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

On March 9, 2022, The Honourable François-Philippe Champagne, Minister of Innovation, Science and Industry, announced federal support through Genome Canada to five Ontario Genomics-led and co-led research and development projects as part of the Genomic Applications Partnership Program (GAPP), that will mobilize genomics out of the lab and deliver real-world benefits.

Round 23

Round 20

Round 19

Round 18

Round 17

Round 16

Round 15

Round 14

Round 13

Round 12

Round 11

Round 10

Round 9

Round 8

Round 7

Round 6

Round 5

Round 3

Round 2

Round 1

GAPP Project Descriptions:

Biopesticide with New Modes of Action for Control of Highly Polyphagous Mite Agricultural Pests

Academic Leader / Institution: Vojislava Grbic (University of Western Ontario)
Receptor Leader / Organization: Ken Narva (Greenlight Biosciences, Inc.), Niki Bennett (Ontario Greenhouse Vegetable Growers)
Genome Centre: Ontario Genomics
Total Funding: $4.1M

Pest management is a top priority for Canada’s horticulture greenhouse sector (with farm gate value of $3.9 billion), which provides Canadians with fresh produce year-round. The two-spotted spider mite (TSSM) presents a particular threat to crop security due to its well-documented resistance to pesticides. This project will develop, register and commercialize RNAi biomiticide (dsRNA biopesticides specific for mites) against the TSSM to effectively manage its outbreaks. Project researchers—the first to demonstrate that RNAi-based silencing operates in TSSM—have already developed protocols for high-throughput screening of RNAi targets, provided proof-of-principle that sprayable RNAi works against TSSM, and identified effective TSSM RNAi targets. The project benefits from Greenlight Biosciences’ experience in commercializing and producing RNAi biopesticides and the Ontario Greenhouse Vegetable Growers’ first-hand knowledge of the needs of Canada’s horticulture greenhouse growers. A potential game-changer for mite control, RNAi biomiticide will not only provide the sector with potential economic benefits of ~$600 million peryear. It will also provide growers with an alternative to synthetic chemical insecticides, thus reducing their environmental footprint.
TOP

Developing Novel Bioleaching Process for Ni Recovery from Pyrrhotite Streams

Academic Leader / Institution: Krishna Mahadevan (University of Toronto)
Receptor Leader / Organization: Jan Van Niekerk (Metso-Outotec)
Genome Centre: Ontario Genomics
Total Funding: $6.0M

Current methods for mining and processing ore and metal recovery are energy intensive. They lead to significant waste streams along with energy-related greenhouse gas emissions, exacerbating the climate crisis. In addition, electrification of the transportation sector is a key part of Canada’s climate strategy. Therefore, we need energy-efficient and environmentally friendly methods for mining and recovering critical minerals, such as nickel, that are key components in batteries and electric vehicles. The project will use genomics and bioleaching technologies to characterize and engineer microbial populations to treat pyrrhotite tailings, waste streams of current mining practices, for nickel extraction. Bioleaching technologies are already commercially used for mining, mainly extracting higher-priced metals (e.g., gold, copper) from sulfidic ores. The team will use genomic solutions to enable the widespread application of bioleaching technology, such as meeting the need for faster bioleaching kinetics, improved selectivity and monitoring methods. Metso-Outotec will work with producers/owners to implement the technology on pyrrhotite tailings from Sudbury basin mines. The extraction of nickel from pyrrhotite tailings in Canada has a potential value of $26 billion, can provide a source of critical minerals for production of electric vehicle batteries, and enable significant (>75%) reduction in waste generation from mining processes.
TOP

Enabling personalized genomics in health with the CanPath Data Safe Haven

Academic Leader / Institution: Phillip Awadalla (Ontario Institute for Cancer Research)
Receptor Leader / Organization: John McLaughlin and Trevor Dummer (Canadian Partnership for Tomorrow’s Health)
Genome Centre: Ontario Genomics
Total Funding: $6.1M

Personalized healthcare programs for Canadians require the collection and integration of high-quality data and biosamples from a vast number of individuals to capture the complex factors that can shape an individual’s health over the course of their lifetime. This data must then be made accessible to both public and commercial health decision-makers. In Canada, the sharing and combining of data across jurisdictions, rather than collecting the data itself, is a main barrier to progress in precision medicine. The Canadian Partnership for Tomorrow’s Health (CanPath) is Canada’s largest population health cohort and a gateway
platform to data worldwide. This project will build upon CanPath’s existing infrastructure to democratize access to the platform. It will develop and pilot a data safe haven (DSH), a secure environment within which researchers, clinicians and industry in Canada can access deeply characterized population health and biobank data. The DSH holds the potential to launch Canada to the forefront of genomic medicine globally. It will also support the development of Canada’s biotechnology sector and industry research as well as create the ability to harmonize with other national precision medicine programs. The ultimate result will be earlier diagnosis of disease and medical interventions for Canadians.
TOP

Lowpass Genomic Instability Characterization as a Comprehensive Cancer and Germline Diagnostic Assay

Academic Leader / Institution: Cynthia Hawkins and Uri Tabori (The Hospital for Sick Children)
Receptor Leader / Organization: Aaron Pollett (Mount Sinai Hospital) and Gino Somers (The Hospital for Sick Children)
Genome Centre: Ontario Genomics
Sector: Health
Fiscal Year Project Launched: 2022-2023
Total Funding:

Mutations in the mismatch repair or DNA polymerase genes lead to replication repair deficiency (RRD), a major cancer mechanism leading to genomic instability, microsatellite instability (MSI) and hypermutagenesis (high tumour mutation burden). RRD is a frequent driver of highly prevalent cancers such as colon, stomach, pancreatic, endometrial, and ovarian in adults, and brain and hematologic in children. There is a need to accurately identify patients with RRD as they are often resistant to chemotherapy but exquisitely sensitive to targeted and immuno-therapies; and have cancer predisposition syndromes so they, and their families, need surveillance. Current screening methods are time consuming, costly, and miss patients due to lack of sensitivity and specificity. This project will develop a sensitive and specific, cost-effective diagnostic tool for clinical RRD testing through a clinically validated lowpass genomic instability characterization diagnostic (LOGIC) assay. Benefits include savings to the health care system as well as potential revenue through the licence of this test to others both nationally and internationally.
TOP

Production of Medium-Chain Length Polyhydroxyalkanoate (mcl-PHA) from Food Waste

Academic Leader / Institution: Hyung-Sool Lee (University of Waterloo)
Receptor Leader / Organization: Bryon Wolff (Ecopoly Solutions)
Genome Centre: Ontario Genomics
Sector: Environment
Fiscal Year Project Launched: 2022-2023
Total Funding:

In Canada, 2.8M tonnes of plastic waste was landfilled or leaked into the environment in 2016. Banning of single-use plastics is driving demand for biodegradable plastic (bioplastic). Medium chain length polyhydroxylalkanoate (mcl-PHA) resin has ideal properties for agriculture and packaging films, showing high flexibility, processability, thermal stability and complete biodegradation into simpler, non-hazardous compounds. High production costs of existing mcl-PHA have limited the market potential and applications. Using technology to efficiently transform food waste into higher quality biodegradable resins (i.e., mcl-PHAs) would be a possible solution. This project will enable scale up and commercialization of low-carbon biodegradable medium-chain length polyhydroxyalkanoate (mcl-PHAs), through validation and enhancement of a two-stage process that consists of mixed culture dry fermentation of food waste into medium-chain length polyhydroxyalkanoates (mcl-PHA) for use as biodegradable plastics.
TOP

YCharOS – Antibody Characterization Through Open Science – From Viruses to Human Proteins

Academic Leader / Institution: Peter S. McPherson (Montreal Neurological Institute and Department of Anatomy and Cell Biology, McGill University)
Receptor Leader / Organization: Chetan Raina (YCharOS Inc.)
Genome Centre: Ontario Genomics, Génome Québec
Sector: Health
Fiscal Year Project Launched: 2022-2023
Total Funding:

Commercially available antibodies are key reagents in laboratory research with global sales estimated to be $2-3 billion USD. However, despite the size of the market and the importance of the product there is no independent, state-of-the-art quality assessment body for antibodies and as a result at least half of the antibodies on the market do not perform as required – leading to billions of dollars of wasted funding and a crisis of experimental reproducibility. YCharOS has developed a standardized process that involves knockout cell lines that do not express the target protein. With these cell lines as controls, and with inventive characterization steps, antibody performance against the cognate target protein can be quantified and compared in a range of commercially relevant applications. The long-term business model involves customers such as research organizations, funding agencies or charities paying YCharOS to perform antibody studies on protein targets selected by one of the customers with a goal of attaining $9M in annual revenue by the end of the project and saving Canadian taxpayers $45M annually by enabling our scientists to order the right antibody for their experiments.
TOP

Fast Track Diagnosis of Stress, Disease, Phenology and Growth (FastPheno)

Academic Leader / Institution: Ingo Ensminger (University of Toronto)
Receptor Leader / Organization: Nathalie Isabel (Natural Resources Canada) and Julie Godbout (Ministère des Forêts, de la Faune et des Parcs du Québec)
Genome Centre: Ontario Genomics, Génome Québec
Sector: Forestry
Fiscal Year Project Launched: 2022-2023
Total Funding:

The field of forest genomics has seen unprecedented advances during the past decade. A suite of genomic resources is now available for enhanced genomic selection and can be used to accelerate breeding cycles and to select genotypes that are better adapted and more resilient to future climate change and diseases. The large-scale phenotyping needed to assess adaptive traits in breeding populations with thousands of trees is now the major bottleneck hindering the rapid identification of the traits that enable trees to cope with climate change. This project will develop a drone-based precision phenotyping tool for assessing conventional and novel adaptive traits to complement the genomic selection research and operational programs of Natural Resources Canada and Ministère des Forêts, de la Faune et des Parcs du Québec. The economic impact of climate change is expected to be significant for Canada’s forest sector. The proposed technology will help the Canadian forest sector take advantage of genomic selection tools that may mitigate the impacts of climate change.
TOP

Cardiovascular Biomarker Translation Team 2 – Atrial Fibrillation

Academic Leader / Institution: Peter Liu (University of Ottawa)
Receptor Leader / Organization: André Ziegler (Roche Diagnostics International Ltd.)
Genome Centre: Ontario Genomics
Sector: Health
Fiscal Year Project Launched: 2020-2021
Total Funding: $6.0M

The early detection and treatment of atrial fibrillation is a high priority for patients and physicians. Atrial fibrillation is the most common cardiac arrhythmia in the world, affecting over 25% of the population over age 70. Patients with atrial fibrillation are at an increased risk of a number of complications, including stroke, cognitive impairment, dementia, paralysis and heart failure. There are currently no established biomarkers to guide the clinical management of patients with atrial fibrillation. This project will develop and validate a diagnostic biomarker panel for atrial fibrillation that will enable the early detection of atrial fibrillation and predict the risk of complications. It will also improve the care of patients with this condition by predicting best treatments and outcomes. The results of the improved decision making in atrial fibrillation is expected to save over $200 million per year in health care costs in Canada alone.
TOP

Development of an Epigenomic Profiling Tool to Facilitate Precision Medicine in Early Breast Cancer

Academic Leader / Institution: John Bartlett (Ontario Institute for Cancer Research)
Receptor Leader / Organization: Seth Sadis (Thermo Fisher Scientific)
Genome Centre: Ontario Genomics
Sector: Health
Fiscal Year Project Launched: 2020-2021
Total Funding: $2.4M

Cancer is responsible for 30% of all deaths in Canada. Over the past two decades, what were once considered to be homogenous diseases of a tissue (e.g., breast cancer) are now known to be heterogeneous even within well-established clinical subtypes. To better understand the individual nature of breast cancer in patients, the implementation of integrated ‘omics solutions are needed to understand the combined effects of genomic and epigenomic changes in driving cancer progression and deliver on the promise of precision medicine. Emerging research in breast cancer implicates epigenomics in the regulation of multiple cancer processes including DNA repair and treatment response. The epigenomics data available across cancer driver genes from different ethnic groups, particularly from women of African descent, which further highlights the diagnostic importance of epigenomic features in patient care. This is critical in the equitable delivery of healthcare to patients, since a significant proportion of patients may not be adequately treated due to molecular processes influenced by differences in ethnicity. This project will develop and validate novel panel-based targeted approaches for the evaluation of epigenetic alterations in breast cancer to address two major needs: improved predictive and prognostic assays for all breast cancer patients and a focused study comparing methylation profiles between cancers in Black and Asian minority ethnic groups and other ethnic groups.
TOP

CLEan plAnt extractioN SEquencing Diagnostics (CLEANSED) for Clean Grapevines in Canada

Project Leaders: Sudarsana Poojari (Brock University), Xuekui Zhang (University of Victoria)
Receptor Leader(s): Mike Rott (Canadian Food Inspection Agency) and Bill Schenck (Canadian Grape Certification Network)
Genome Centre: Genome British Columbia, Génome Québec, Ontario Genomics
Sector: Agriculture and Agri Food
Fiscal Year Project Launched: 2020-2021
Total Project Funding: $6.3 million

Grapevine virus disease management has been identified by the grape grower and wine industries as a top priority for long‐term sector sustainability. Losses of over $23 million per year are currently incurred by grape growers due to reduced yield of infected grapes and increased fruit rejection by wineries. To replace the currently infected acreage and meet ongoing renewal of vineyards the industry needs access to 6.7 million domestically produced, virus free vines/year. There will be two separate pathways for implementation and commercialization. To accommodate these demands, the Canadian Food Inspection Agency (CFIA) Sidney Centre for Plant Health (CPH) requires a rapid, cost effective genomic solution to replace the over 30 molecular and bioassays currently performed on , which can take up to three years to complete. By implementing a high throughput sequencing method at the CFIA the costs of analysis will be reduced and analysis time will be reduced for industry priority varieties imported into Canada as well as audit testing from certified foreign sources destined to commercial planting. Reducing the testing time to 10 days allows grape growers to rapidly improve the health of their vineyards. Domestically, the Canadian Grape Certification Network (CGCN) is commercializing high throughput sequencing through its partner Cool Climate and Oenology Viticulture Institute for the certification of propagation material in nurseries and grapevines obtained through CPH, and for monitoring of production vineyards.
TOP

Stopping Enteric Illnesses Early (Sentinel)

Project Leaders: Lawrence Goodridge (University of Guelph), Roger Levesque (Université Laval)
Receptor Leader(s): Chrystal Landgraff (Agence de la santé publique du Canada)
Genome Centre: Ontario Genomics, Génome Québec
Sector: Health
Fiscal Year Project Launched: 2020-2021
Total Project Funding: $6.4 million

In Canada, consumption of contaminated food causes 4 million illnesses, 14,150 hospitalizations and 323 deaths each year, with an estimated annual economic burden of approximately $4 billion, and a major impediment to the identification of contaminated food is that current surveillance methods rely on sick people to seek medical help. The Public Health Agency of Canada (PHAC), in partnership with the University of Guelph and Université Laval, aims to develop a novel, integrated approach to improved foodborne outbreak detection, beginning with metagenomic detection of foodborne pathogens in raw sewage within geographically localized monitoring sites (Quebec City, Guelph, Winnipeg), and monitoring of social media for keywords associated with enteric illness. The tools, methods and datasets generated through this project will be translated for downstream operational use into the network of Canadian foodborne surveillance programs through collaborations between PHAC and its federal/provincial/territorial partners. Implementation is expected to result in a reduction in the amount of illnesses and hospitalizations and economic savings due to a reduction in food recalls through faster detection of outbreaks. A key advantage of this flexible ‘omics and social media surveillance approach is that it can be scaled for rapid detection of other pathogens, and will be immediately utilized to monitor levels of SARS-CoV-2 (the COVID-19 virus) in wastewater, as an early indicator of changing case numbers prior to clinical presentation.
TOP

Caribou Genomics: A National Non-Invasive Monitoring Approach for an Iconic Model Species-At-Risk

Project Leaders: Paul Wilson (Trent University), Micheline Manseau (Environment and Climate Change Canada and Trent University)
Receptor Leader(s): Roxanne Comeau (Environment and Climate Change Canada)
Genome Centre: Ontario Genomics
Sector: Environment
Fiscal Year Project Launched: 2020-2021
Total Project Funding: $4 million

Caribou has been identified as a priority species for recovery by Environment and Climate Change Canada (ECCC) in consultation with provinces, territories, and Indigenous groups. Significant efforts are being made by all levels of government to gain a better understanding of the factors affecting this iconic species, including climate change, and identify the best options for monitoring the effectiveness of recovery options. The goal of this project is to build upon their established caribou genetics research program to implement a genomics platform that will enable i) long-term, non-invasive genomic monitoring of boreal caribou, ii) allow for compatibility among different data generators and, iii) house data in an open access repository that supports analytical toolkits for use by partners. Investing in the implementation of such a genomic platform will allow comparisons through space and time to monitor the recovery of caribou populations and inform conservation efforts.
TOP

Strain development for butanol process addition to existing biodiesel plants

Project Leaders: Lars Rehmann (University of Western Ontario), Nak Paik (World Energy, Hamilton Facility)
Genome Centre: Ontario Genomics
Total Project Funding: $796,500

Biodiesel production from agricultural crops generates a considerable amount of crude glycerol as a byproduct each year. The purification costs for this crude glycerol are high and market demand for refined glycerine is low, resulting in a large fraction of the crude glycerol being incinerated, adding to climate emissions and production costs. World Energy intends to commercialize the production of bio-butanol, a superior biofuel and chemical commodity, from this waste glycerol. A process has previously been developed for the conversion of glycerol to butanol using Clostridium pasteurianum, however the genetic changes that have occurred and the stability of the new strains are not well understood. The aim of this project is to improve the continuous fermentation process by gaining a better understanding of the genetic changes that have occurred in the engineered bacterial strains as well as enhance biobutanol production and fatty acid tolerance through additional genetic modifications. Process scale up is also planned. World Energy generates approximately 66,000 MT of glycerol annually that can be used for bio-butanol production. With initial goals of 30% of the carbon from waste glycerol being converted to bio-butanol, up to $3.7 million additional revenue could be incurred per facility per year.
TOP

Targeting fungal stress responses to provide first-in-class treatment for drug resistant fungal pathogens

Project Leaders: Leah Cowen (University of Toronto), Dominic Jaikaran (Bright Angel Therapeutics)
Genome Centre: Ontario Genomics
Total Project Funding: $6.0 million

The impact of fungal infections on human health in Canada is profound, with recent epidemiological reports of approximately 3,000 invasive fungal infections annually, resulting in approximately 1,000 deaths, with immunocompromised individuals being the most vulnerable. Only three major classes of antifungal drugs are currently available and resistance to each class is increasing at an alarming rate.
This team has established that fungal stress responses are critical for fungal drug resistance and virulence traits and has identified potential antifungal inhibitors of the molecular chaperone and stress response regulator Hsp90. This project couples Schrödinger’s computational drug discovery expertise with the Cowen lab’s expertise in fungal genomics and Hsp90 to enable Bright Angel Therapeutics to rapidly translate existing data supporting the benefit of targeting fungal Hsp90 into an IND-ready drug candidate. The project will pursue a 3-task development approach based on computational design, targeted medicinal chemistry, and biological verification/validation. The project gives Canada a chance to be a global leader in antifungal research. The drug coming to market would be expected to reduce morbidity and mortality due to fungal infections and provide significant savings to the Canadian health care system, which currently spends $345 million on invasive fungal infections.
TOP

Beyond Genomics: Assessing the Improvement in Diagnosis of Rare Diseases using Clinical Epigenomics in Canada (EpiSign-CAN)

Project Leaders: Bekim Sadikovic (Lawson Health Research Institute/Western University), Mike Kadour (London Health Sciences Centre)
Genome Centre: Ontario Genomics
Total Project Funding: $4.8 million

This project will be validating a test, called EpiSign, a proprietary machine learning algorithm built on rare genetic disease datasets (EpiSign Knowledge Database) which analyzes data obtained from wholegenome methylation arrays. This approach is expected to increase diagnostic yield above that of current genetic analyses. This project will validate the conditions for maximizing patient and health system impact and assess the evidence for first-visit and reflex scenarios for adoption of genome-wide DNA methylation testing within Canada. Future clinical adaption would see EpiSign implemented as a bioinformatics service with tertiary genetic centres engaging with their patients and performing the wet lab methylation array data production locally. These centres would then utilize a secure web-based portal to have their data interpreted by the EpiSign Knowledge Database. Expected benefits to Canada include improved quality of life to patients and families who will receive a long-awaited definitive diagnosis. Providing patients with a diagnosis sooner will also have cost benefits, as many tests will be avoided in addition to reducing the reliance on out-of-country commercial laboratories.
TOP

Optimization and Implementation of a Clinical Genome-Wide Sequencing Service for Rare Disease Diagnosis in Ontario

Academic Leader / Institution: Kym Boycott (CHEO Research Institute, University of Ottawa), Martin Somerville (SickKids Research Institute, University of Toronto)
Receptor Leader / Organization: Neeta Sarta (Ontario Ministry of Health)
Genome Centre: Ontario Genomics
Sector: Health
Fiscal Year Project Launched: 2022-2023
Total Funding:

Currently, more than one third of Ontarians with a rare disease lack a genetic diagnosis, despite lengthy and costly investigations. Fortunately, genome-wide sequencing (GWS), in the form of exome sequencing (ES) and genome sequencing (GS), has transformed our ability to achieve a timely diagnosis for rare disease patients. Prior to April 2021, clinical GWS for Ontario patients was only available via an exceptional access program (EAP) and completed in laboratories outside Canada. The EAP program was designed as a ‘safety net’, rather than a regular service delivery model, and presented significant challenges including lack of oversight of turnaround time, diagnostic yield and impact, timing, and outcome of exome vs. genome. To address these challenges, CHEO and The Hospital for Sick Children (SickKids), in collaboration with the Ontario Ministry of Health, developed and is delivering an optimized clinical GWS service as a two-year pilot for individuals with rare diseases that is equitable, accessible, sustainable and performed in Ontario. The pilot project will provide GWS in the form of both ES (n=325 trios) and GS (n=325 trios) to 650 families from CHEO and SickKids. This work will enable robust assessment of diagnostic utility, cost effectiveness, and timeliness of ES and GS to inform provincial and cross-provincial policy related to the long-term organization, delivery, and reimbursement of genome-based diagnostics for rare disease.
TOP

Validating and Improvement of in silico Proteome Screening and Drug Design Technologies by Experimental Drug Discovery for Neurodegenerative Diseases

Project Leaders: Angus McQuibban (University of Toronto), Zheng Li (Cyclica Inc.)
Genome Centre: Ontario Genomics
Total Project Funding: $2.3 million

An important contributor in the decline of productivity in pharmaceutical development is the traditional focus on single target drug design, in which molecules are designed for one protein target. In practice, however, a drug is likely to interact with a number of proteins, sometimes up to 300 in the body, leading to unforeseen and adverse side effects. Cyclica intends to mitigate this problem by using their proprietary Ligand Design™ and Ligand Express®  drug discovery platform. Ligand Design is a multi-targeted and multi-objective in silico drug design platform, and Ligand Express is a cloud-based and AI-augmented off-target profiling and target deconvolution platform that computationally determines polypharmacological profiles. Taken together, Ligand Design and Ligand Express offer an integrated platform to design advanced lead like molecules that minimize off-target effects, while providing insights into structural pharmacogenomics. The team at Cyclica and McQuibban Lab will seek to identify novel solutions for Parkinson’s disease, which will be commercialized jointly by Cyclica and Rosetta Therapeutics. The McQuibban Lab has established assays to substantiate the Cyclica AI predictions. It is expected that these validated platforms will assist Cyclica in further quantifying the benefits of their platforms, including the potential time and resources saved during drug development.
TOP

Systematic evaluation and optimization of immune-targeting modalities for GBM and brain metastases

Project Leaders: Jason Moffat (University of Toronto), Sheila Singh (Empirica Therapeutics)
Genome Centre: Ontario Genomics
Total Project Funding: $4.6 million

There are currently no successful therapeutic regimens for patients with recurrent/refractory glioblastoma (GBM), and brain metastases (BM). Partnering with Dr. Jason Moffat at the University of Toronto and collaborators at McMaster University, Empirica has used genomic screening technology to identify CD133 as a promising target for effective treatment in both in vitro and in vivo models using Chimeric Antigen Receptor (CAR)-T cell therapy.  The overall goal of the project is to design and validate next-generation CD133 CAR-Ts that are genetically engineered to be manufactured “off-the-shelf”- thus less costly – and are less susceptible to immune suppression.  GBM accounts for more than 50% of the approximately 22,850 cases of brain and other nervous system cancers that were diagnosed in 2015. As one of the most aggressive cancer types, with inevitable recurrence, the global GBM market was US $416.8 million in 2015 and is forecast to reach US $1.15 billion by 2024 as the global population increases. In Canada, costs of cancer care have been steadily on the rise, and this project aims to provide more effective and universal treatments for recurrent GBM that can alleviate this economic burden.
TOP

Field Validation of Technologies for Anaerobic Benzene and Alkylbenzene Bioremediation

Project Leaders: Elizabeth A. Edwards (University of Toronto), Sandra Dworatzek (SiREM, a Division of Geosyntec Consultants International Inc.)
Genome Centre: Ontario Genomics
Total Project Funding: $3 million

There are thousands of sites in Canada contaminated with benzene, and the alkylbenzenes toluene, ethylbenzene, and xylenes (collectively known as BTEX), negatively impacting soil and groundwater resources. Current BTEX remediation technologies are often too costly and not applicable at the many sites with prevailing anoxic conditions. Building on previous research that developed, characterized and scaled-up a single methanogenic benzene-degrading culture, this GAPP project’s goal is to demonstrate the efficacy of a broader set of novel and specialized anaerobic bioaugmentation cultures in pilot trials at three different benzene contaminated sites. The team will use metagenome-enabled analysis, groundwater modeling, and tracking of the microbial populations and functional genes associated with anaerobic BTEX biodegradation in the subsurface to improve overall remediation outcomes and to restore ecosystem health.
TOP

Targeted Next Generation Sequencing Panels for Clinical Disease Management

Project Leaders: John Bartlett (Ontario Institute for Cancer Research), Seth Sadis (Thermo Fisher Scientific)
Genome Centre: Ontario Genomics
Total Project Funding: $6 million

Over the past 2-3 years, the Ontario Institute for Cancer Research (OICR) and Thermo Fisher Scientific (TFS) have partnered in developing genomic solutions for rapid adoption into the clinic. OICR’s collaboration with TFS resulted in the commercial launch of the Oncomine™ Comprehensive Assay (v3).  The current project is focused on developing new biomarker signatures based on combined RNA and DNA sequencing with clinical utility in well-characterized patient cohorts to develop clinical diagnostic tests in cancers for pancreatic, prostate and breast cancer patients, and provide a model for adoption in other disease settings.
TOP

NanoString nCounter Vantage 3D platform-based complementary diagnostic tests for precision medicine in pediatric cancers

Project Leaders: Cynthia Hawkins (The Hospital for Sick Children), Sean Ferree (NanoString Technologies)
Genome Centre: Ontario Genomics
Total Project Funding: $4 million

DNA-based next generation sequencing provides important information about DNA alterations however, most oncology drugs are designed against defined molecular targets at the protein level. There is a pressing need for novel diagnostics that interrogate all levels of cellular information, protein, RNA and DNA, in order to best guide therapeutic choices.  This project aims to amalgamate proteomic data with genomic and transcriptomic information to develop laboratory developed (LDT)-complementary diagnostics for the most common pediatric cancers.  Furthermore, the partnership between NanoString Technologies and the SickKids Department of Paediatric Laboratory Medicine will leverage their combined technological, clinical and business expertise.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

Genomics Driven Engineering of Hosts for Bio-Nylon

Project leaders: Deepak Dugar, Visolis Inc. (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 environmentally friendly or sustainable. Therefore, there is strong demand for nylon produced from renewable resources, which requires less energy and results in fewer greenhouse gas emissions. Visolis is developing processes to manufacture renewable polymer such as nylon. Dr. Radhakrishnan Mahadevan from BioZone at the University of Toronto is using a genomics-driven bioengineering approach to convert sugars derived from forestry or agricultural feedstocks 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, Visolis 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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP

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.
TOP