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

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Overview

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.

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

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Overview

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.

Translating OMICS for competitive dairy products

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Overview

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.

Increasing Yield in Canola Using Genomic Solutions

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Overview

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.

Genomics Driven Engineering of Hosts for Bio-Nylon

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Overview

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.

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

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Overview

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.

Validation of TAC receptors for use against liquid and solid tumours

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Overview

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.

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

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Overview

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.

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

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Overview

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.

Broad-range disease resistance in greenhouse vegetables

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Overview

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.