Genomic Applications Partnership Program (GAPP)

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

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 1

Round 2

Round 3

Round 5

Round 6


GAPP Project Descriptions:

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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.

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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.

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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.

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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.

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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.

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