, BTEX compounds frequently pollute groundwater in all industrialized regions of the globe.

In Canada and elsewhere, remediation of contaminated sites is difficult and costly. When possible, affected soils are dug up and treated or disposed of offsite. Dr. Elizabeth Edwards of the University of Toronto is working with SiREM, a Canadian leader in bioremediation, to scale up and commercialize anaerobic bioaugmentation cultures for in situ BTEX remediation. These cultures were developed in Dr. Edwards’ lab where genomic knowledge was used to identify novel benzene-depleting microbial strains. Bioaugmentation, or the injection of specific microbes into contaminated sites, could significantly accelerate the rate of biodegradation, leading to the cleanup of these sites. How well the cultures perform this biodegradation should be understood in 1-3 years, leading to a cost-effective approach for cleanup of BTEX-contaminated sites.

If successful, this project would be the first commercial application of bioaugmentation for anaerobic BTEX degradation. It would lead to more widespread cleanup of contaminated sites where currently technologies are not feasible or too expensive. It will enable remediation of soils in-place, as opposed to excavation and removal. There are also significant economic benefits, as the global bioremediation market was conservatively estimated at $1.5 billion in 2009 and is now probably greater than $10 billion and continuing to grow.

Preclinical development of drugs for Intracerebral Hemorrhage (ICH)

Academia-User Partnership: Xiao-Yan Wen, St. Michael’s Hospital; R. Loch Macdonald, Edge Therapeutics, Inc.
Start Date: April 1, 2016
End Date: March 31, 2019
Total Project Funding: $5.9 Million

Intracerebral hemorrhage (ICH) is a form of brain hemorrhage responsible for 10 per cent of all strokes. It affects about 90,000 people in North America each year, more than half of whom either die or are disabled. Anywhere from one-quarter to 44 per cent of those who survive have recurring ICH. The annual economic burden of ICH is estimated at $300 million to Canada and $6 billion to the United States. Apart from treating hypertension, which is one of the causes of ICH, there is currently no way to prevent recurrent ICH.

Dr. Xiao-Yan Wen, director of the Zebrafish Centre for Advanced Drug Discovery (ZCADD) and his team at St. Michael’s Hospital, used genomics-driven research tools to identify several existing drugs that are already approved by the US Food and Drug Administration (FDA) that have shown the ability to prevent ICH in zebrafish models. In this project, Edge Therapeutics is partnering with Dr. Wen to perform preclinical studies on the most potent anti-ICH molecules known as EZF-0100 for treatment of ICH and brain microhemorrhages (BMH). Depending on the results of these studies, Edge may explore the use of its Precisa™ technology to develop a way to administer the drug in a sustained release profile and may also synthesize and test analogs of EZF-0100 to determine the best drug candidate for preclinical development and clinical study in Canada and the US.

The project will reinforce ZCADD’s leadership in drug development, attracting new partnerships, investment and revenue generation for the Centre. It will also train next-generation scientists and entrepreneurs and create new jobs for Canadians.

SIRPaFc: Translating genomics research into a novel cancer immunotherapy

Academia-User Partnership: Jean Wang, University of Toronto and University Health Network; Robert Uger, Trillium Therapeutics Inc. (user)
Start Date: December 12, 2014
End Date: June 30, 2018
Total Project Funding: $3.4 Million

Nearly all (96 per cent) people aged 65 or older diagnosed with acute myeloid leukemia (AML) die within five years, as do two-thirds of younger patients. Because it primarily affects older people, the incidence of this aggressive cancer is expected to rise in coming years as the population ages. Chemotherapy regimens for AML have remained essentially unchanged since the 1970s. With standard treatment, many patients can achieve remission, but most will relapse; following relapse two-thirds of patients will die within 3 years.
One of the reasons for the high rate of relapse in AML is that standard chemotherapy does not kill leukemia stem cells, leaving them to grow and mature into new leukemia cells. Leukemia stem cells express high levels of a protein called CD47. This protein sends a “do not eat” signal that stops white blood cells of the immune system called macrophages from surrounding and “eating” cancer cells.
With previous support from Genome Canada and Trillium Therapeutics Inc. (TTI), a publicly traded biotech company in Toronto, Canada, Dr. Jean Wang and team at the Princess Margaret Cancer Centre, University Health Network, and Dr. Jayne Danska and team at SickKids have developed SIRPaFc, a novel therapeutic that blocks the “do not eat” signal, freeing the immune system to attack leukemia stem cells. TTI is completing formal preclinical studies and will carry out clinical trials aimed at demonstrating SIRPaFc’s safety and efficacy. The collaboration between Drs. Wang and Danska and TTI will assist in realizing the commercial potential of this promising discovery.

Toward a national framework for clinical cancer genome profiling in Canadian hospitals

Academia-User Partnership: Suzanne Kamel-Reid, Princess Margaret Cancer Centre (University Health Network); Jeff Sumner, LifeLabs Medical Laboratory Services
Start Date: April 1, 2015
End Date: March 31, 2018
Total Project Funding: $6 Million

Approximately 200,000 Canadians are diagnosed with cancer each year. More than one in four of these patients can benefit from targeted treatment based on a genomic analysis of their tumours. Indeed, genome-based tumour profiling helps treat patients with the right drug at the right time, improving outcomes and saving lives. However, at present this breakthrough testing is not widely available and is currently only being used in a clinical trial setting for patients with advanced cancers at one Toronto Hospital, and its collaborators.
This genomics project between Dr. Suzanne Kamel-Reid of Princess Margaret Cancer Centre (University Health Network) and LifeLabs Medical Laboratory Services, Canada’s leading diagnostic lab company, is the first step in providing national market access to this potentially vital information.
In addition to saving lives, personalized cancer medicine data can reduce healthcare costs significantly, as the cost of treatment can be up to 10 times more than the cost of laboratory genomic cancer testing. Projected to total Canadian healthcare expenditures, genomic tumour profiling is expected to save the healthcare system hundreds of millions of dollars annually.

Novel rapid diagnostic tools for lung transplantation: Bringing omics to the bedside

Academia-User Partnership: Shaf Keshavjee, University of Toronto; Thomas Hartnett, United Therapeutics (Lung Bioengineering Inc.)
Start Date: April 1, 2015
End Date: March 31, 2018
Total Project Funding: $6 Million

A considerable number of patients needing a lung transplant die due to a lack of donor organs deemed suitable for transplant. Now, a proposed genomics approach to assessing donor lungs has the potential to save thousands of lives while reducing healthcare costs.
The project, led by Dr. Shaf Keshavjee of Toronto’s University Health Network (UHN) in collaboration with the U.S. biotech firm Lung Bioengineering Inc., a subsidiary of United Therapeutics Corp., intends to develop a genomics-based diagnostic test to determine whether a donor lung meets transplant requirements. At present, such evaluations are based on physiological assessments alone. As a result, less than 15 per cent of lungs, the healthiest, are deemed suitable for transplant, leaving unused countless “marginal” lungs that also could save lives. A genomics-based analysis could increase the number of transplant-acceptable lungs to nearly 50 per cent, resulting in a greater number of patients receiving this life-saving intervention. Using diagnostic test kits, donor lung conditions would be precisely monitored through biomarker analyses. Under Dr. Keshavjee’s research leadership, some biomarkers have already been isolated that can predict lung quality. Building on these findings, this new initiative will result in the creation of rapid diagnostic tools that could be used in transplant centres around the world.
The world’s first successful clinical lung transplant took place at Toronto General Hospital in 1983. Today’s genome project has the potential to further cement Canada’s global leadership in this high-tech medical sector. This initiative may also reduce the economic burden on the Canadian healthcare system while improving overall quality of life for lung-transplant patients.

Clinical utility and enhancements of a pharmacogenomic decision support Tool for Mental Health Patients

Academia-User Partnership: James Kennedy, Centre for Addiction and Mental Health; C. Anthony Altar, Assurex Health.
Start Date: October 1, 2014
End Date: September 30, 2017
Total Project Funding: $6 Million

One in five Canadians will experience some form of mental illness in their lifetime. Treatments are available but each person responds differently to them, in part because of their genes. A clinically proven genetic test, called GeneSight, analyzes an individual’s genes and recommends the optimal drugs for that person along with dose adjustments among the 33 most commonly prescribed antidepressant and antipsychotic drugs. Clinical testing in the United States has shown that GeneSight doubles the odds of a patient responding to antidepressant medication. More than 100,000 patients have received GeneSight tests in the United States.
Now, Assurex Health, the company that developed GeneSight, is partnering with scientists at Toronto’s Centre for Addiction and Mental Health (CAMH) to develop the Enhanced GeneSight (E-GeneSight) genomic test. E-GeneSight will incorporate new genomic markers that scientists at CAMH have identified and characterized for their association with patient responses to psychiatric medications. Assurex Canada and CAMH will together validate these markers for their ability to predict efficacy and side effects of psychiatric medications; the most predictive markers will be integrated into E-GeneSight. E-GeneSight, when launched in 2017, is anticipated to reduce the need for “trial-and-error” approaches to prescribing and increase the likelihood that people will respond optimally to the medications prescribed for them, while reducing side effects.
This will increase the proportion of patients who stay on their medications and improve their quality of life. It will also save the Canadian healthcare system $4,000 per year per treatment-resistant patient and will generate royalty revenues for CAMH as E-GeneSight is marketed internationally.

Developing Vasculotide, a genomic/proteomic-derived treatment to target vascular inflammation and destabilization

Academia-User Partnership: Dan Dumont, Sunnybrook Research Institute; Parimal Nathwani & Paul Van Slyke, Vasomune Therapeutics
Start Date: July 1, 2014
End Date: December 30, 2015
Total Project Funding: $1.5 Million

More than one million cardiac surgeries are carried out each year, usually successfully. Nearly one-third of high-risk patients, however, will experience a rapid loss of kidney function after surgery, known as Acute Kidney Injury, or AKI. AKI is the result of short-term interruptions in blood flow during surgery; 11 percent of patients who develop AKI after bypass surgery will die, compared to 2 percent of those who do not. Those who survive AKI are at risk of developing longer term kidney complications such as chronic kidney disease or End Stage Renal Disease. There is, therefore, a pressing need for better ways to prevent or treat AKI.
Drs Dumont and Van Slyke conceptualized and designed a drug called Vasculotide (VT) that binds to the Tie2 receptor, which is responsible for maintaining vascular health (and thus blood flow). Vasomune Therapeutics, the company developing and commercializing the drug, is partnering with these researchers to develop VT to the point where it is ready for human clinical trials. At that point, Vasomune will be positioned to seek venture capital for further development.
Within three-to-five years of the end of the project, Vasomune will be a venture-backed Ontario biotech company with a Phase II clinical program in renal disease. Being able to prevent or reverse AKI will save the healthcare system as much as $1 billion each year, in part because fewer patients will develop chronic kidney disease. Canadians will also have earlier access to VT. Commercializing VT will also bring financial returns to Canada and provide training and create jobs for highly qualified personnel.

Cardiovascular Biomarker Translation (CBT) program

Academia-User Partnership: Peter Liu, University of Ottawa Heart Institute; Gabriela Bucklar-Suchankova, Roche Diagnostics International Ltd.
Start Date: October 1, 2014
End Date: September 31, 2017
Total Project Funding: $5.9 Million

Heart failure (HF) is the most costly chronic disease in developed and developing countries. More than 26 million people worldwide are suffering from HF, placing great stresses on patients, caregivers and health care systems. The number of patients will be increasing in the next decades due to ageing populations, therefore improved diagnosis and therapy of HF are important goals of major healthcare organizations.
In keeping with its mission to identify areas of unmet medical needs and develop innovative health care solutions, Roche Diagnostics is partnering with the University of Ottawa Heart Institute (UOHI) to develop a better way to identify and classify HF, based on testing novel biomarkers for the disease. To date, with previous Genome Canada funding, UHOI, University of Toronto and Roche Diagnostics have identified eight novel biomarker candidates for HF characterization and have filed for global patents for these candidates. Now, the partners will conduct further clinical evaluation of the biomarkers, with the intent of developing a HF biomarker panel and an accompanying clinical development program to translate the findings from basic research to clinical benefit of patients. Partnering with Roche has the strategic advantage that their diagnostic test might run on more than 40,000 Roche Diagnostic instruments worldwide.
The Panel aims to assist physicians in earlier identification and classification of HF and support personalized HF treatment that might result in more effective therapies and better outcomes for HF patients. These are important aspects in view of patient burden and costs associated with HF, with particular focus on minimizing length of hospitalization, re-admissions, unnecessary treatments and adverse events. The project aims at promoting Canadian leadership in medical innovation and attracts additional partnerships and investments from major leaders in the global biotech industry.

Development of low cost diagnostic platform for infectious disease testing

Academia-User Partnership: Shana Kelley, University of Toronto; Graham Jack, Xagenic Canada Inc.
Start Date: April 1, 2014
End Date: March 31, 2017
Total Project Funding: $5.9 Million

Conventional lab testing for infectious diseases such as Hepatitis C, malaria and tuberculosis is inefficient and not cost-effective, particularly in developing countries. The development of fast and accurate point-of-care testing for these infections would significantly improve the clinical management of infectious diseases.
For this research, Xagenic will partner with Dr. Shana Kelley, a leading academic from the University of Toronto, to leverage expertise in viral assay development, sensor technology and plastic chip fabrication.
This project will lead to a single affordable and accurate genotyping test to screen for infectious pathogens, and will provide a new solution for rapid disease diagnosis. The low-cost, disposable, battery-powered testing device will identify pathogens in human blood in minutes, which could reduce infectious disease in Canada and around the world, and dramatically improve disease management. The launch of this new product line by Xagenic will result in increased revenues and significant job creation within the company.

Genomics for a competitive greenhouse vegetable industry

Academia-User Partnership: Keiko Yoshioka, University of Toronto; Daryl J. Somers, Vineland Research and Innovation Centre
Start Date: April 1, 2014
End Date: March 31, 2017
Total Project Funding: $2.4 Million

Tomatoes, peppers and cucumbers generate more than $1 billion in annual sales for the Canadian greenhouse vegetable industry. These plants are susceptible to a number of diseases, which threaten crops and decrease profits for producers. In order to maintain a competitive edge, create growth and ensure future success, Canada’s greenhouse vegetable industry needs plant varieties that are resistant to disease.
To address this challenge, Vineland Research and Innovation Centre will partner with Dr. Keiko Yoshioka, a leading academic from the University of Toronto, who has discovered a key gene involved in plant disease resistance.
By using proven gene technologies to enhance disease resistance in greenhouse vegetables, this project aims to develop new commercial traits and varieties for Canada’s vegetable industry.
These technologies will benefit Canada’s greenhouse vegetable industry by adding value to Canadian greenhouse vegetables, and fostering economic growth, increased exports, reducing competition from imports.

SALMON and CHIPS – Commercial application of genomics to maximize genetic improvement of farmed Atlantic salmon on the East coast of Canada

Academia-User Partnership: Elizabeth G. Boulding, University of Guelph; Keng Pee Ang, Cooke Aquaculture Inc. and Kelly Cove Salmon Ltd.
Start Date: April 1, 2014
End Date: March 31, 2017
Total Project Funding: $3.8 Million

Aquaculture companies are increasingly incorporating genomics technology into their breeding programs to develop desirable stock traits for improved growth and disease resistance.
To retain its ability to compete internationally, Cooke Aquaculture/Kelly Cove Salmon will partner with Dr. Elizabeth Boulding and her academic group from the University of Guelph to incorporate genomics marker technology into Kelly Cove Salmon’s current breeding program. This will allow the company to improve the effectiveness of its breeding program and increase the resistance of its salmon to diseases and parasites.
The company aims to implement an advanced genomics technology known as SNP-chips, which when blended with conventional animal breeding techniques, can yield significant increases in the survival rates of eggs and juvenile stages, as well as improved saltwater performance.
The implementation of this genomics technology is expected to increase the quality and sales of Kelly Cove’s salmon, and improve profitability by reducing expenditures on vaccines and medication. Strengthening Kelly Cove Salmon and its parent company, Cooke Aquaculture, will be good news for the more than 1,700 current employees in Atlantic Canada, and will lead to increased employment in rural and coastal communities.