Streamlined care for Canadians with mismatch repair deficient cancers through full-service genetic and epigenetic DNA sequencing


Inherited mismatch repair (MMR) deficiency (also known as Lynch Syndrome, LS) affects at least 1 in 300 Canadians. It is a feature of families with heightened risk of colon, brain and gynaecological cancer. Despite a tenfold increased risk, the majority of LS patients are not well identified by the Canadian health system, which takes a piecemeal and overly complex approach to testing, including an excessive use of often-limited tumour tissues. As a result, the length of time to diagnosis is currently 1-3 years in Ontario and up to 6 years in other provinces. While they wait, many Canadians are developing advanced cancers. There is an urgent need for a more efficient, comprehensive MMR screening protocol to identify and treat high-risk patients earlier.

MMR tumours all display a biological feature (microsatellite instability, MSI) that leads to the accumulation of 10,000s of DNA mutations. The project aims to commercialize a MultiMMR tumour test previously developed by the researchers involved. In a single cost-efficient test, this comprehensive DNA sequencing method queries the MMR genes for germline and somatic mutations, MSI status and promoter methylation. MultiMMR conserves tissue, eliminates the need for serial molecular testing and helps differentiate LS from other hereditary cancers.

In partnership with the health solutions company Dynacare, the team will test and clinically validate the MultiMMR panel through a pilot study with various clinics nationally, and validate a new application of MultiMMR to blood cell-free DNA for proactive cancer screening in LS and constitutional mismatch repair deficiency (CMMRD) carriers. Within 3-5 years of completion, the project will reduce LS/CMMRD diagnosis time from 1-6 years to 4 months, saving 50-75% of patients from lifelong cancer screening. It will also reduce healthcare spending on molecular testing by more than 10%, and ultimately improve patient experiences and outcomes.

Advancing Patient Care in Oncology: Integrating Multiscale Transcriptomics for Sarcoma Classification, and Beyond


Cancer is responsible for more than 1 in 4 deaths in Canada, with more than 600 new cases diagnosed daily. Sarcomas – tumours of the bone and soft tissue – are the most challenging cancers to diagnose. The many sarcoma types all have intrinsically different molecular pathogenesis (the process by which a disease develops). Patients with sarcomas, which are proportionately more common in children, face delays of weeks to months until they can be referred to a specialist centre and there are few clinical trials. Current histomorphology and immunohistochemistry approaches to diagnosis are also extremely subjective, requiring clinicians to order 10-20 tests per patient. These challenges lead to ultimately higher health system costs and lower patient survival rates.

Pathologists need a comprehensive approach with better tools to diagnose sarcoma. Project researchers have recently developed a platform to accurately diagnose (with 85-95% accuracy) any sarcoma using its ribonucleic acid (RNA). The highly scalable RNA-Seq-based tumour classification system has been trained on >13,000 tumours and normal samples, and improves with every sample analyzed. This project will validate and implement the platform at two major Toronto hospitals, which together treat around 1,000 patients with tumours of soft tissue and bone each year. The team will implement the initial web platform and will work with two commercial partners: DNAstack to expand the platform to the cloud; and Illumina to expand access to this platform outside of Ontario. It will also compare the platform to World Health Organization classifications to support future global adoption of the platform. In 3-5 years, the platform will be expanded to other types of cancer and altogether better streamline the diagnosis of sarcomas of cancer patients.

A synthetic biology platform to support fungal drug discovery


Fungi have been the source of some of the most effective medicines in history, such as penicillin. However, producing the active medicinal ingredients at scale for R&D has been a key challenge to further fungal drug discovery. This project aims to create a flexible, scalable and cost-efficient synthetic biology platform that supports the synthesis of diverse fungal molecules and produces sufficient compound. It will leverage Kapoose Creek Bio’s (KCB’s) proprietary AI-enabled drug discovery platform (unEarth Rx), which mines nature for new therapeutic drug leads. The platform will use genomics and metabolomics solutions to develop a biosynthetic expression system for genetically-encoded fungal compounds.

The implementation of an in-house synthetic biology platform at KCB will provide a significant competitive advantage, both to accelerate the drug discovery program and enable future clinical-stage partnerships. The project is anticipated to catalyze KCB’s growth and position the company to bring new therapies to market with the potential to counteract cognitive impairment, a major health burden for Canadians, particularly as they age.

Improving patient matching to therapy (PMATCH): streamlining clinical trial criteria to guide precision oncology


Clinical trials are a crucial element of the modern health system. Cancer patients in Canada, however, face substantial barriers to accessing state-of-the-art precision therapies. This is because matching patients to trials is an increasingly resource-intensive and time-consuming task. The disjointed nature of the digital infrastructure means that already overworked clinicians have to spend time parsing through complex eligibility criteria and clinical diagnostic data.

The result is fewer patients are enrolled in trials for which they are eligible. This project will develop PMATCH, an innovative open-source software platform using powerful machine learning techniques to search through complex clinical and genomic eligibility criteria along with the data generated by each patient during their cancer journey, e.g., blood tests, surgery, family history.

Clinicians will be able to match their patients with the best clinical trials for each individual in near-real-time. PMATCH will also standardize the clinical and sequencing data and ensure their FAIRness (findability, accessibility, interoperability and reusability).

Expected benefits of the PMATCH pilot include a 50 per cent increase in patients matched to precision medicine trials across Ontario, acceleration of the identification of actionable biomarkers, increased pharmaceutical support for academic clinical trials, and improved patient experience in trials.

EpiSign International: Health system impact assessment and expanding clinical utilization of epi/genomic testing in rare diseases and beyond


An estimated 1 in 15 children is born with a rare genetic disease. Since 75 per cent of the 4,000 diseases manifest in childhood, children affected by them occupy 25 per cent of pediatric hospital beds in Canada, with diagnostic assessments often exceeding $10,000 per child. Despite advances in genome sequencing, most people with rare disorders remain undiagnosed, resulting in a significant socioeconomic burden related to the so-called “diagnostic odyssey”, impacting treatment, reproductive planning and access to specialized care services. In addition to genetics, a significant cause of birth and neurodevelopmental defects involves prenatal exposures to teratogenic toxins including lifestyle choices, drugs and pathogens.

Toxic exposures are challenging to resolve due to the lack of genetic biomarkers that can be detected with standard molecular tests. In partnership with Canadian biotech start-up EpiSign Inc., London Health Sciences Centre’s Dr. Bekim Sadikovic has developed the first technology, called EpiSign, that uses a patient’s epigenome to diagnose both genetic and teratogenic disorders.

EpiSign’s proprietary and continuously evolving AI-based algorithms compare Illumina microarray-generated epigenetic DNA methylation profiles in a patient’s blood to the EpiSign Knowledge Database, the largest, rare disorder DNA methylation database.

This project will expand clinical adoption of EpiSign as a Tier I test, using new Illumina technology. The project will advance molecular diagnostics of rare disorders and enhance Canada’s leadership in clinical epigenomics. Improved and earlier diagnosis will give patients better access to care options and support networks, while improving health equity and socioeconomic impacts on healthcare systems in Canada and internationally.

Genomic Applications Partnership Program (GAPP)

DNA Banner image for Ontario Genomics

The Genomic Applications Partnership Program (GAPP) funds downstream research and development (R&D) projects that address real-world opportunities and challenges defined by “Receptor” organizations such as industry, government, or not-for-profit entities. These organizations should have the expertise, resources and commitment to commercialize or implement the project’s outcomes. Projects must be active collaborations between the Receptor organization (Canadian or international) and a Canadian academic researcher. Both must play an integral role in the project. These projects are co-funded by Receptors and other stakeholders and must have the potential to generate significant social and/or economic benefits for Canada. The GAPP aims to:

  • Accelerate the application of Canadian genomics-derived solutions from academia to real-world opportunities and challenges defined by industry, not-for-profit and public-sector Receptors.
  • Channel Canada’s genomics capacity into sustainable innovations that benefit Canadians.
  • Enhance the value of Canadian genomics technologies by de-risking and incentivizing follow-on investment from industry and other partners.
  • Foster mutually beneficial collaboration and knowledge exchange between Canadian academia and technology receptors.

GAPP is open to projects across all sectors. For examples of previously funded projects, see Funded GAPP Projects

Key Parameters of the Program:

  • Total project size: $300,000 to $6 million.
  • Co-Funding: Up to 1/3 investment from Genome Canada; Receptor co-funding (cash and/or in-kind) that is equal to or greater than Genome Canada’s contribution; and any remaining co-funding from other eligible sources. For more information, see Section 4 and Appendix 2 of the GAPP Investment Strategy and Guidelines.
  • Project term: 2 – 3 years. Shorter or longer terms will be considered only if strong rationale is provided.
  • Project stage: Small-scale proof-of-concept / pilot projects through to large-scale projects will be accepted. Projects should not be in discovery phase.

Project Eligibility:

To be eligible for the GAPP, a project must:

  • Develop and apply a genomics-derived or genomics-enabling tool, product or process to an opportunity or challenge defined by the Receptor(s);
  • Focus on late stage R&D that will position the innovation for near-term implementation/commercialization;
  • Be co-led by an academic and a Receptor organization in partnership, with active and necessary roles for both; and
  • Demonstrate the potential to generate significant social and/or economic benefits for Canada.

Receptor Definition

A Receptor is defined as an organization that intends to put the resulting innovation into practice (in internal operations, by commercialization, or otherwise making it available to its ultimate users). Eligible Receptors include:

  • Companies (private / public, Canadian / foreign-owned);
  • Industry consortia;
  • Government departments and agencies (federal, provincial and municipal);
  • Healthcare organizations; and
  • Not-for-profit organizations

Small or start-up companies may be considered, as per the Investment Strategy Guidelines.

Application Process:

There is a three-stage, gated application process for this program:

  • Expression of Interest (EOI)
  • Project Pitch
  • Supplementary Proposal

Note that the EOI and Project Pitch content resembles a business case for the proposed project. At each of the above stages, Ontario Genomics has developed a review process, where a panel of industry experts and entrepreneurs provide feedback to help teams navigate the application and increase their competitiveness. These reviews are mandatory for all Ontario projects. Applicants should anticipate the following phases in the application process:

  • Register your intent to apply to Ontario Genomics and obtain EOI form.
  • Complete a draft EOI and submit to Ontario Genomics.
  • Present a face-to-face business pitch to Ontario Genomics’ GAPP Review Panel.
  • Develop the final EOI through active collaboration with Ontario Genomics.
  • Submit EOI to Genome Canada via Ontario Genomics.
  • For teams invited to Project Pitch stage:
    • Present practice pitch to Ontario Genomics before official pitch to Genome Canada.
  • For teams invited to Supplementary Proposal stage:
    • Submit draft applications to Ontario Genomics for panel review before submission to Genome Canada.

Funded 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.

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


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.

Genomics for a competitive greenhouse vegetable industry


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.

Development of low cost diagnostic platform for infectious disease testing


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.