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A synthetic biology platform to support fungal drug discovery

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Overview

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

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Overview

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

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Overview

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.

Leveraging Genomics to Achieve Dairy Net-Zero

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Overview

The Canadian dairy industry supported $7.5 billion in total net farm cash receipts and $16.8 billion in dairy products in 2021, contributing $35 billion to the national GDP. At the same time, dairy accounts for around 1.2-1.4 per cent of total emissions—primarily via methane and nitrous oxide (36 per cent of all livestock emissions). The industry has committed to a Dairy Net-Zero Pledge by 2050. The project goal is to integrate cutting-edge knowledge in genomics and nutrition to deliver a mitigation roadmap for greenhouse gas (GHG) management in dairy production. This includes a comprehensive farm toolbox which will be used to quantify emissions and apply nutritional and genetic strategies to reduce GHG, as well as to inform policy. The roadmap will allow a 55 per cent reduction in GHG emissions from Canadian dairy (30-40 per cent from nutrition and 30 per cent from genomic strategies) at an estimated value of $338 million, with additional potential reduction in beef. A further $100 million in annual net savings is expected through correlated genetic gain in production efficiency and enhanced animal welfare. The shared roadmap for dairy production will inform and align producers, industry stakeholders and policymakers.

Omics Guided Technologies for Scalable Production of Cell-Cultivated Meat

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Overview

The demand for dietary protein is growing with the global population. Since intensive beef farming contributes significant greenhouse gas (GHG) emissions to the atmosphere, cell-cultivated meat is emerging as a complementary protein source to meet this increasing demand with potentially a small fraction of the environmental impact. Similar to how yoghurt and beer are made, these products are cultivated directly from biological cells in a nutrient-rich medium in stainless steel bioreactors. Formation of meat-like textures are triggered by seeding cells into organic scaffolds. To reach cost parity with animal-based meat, however, the cultivating process must become more efficient and less expensive. This project will use genomic, proteomic, metabolomic and GE3LS (genomics and its ethical, environmental, economic, legal and social aspects) approaches to address technical, economic and social barriers to scaling and commercialization of cell-cultivated meat in Canadian and export markets while minimizing the carbon footprint of production. It will do so by creating a catalogue of cells grown from tiny muscle biopsies of beef cattle to find the cell types best suited for cultivated meat production. This will make cell-cultivated meat nutritious and affordable, with the potential to incorporate agricultural by-products into certain stages of production. The project will optimize bioreactor conditions for growing large numbers of cells and develop protein scaffolds that replicate the taste and texture of animal meat to produce meat patty and slab meat (steak-like) prototypes. The project will bring academia, industry, government and NGOs together in a Canadian Cultivated Meat Consortium. This collaboration will enable rapid mobilization of new knowledge, resulting in efficient implementation by Canadian small and medium-sized enterprises. This research will also have wider applications in the production of cell-cultivated chicken, fish and seafood.

Bio-Inoculants for the Promotion of Nutrient use Efficiency and Crop Resiliency in Canadian Agriculture-BENEFIT

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Overview

Many root-associated microbes play an essential role in the way plants extract nutrients from the soil, grow and resist stressors. The BENEFIT project will use genomics to identify Canadian soil microbes, examine their interaction with cereals, brassicas and legumes, develop strains that interact better with crops, and help improve crop productivity. The project team will also investigate genetic factors within the microbes that help them survive the processes used to manufacture, store and deliver bioinoculants. It will also investigate the economics, environmental impacts and social factors associated with inoculant production, application and uptake. By improving crop nutrition and stress resistance using microbes, the requirement for high fertilizer levels, whose production and usage lead to greenhouse gas emissions, will be significantly reduced.

Climate Action Genomics Initiative Climate-Smart Agriculture and Food Systems

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Ontario Genomics is pleased to announce that Genome Canada has launched the Climate Action Genomics Initiative.
Climate change poses a significant risk to our agricultural systems, impacting the availability of food and other vital resources, from fuels to the raw materials used to develop everyday products. In response to this major challenge, Genome Canada’s latest large-scale genomics initiative supports climate change mitigation, and adaptation that leads to mitigation, through strategic investments in climate-smart agriculture and food systems.

The new opportunity, called the Climate-Smart Agriculture and Food Systems initiative, is investing $30 million in cutting-edge genomics research and innovation to reduce greenhouse gas emissions and the carbon footprint of Canada’s food production systems—building their resiliency, environmental sustainability and economic viability.

A distinguishing feature of the Initiative is that it will fund a portfolio of interdisciplinary projects and helps coordinate and connect their efforts with cross-cutting programs for knowledge mobilization, data coordination and implementation across Canada. This portfolio approach allows benefits from one solution to translate into other food production systems or supply chains and cascade impact throughout the broader food system.

The Initiative will deploy a number of funding opportunities that will make up the portfolio.

At the outset, these will include:

Interdisciplinary Challenge Teams 2023 (ICT) Funding Opportunity

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Ontario Genomics is pleased to announce Genome Canada’s new Climate Action Genomics Initiative – Climate-Smart Agriculture and Food Systems funding opportunity, launched in May 2022. Interdisciplinary Challenge Teams (ICTs) represent the largest, key component of the initiative. ICTs are integrated teams of researchers from different disciplines and users who work together to address specific questions, achieve relevant deliverables and, ultimately, reduce the carbon footprint and greenhouse gas emissions of Canada’s agriculture and food systems. As part of the Initiative portfolio, the teams will work toward broader national impacts that manifest value beyond each individual project. The ICTs will provide genomic solutions to help implement agriculture and food production systems that are climate-resilient, socially responsible, economically viable and environmentally sustainable, and that contribute to the mitigation of climate change impacts.

Objectives

The ICT funding opportunity aims to support teams that use genomic approaches to achieve the overall objective of the Initiative, which is to develop and apply genomic tools and technologies to reduce greenhouse gas emissions and mitigate the carbon footprint of Canada’s food systems to ensure they are resilient, economically viable and environmentally sustainable.

The scope of this funding opportunity will include areas where genomic technologies are used to help achieve net-zero emissions by 2050 and reduce the carbon footprint of Canada’s agriculture and food production system. Projects should seek solutions that will increase the value created by production systems without increasing greenhouse gas emissions or amplifying negative impacts on the natural environment. Furthermore, projects should demonstrate how their outputs could be translated into reduced emissions by taking into account the various dimensions of the food system value chain, including production, processing, distribution and consumption.

Applicants must demonstrate how their proposal has significant potential to achieve concrete deliverables by the end of the funding period. Proposals that make a strong case that their deliverables will translate into significant social and/or economic benefits that align with the Initiative’s overall intended impact (i.e., the reduction of greenhouse gas emissions to lessen the carbon footprint of Canada’s agriculture and food production systems) within the shortest time frame possible after the end of the project are particularly encouraged. Consideration will be given to what is reasonable for different research areas.

See example projects here.

To ensure that the objectives of the funding opportunity are met, all applications must address the evaluation criteria established for the competition (see Appendix 1 of funding opportunity).

Available funding and term

  • There is approximately $24 million available for the ICTs from Genome Canada.
  • Genome Canada’s maximum contribution to an approved project will be $3 million.
  • There must be a minimum contribution of $1 million from Genome Canada to each approved project.
  • A project’s eligible costs must be co-funded from eligible sources such that the co-funding is at least equal to the Genome Canada contribution. See the Genome Canada Guidelines for Funding for more details.
  • Successful teams will be awarded funding for a term of up to four years.

It is anticipated that eight to ten ICTs will be funded as part of this Initiative portfolio. The portfolio will also include a Data Coordinating Centre (DCC) as well as a Knowledge Mobilization and Implementation Coordinating Centre (KMICC).

Eligibility

Genome Canada funds can only be awarded to individuals affiliated with one or more of the following types of organizations:

  • Canadian universities, colleges and affiliated institutions including research hospitals and research institutes
  • Not-for-profit organizations (including community or charitable organizations) with an explicit research mandate
  • Canadian non-federal government departments or agencies

See ICT Funding Opportunity and Guidelines for Funding Research Projects for complete eligibility requirements.

Data Coordination and Collaboration Hub (Data Hub) Funding Opportunity

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Ontario Genomics is pleased to announce new funding opportunities in Genome Canada’s Climate-Smart Agriculture and Food Systems Initiative. This Initiative will create a portfolio of projects that will be managed for integration of activities and objectives across the various portfolio elements.

Data are a central component of the Initiative. Data will act as a bridge or connector between projects and as an output supporting the ability to achieve and measure impact across a diverse portfolio of projects.

To that end, this Initiative will fund two cross-cutting coordination Hubs: the Data Coordination and Collaboration Hub (Data Hub) and the Knowledge Mobilization and Implementation Coordination Hub (KMIC Hub). The cross-cutting, coordinating Hubs are designed to support and maximize the impacts produced by a portfolio of selected Interdisciplinary Challenge Teams (ICT) projects.

These Hubs will provide administrative, technical and coordination leadership to the project portfolio with a focus on:

  • Intentionally connecting projects across the ICT portfolio.
  • Supporting the coordination and alignment of portfolio activities across projects.
  • Engaging stakeholders and end users at the portfolio level.
  • Adding value to project outputs.
  • Addressing gaps to create portfolio coherence in achieving impacts

A single pan-Canadian team will be selected to provide data coordination and technical expertise for the portfolio of projects. This team will work with the ICTs and other partners to develop and implement a portfolio data plan.

Data Coordination and Collaboration Hub (Data Hub)

The Data Hub will be responsible for coordinating the scientific data within the portfolio that are required to validate and replicate research findings. Beyond genomic datasets, relevant scientific findings will include information about how the data were generated (e.g., software, workflows and protocols) and the context in which the data should be interpreted (e.g., metadata, policy, socio-economic measures, etc.). Collectively, scientific data outputs from the Initiative will be referred to as “data assets.”

The Data Hub intends to leverage existing digital research infrastructure or software platforms and focus on adding value to these, as opposed to engineering new software. Moreover, the intent is to support the success of individual projects by providing data resources and broader connections to stakeholders. To facilitate climate impact, the Data Hub will help provide a common framework for portfolio outputs. It will not link disparate projects under one overarching research question.

The Data Hub will be responsible for data governance, research data management and analytics. Data governance will ensure that the appropriate data stewardship and data sharing policies are implemented for access, security, and privacy. Research data management will focus on the infrastructure for data storage, processing, and data sharing. This will include advancing data interoperability standards so that data flow and data linkages are optimal. Data analytics will provide value to the portfolio through expertise in statistics, machine learning and artificial intelligence (AI). Analytics would include developing tools and workflows that support ICTs and/or that make the data more useful to external partners.

This funding opportunity aims to support a single pan-Canadian team that will develop and implement a data plan for Genome Canada’s Climate-Smart Agriculture and Food Systems Initiative. First, the team will internally coordinate data-related activities across the interdisciplinary research teams to add value and consistency to the genomic data assets that are being generated. Second, the team will help the projects leverage these data assets to externally advance genomic technologies and policies that have the potential to measurably mitigate climate change, such as by reducing greenhouse gas emissions and/or increasing carbon sequestration.

The broader vision is to co-develop the foundation of a collaborative Canadian climate genomic data hub.

To ensure that the objectives of the funding opportunity are met, all applications must address the review criteria established for the competition (see Appendix 1 of funding opportunity).

Available funding and term

  • Genome Canada will fund one pan-Canadian team.
  • There is up to $4 million available for the Data Hub from Genome Canada (phased approach – see funding opportunity).
  • Co-funding at least equal to the Genome Canada contribution is required (phased approach – see funding opportunity). 
  • The successful team will be awarded funding for a term of up to five years.

Eligibility Criteria

  1. The team must be pan-Canadian with representation from at least three provinces.
  2. The team must include relevant expertise in:
    1. Data governance (i.e., data-sharing, access, security and privacy policy).
    2. Data management (i.e., standards, metadata, data portals and cloud computing).
    3. Data analytics (i.e., bioinformatics, statistics, and AI).
    4. Agriculture science (e.g., crops and livestock).
    5. Climate science (e.g., carbon accounting, climate modelling, geographic information systems).
  3. The project must include public or private sector partner(s) to:
    1. Support computational infrastructure and longer-term sustainability.
    2. Facilitate the downstream use and/or impact of the data resources.
  4. Project leaders from the ICT teams cannot be Project Leaders of the Hubs. However, members of the ICT teams can be involved in the Hub team as co-applicants.

See Data Hub Funding Opportunity for complete eligibility requirements.

Knowledge Mobilization and Implementation Coordination Hub (KMIC Hub) Funding Opportunity

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Ontario Genomics is pleased to announce new funding opportunities in Genome Canada’s Climate-Smart Agriculture and Food Systems Initiative. This Initiative will create a portfolio of projects that will be managed for integration of activities and objectives across the various portfolio elements.

Knowledge mobilization and implementation will be critical to the Climate-Smart Agriculture and Food Systems Initiative. The projects within the portfolio will intentionally and regularly connect, convene and learn from each other to drive greater collective impact.

To that end, this Initiative will fund two cross-cutting coordination Hubs: the Knowledge Mobilization and Implementation Coordination Hub (KMIC Hub) and the Data Coordination and Collaboration Hub (Data Hub). The cross-cutting, coordinating Hubs are designed to support and maximize the impacts produced by a portfolio of selected Interdisciplinary Challenge Teams (ICT) projects.

These Hubs will provide administrative, technical and coordination leadership to the project portfolio with a focus on:

  • Intentionally connecting projects across the ICT portfolio.
  • Supporting the coordination and alignment of portfolio activities across projects.
  • Engaging stakeholders and end users at the portfolio level.
  • Adding value to project outputs.
  • Addressing gaps to create portfolio coherence in achieving impacts

A single pan-Canadian team will be selected to develop and implement a portfolio-level knowledge mobilization and implementation plan for Genome Canada’s Climate-Smart Agriculture and Food Systems Initiative.

Knowledge Mobilization and Implementation Coordination Hub (KMIC)

The KMIC Hub will have broad and specific knowledge, skills, and expertise in Genomics In Society (GIS) – a field that encompasses the environmental, economic, ethical, legal and social aspects of genomics (GE3LS) research – as well as skills in stakeholder relations, partnership development, project management, stakeholder and end-user engagement, policy and regulation, economics, and implementation science. These skills and knowledge areas will equip the KMIC Hub to lead and coordinate cross-cutting GE3LS research and activities at the portfolio level and to launch and manage other knowledge mobilization activities that will help drive the adoption of genomic solutions and mobilize knowledge to help the portfolio deliver net carbon reduction.

The KMIC Hub will focus initially on developing mechanisms and structures to enable the ICT teams to connect with the Hub. The Hub will work with ICTs to refine, cocreate and harmonize project-specific knowledge mobilization and implementation plans into a single unified portfolio plan. This plan should describe an ambitious yet practical vision of what a Canadian KMIC Hub for climate genomics could be and how it will work across the portfolio of projects to support Canada’s goals to achieve net-zero emissions by 2050 and to reduce the carbon footprint of its agriculture and food production system.

The objective of this funding opportunity is to support a single pan-Canadian team that will develop and implement a portfolio-level knowledge mobilization and implementation plan for this Initiative. The team will coordinate knowledge mobilization and implementation activities to ensure that research and investments produce the intended impact and outcome. Consistent with the overall initiative objective, this will include undertaking key GE3LS research at the portfolio level and advancing genomic technologies and policies that have the potential to measurably mitigate climate change by reducing carbon emissions and increasing carbon sequestration.

To ensure that the objectives of the funding opportunity are met, all applications must address the review criteria established for the competition (see Appendix 1 of funding opportunity).

Available funding and terms

  • Genome Canada will fund one pan-Canadian team.
  • There is up to $2.1 million available for the KMIC hub from Genome Canada (phased approach – see funding opportunity).
  • Co-funding at least equal to the Genome Canada contribution is required (phased approach – see funding opportunity).
  • The successful team will be awarded funding for a term of up to five years.

Eligibility Criteria

  1. The team must be pan-Canadian with representation from at least three provinces.
  2. The team should be multidisciplinary and include representatives who have expertise, skills and knowledge in areas such as:
    1. Knowledge mobilization and implementation (e.g., implementation science, knowledge translation and exchange, knowledge brokering).
    2. Research (e.g., implementation science, GE3LS).
    3. Policy and regulation (e.g., shaping and influencing policy, understanding federal and provincial or territorial governments and processes).
    4. Stakeholder engagement and outreach (e.g., consultations, public engagement).
    5. Partnership development (e.g., the ability to identify, establish and maintain partnerships with public, private, non-governmental and academic sectors).
    6. Science communications and marketing.
    7. Economics and economic evaluation.
    8. Evaluation and measurement.
    9. Inclusion, diversity, equity and access (IDEA) and Indigenous knowledge and engagement.
    10. Climate and agriculture science (e.g., genomics in society, crops, livestock).

Please note that different sources of expertise and experience can be pulled in at different phases; the full complement is not necessarily expected at the start of the project.

  1. The project must include partner(s) from the public, community or private sector to facilitate the use and/or impact of the Initiative.
  2. Project Leaders from the ICT teams cannot be Project Leaders of the Hubs. However, members of the ICT teams can be involved in the Hub team as co-applicants.

See KMIC Funding Opportunity for complete eligibility requirements.

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