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A Thriving and Resilient Dairy Cattle Industry

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Canada is the world’s fifth largest exporter of agricultural products. Canadian farmers are poised to play a decisive role in meeting the 70% increase in world food demand expected by 2050. Dairy cow growth, milk production, and reproduction, as well as their overall health and welfare, can be strongly influenced by changes in air temperature, humidity, and other environmental factors, including climate change.

Genetic selection plays an essential role in breeding livestock to better cope with rapidly changing climate and environmental factors. In collaboration, Semex Alliance and the University of Guelph will provide innovative methods to select the right genetic traits to breed robust dairy cows that are resilient to environmental stressors, such as extreme hot or cold temperatures while maintaining health, production, and reproductive efficiency.

This proof-of-concept project integrates phenotypic data collected using automated sensor technologies with high-throughput genotypes of dairy cows. By applying genomics-derived processes for identifying healthy, fertile, resilient animals for use in genomic selection programs, this project strengthens Ontario’s dairy sector leadership and provides opportunities for large-scale application in Canada and around the world.

“Breeding animals resilient to heat stress and other environmental challenges exacerbated through climate change is a very important goal that will ensure a safe and sustainable food supply in a changing environment.”

— Dr. Christine Baes, Assistant Professor at the University of Guelph & Canada Research Chair at Livestock Genomics


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Improving Pediatric Cancers Diagnoses and Treatment with Precision Medicine

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The past decade has seen many high-impact, genomics-driven discoveries that have ushered precision medicine as an emerging treatment for pediatric cancer. Pediatric tumours have a different genetic make-up and fewer actionable molecular targets than adult tumours, therefore, precision oncology designed for children promises to greatly improve survival.

There is currently a disconnect, with diagnostic analysis at the DNA level and oncology drugs targeting specific molecular targets at the protein level, leading to response rates of 15-20%. Therefore, there is a pressing need for novel diagnostic tests that examine all levels of cellular information – protein, RNA, and DNA — to accurately guide therapeutic decisions.

The Hospital for Sick Children and US-based NanoString Technologies have collaborated to develop next-generation molecular tools for characterizing children’s cancer. This technology interrogates DNA, RNA, and protein simultaneously, providing better analysis of the patient’s cancer and the information needed to determine the personalized care and accurate assignment of the best class of drugs for each patient. By delivering essential information in a targeted, cost-effective, and timely manner, this diagnostics solution for pediatric cancers will benefit patients, the regional economy, and the healthcare system.

This technology also has the potential in the future as a diagnostic tool for adult cancers. In a previous, successful GAPP project involving the same partners, their commercialized pediatric low-grade glioma (pLGG) and sarcoma tests were recently licensed by the Ontario Ministry of Health and the intellectual property (IP) has been licensed to Singapore and Hong Kong, with interest from Brazil as well. The work performed has created an evidence base for these tests and has resulted in over $1M in instrument and consumable sales for NanoString.

“Our lab is dedicated to improving outcomes for children with cancer. This project will enable us to better predict which drugs will work best for each child’s cancer.”

— Dr. Cynthia Hawkins, Senior Scientist & Principal Investigator, The Hospital for Sick Children


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Upcycling Plastics with Genomics for a Zero-Waste Future

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Over 29,000 tons of plastic leak into the Canadian environment and oceans annually, creating severe environmental problems, including killing 100,000 marine mammals annually. Another 2.8 million tons of plastic are sent to Canadian landfills, which creates a latent problem for future generations, with only 9% of plastic being recycled.

With growing awareness of the detrimental impacts of plastic, governments and manufacturers are working towards a zero-plastic waste future. Under this paradigm, plastics will be made with recycled or biodegradable components. In this project, a Canadian-led team consisting of multiple universities, governments, and industries will drive a shift to a zero-plastic waste future by harnessing genomics technologies to create a circular economy for plastics.

This team will identify and engineer bacteria and enzymes that can break down plastics into recyclable components or valuable fine chemicals more effectively than chemical conversion-based technologies. Additionally, they will conduct a holistic investigation into the impact of these new plastic biotechnologies on society, the economy, and the environment.

Preliminary estimates indicate recycling could save Canada $500 million annually in costs and create 42,000 jobs in new industries. The market for recovered waste plastic in the textiles sector alone is over $600 million per year. We could also save 1.8 million tons of CO2 equivalents per year in greenhouse gas emissions, ensuring that plastics continue to contribute to the economy without adversely impacting the environment.

“To reach zero plastic waste in Canada by 2030, the Open Plastic consortium will develop novel microbiological technology to support the breakdown of plastic waste into marketable recycled products. Our open science framework will empower trainees of the program and existing companies to build ventures for Canada and export.”

– Dr. Laurence Yang, Assistant Professor, Queen’s National Scholar in Systems Biology, Queen’s University.


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Stopping Foodborne Outbreaks Early

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In Canada, consumption of contaminated food causes 4 million illnesses, over 14,000 hospitalizations, and more than 300 deaths each year, with an estimated annual economic burden of approximately $4 billion.

A major impediment to identifying contaminated food is that current surveillance methods rely on sick people to seek medical help instead of public health mechanisms detecting foodborne outbreaks.

The Public Health Agency of Canada (PHAC), the University of Guelph, and Université Laval, are developing a novel, integrated approach to improved foodborne outbreak detection, beginning with genomic detection of foodborne pathogens in raw sewage 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, and territorial partners.

Implementation will reduce the number of illnesses and hospitalizations and increase economic savings due to decreased food recalls through faster detection of outbreaks. Another advantage is that this project can be scaled-up for rapid detection of other pathogens and is currently being utilized to monitor levels of SARS-CoV-2, the virus that causes COVID-19, in wastewater, as an early indicator of changing case numbers before clinical presentation.

“As the COVID-19 pandemic continues, we are seeing increasing emergence of variants of concern (VOCs) and variants of interest (VOIs) which threaten the health and wellbeing of Canadians. The funding provided by Ontario Genomics and Genome Canada is helping my team to develop a genomics-based surveillance platform based on analysis of wastewater, providing a customizable tool for use in controlling the spread of infectious diseases, whether they be food or waterborne, or respiratory borne like COVID-19.”

– Dr. Lawrence Goodridge, Director at Canadian Research Institute for Food Safety, University of Guelph.


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Precision Medicine in Early Breast Cancer

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Breast cancer accounts for approximately 25% of new cancer cases each year and 13% of all cancer deaths in Canadian women. Breast cancer, which was once considered a homogenous tissue disease, is now known to be a complex, heterogeneous disease. Breast cancer in patients is individual and has different molecular make-ups; therefore, precision oncology promises to significantly improve treatment options.

To better comprehend the individual nature of breast cancer in patients, the implementation of integrated ‘omics solutions is 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 treatment response. Additionally, epigenomics data across cancer driver genes from different ethnic groups shows that molecular processes are influenced by differences in ethnicity. This highlights the diagnostic importance of epigenomic features for equitable delivery of healthcare to patients.

Ontario Institute for Cancer Research (OICR) and Thermo Fisher Scientific have collaborated to 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 ethnic minority groups.

“We’re investigating the impact of ethnicity in the biology of breast cancer. We are developing new tools to improve the diagnosis of breast cancer patients and accelerate personalized treatment based on the biology of their disease.”

– Dr. Melanie Spears, Principal Research Scientist, Ontario Institute for Cancer Research.


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Ontario Genomics & CANSSI Ontario Announce $200K for Postdoctoral Fellowships in Genome Data Science

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TORONTO, ON. — Ontario Genomics and CANSSI Ontario have awarded two fellowships of $200,000 total for early-career scientists to pursue work in the areas of statistical genetics, environmental genetics, or the economics and impacts of genomic technologies, in a climate-changing world.

The Ontario Genomics-CANSSI Ontario Postdoctoral Fellowship in Genomic Data Science, originally conceived as a single fellowship in 2021, has since evolved into two awards in 2023.

2023 recipients of Postdoctoral Fellowships in Genome Data Science

The Fellowship offers two-year salary support for up to $50,000 per year. We are delighted to congratulate the recipients of this Fellowship:

1. Dr. Ander Díaz-Navarro, Department of Molecular Genetics, University Toronto
Supervisors: Drs. Lincoln Stein and Bo Wang (University of Toronto)
Project: In Silico Generation of Synthetic Cancer Genomes Using Deep Learning Algorithms

2. Dr. João Pedro Fontenelle, Institute of Forestry and Conservation, Daniels Faculty of Forestry, University of Toronto
Supervisors: Drs. Patrick James (University of Toronto) and Catherine Cullingham (Carleton University)
Project: The Influence of Cyclic Population Outbreaks on Population Genetic Structure Inferences

Drs. Díaz-Navarro and Fontenelle, are profiled, along with information about their background, research, and proposed research projects, here: Díaz-Navarro | Fontenelle

Ontario Genomics is proud to be a partner with CANSSI Ontario to help build research capacity in data science and genomics in Ontario.

About

The Ontario Genomics-CANSSI Ontario Postdoctoral Fellowship in Genome Data Science was created to support research projects that deepen our understanding of genomic epidemiology of infectious disease, using genomics for pathogen surveillance or host-virus genetic interaction by providing salary support for up to two years for an early career investigator pursuing research in the areas of statistical genetics or genetic epidemiology.

About Ontario Genomics:
Established in 2000, Ontario Genomics is a not-for-profit organization leading the application of genomics-based solutions to drive economic growth, improved quality of life, and global leadership for Ontario. As part of its strategic vision, Ontario Genomics (OG) is dedicated to supporting the development of educational resources that demonstrate how genomics plays a vital role to address key challenges in our society. Ontario Genomics also plays a role in advancing genomics projects and programs across the province by supporting the development of proposals, helping researchers access diverse funding sources, and finding the right industry partners to take this research out of the lab to apply it to the world’s most pressing challenges. Since its inception, Ontario Genomics has raised more than $1.27 billion for genomics applied research in Ontario and directly supported more than 9,100 trainees and jobs. OG supports 110+ active projects, 500+ impactful partnerships and has secured $1.34 billion in follow-on investments.

About CANNSI Ontario:
CANSSI Ontario is the Ontario Regional Centre of the Canadian Statistical Sciences Institute (CANSSI). Its goal is to strengthen and enhance research and training in data science by developing programs that promote interdisciplinary research and enable multidisciplinary collaborations.

It\’s Not Magic, It\’s Genomics – Ontario Genomics Annual Report 2021-2022

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Ontario Genomics is pleased to launch our 2021-22 Annual Report

The theme of this year’s annual report, “It’s Not Magic, It’s Genomics”, captures the essence of what is truly possible in this revolutionary, cutting-edge space. Although sometimes it may seem like magic, genomics offers scientifically sound and proven solutions to some of humanity’s biggest challenges: climate change, food insecurity, and acute and chronic disease.

This year, our advancements in agriculture and food have been a particular source of pride for Ontario Genomics. Expanding on our 2020 white paper: Engineering Biology – A platform technology to fuel multi-sector economic recovery and modernize biomanufacturing in Canada, we examined Canada’s opportunity in food innovation and food export. In 2021 we released a first-of-its-kind Canadian report that examines the growing global demand for diversified food production while complementing traditional agricultural approaches, thereby creating up to $12.5B per year in new economic opportunity for Canada.

Ontario Genomics’ multi-sector vision of healthy people, a healthy economy, and a healthy planet through genomics innovations depends on Ontario’s greatest strength to make it all happen: our talent. This year’s annual report features a special overview of our work to prepare the greater public and our future workforce for the transdisciplinary and entrepreneurial jobs of today and tomorrow.

And we are only just getting started. With the power of genomics, we can take the seemingly magical and make it the foundation of Ontario’s economic strength and prosperity for generations to come.

Report – Clean DNA: How Genomics Can Reduce Emissions and Drive Economic Growth for Canada

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The climate crisis demands innovation and new strategies. Scientists are finding potential solutions from an unexpected place: biology. The mapping of the human genome led to breakthroughs in medicine, but gene mapping can apply to many other fields, including agriculture, food, resource extraction and manufacturing.

It’s now possible to harness natural micro-organisms such as bacteria, yeast and micro-algae to manufacture many of the world’s physical materials, potentially with improved performance and fewer emissions. Bacteria is engineered to make proteins. Meat and fish cells are cultivated for burgers, nuggets or sushi. Sugar-based substances can replace petroleum in nylon. Researchers are developing ways to use microbes to devour toxins and bacteria to consume methane.

A recent McKinsey Global Institute report found that 60 percent of physical inputs to the global economy could, in principle, be produced biologically — with an economic value of at least U.S. $2 trillion between 2030 and 2040. This would represent a turn toward more biology-based processes, away from petroleum-based synthetic chemistry, says Bettina Hamelin, president and CEO of Ontario Genomics.

Hamelin notes that nature has made chemicals and proteins for billions of years. Science can reproduce those processes to make products we want and need. “We are building on what is happening in nature,” she says. “Biology, and biotechnology, is the only way toward a sustainable and prosperous future.”

Canada is a world leader in genomics, engineering, chemistry, mathematics, big data, AI and biotechnology. We have all the ingredients for a successful industry, but we risk falling behind other jurisdictions that benefit from significant public and private investment in the sector.

Moving swiftly to a low-carbon society will require enormous effort by governments, businesses and individuals. That should include measures that allow Canadian startups in genomics and biological engineering to scale up their technologies, from public-private partnerships and talent development, to community engagement and building product trust.

Save the Date for Canada SynBio Conference (June 13-15, 2023)

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Ontario Genomics is pleased to announce that our annual Canada SynBio Conference is back for a special fifth-anniversary edition!
Save the Date: June 13-15, 2023

The brings together researchers, industry, government and students to showcase the successes and opportunities of engineering biology in Canada and the world. (Sign Up for Updates)

Canada is at the next frontier of innovation through engineering biology. As the global bio-revolution accelerates around us and Canada embarks on a Canadian genomics strategy, our goal is to continue to foster the connections, networks and communities that will advance a common vision and Canada’s position as a leader in engineering biology.
This conference plays a pivotal role in catalyzing new partnerships, technological development, and attracting investment from multiple sources.

This is a one-of-a-kind conference that brings together national and international leaders in the field of engineering biology to foster inter-sector partnerships and contribute to establishing Canada as an international powerhouse in the bioeconomy.

The 2022 edition of Canada SynBio gathered over 350 national and international leaders and had a vast social media reach of over 272k. Learn more about previous SynBio Conferences.

Join us as we explore emerging themes in engineering biology through a series of engaging presentations, dynamic workshops and interactive networking events.

We look forward to working together to continue the momentum of Canadian engineering biology.

Save the date for the most engaging engineering biology conference you’ll attend all year!