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Ontario Genomics welcomes two new board members and appoints Interim Chair

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Ontario Genomics is pleased to announce the appointment of Dr. Tom Corr and Dr. Diane Gosselin to its Board.

These highly accomplished individuals bring a wealth of insight, experience and expertise in areas crucial to our business that will contribute to fulfilling the mission and achieving the strategic objectives of Ontario Genomics.

Tom Corr is President and CEO of Ontario Centres of Excellence and brings more than 40 years of experience in the technology transfer, ITC, entrepreneurship, academic and venture capital sectors; and Diane Gosselin is President and Chief Executive Officer of CQDM. As a scientific and accomplished leader, Diane has been passionately committed to the financing of innovative biomedical research for over 20 years.

Ontario Genomics is also pleased to announce the appointment of Dr. Jack Gauldie as Interim Chair of the Board, following the retirement of Dr. Brian Underdown who has served as Board Chair since 2011. Jack Gauldie has been an esteemed member of the Ontario Genomics’ Board of Directors for the last seven years.

“The experience and skills of our new members are a fantastic complement to the strengths of our current Board and will assist us as we work towards Ontario Genomics’ future. I look forward to working closely with the Board to develop and execute on a vision that will position genomics technologies as promising solutions to some of our most pressing challenges across Ontario’s economy,” said Dr. Bettina Hamelin, President and CEO of Ontario Genomics.

Ontario Genomics thanks retiring Chair, Dr. Brian Underdown, for his sage leadership, and Board members Dr. Maurice Bitran, Dr. Scott Tanner, and Dr. Cal Stiller for their invaluable service and contributions to Ontario Genomics and the province’s genomics ecosystem.

For more information and detailed biographical notes visit our Board of Directors page.

The Genetic and Molecular Epidemiology Laboratory (GMEL) – Advancing the promise of personalized medicine

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The Genetic and Molecular Epidemiology Laboratory (GMEL) at McMaster University is a premier genomics and proteomics facility offering a broad range of analytical services for academic and industry scientists. Established in 2009 by Guillaume Paré, MD, GMEL offers a broad array of cutting-edge “omics” platforms and technologies for high-throughput analyses of nucleic acids and protein biomarkers. Among the key services that GMEL offers are high-throughput DNA/RNA extraction, quantitation and quality assessment, microarrays (genotyping, gene expression, methylation), next-generation sequencing (exome, RNA, custom target, low-pass whole-genome), and multiplexed protein biomarker assays (>982 biomarkers simultaneously).

GMEL is affiliated with Hamilton Health Sciences’ Population Health Research Institute (PHRI), Thrombosis and Atherosclerosis Research Institute (TAaRI), and McMaster University. GMEL specializes in large-scale population genetic studies, and as such, is capable of handling project sizes ranging from single samples to >10,000 samples. With in-house Principal Investigators, project managers, statisticians, and bioinformaticians, GMEL provides support for experimental design, bioinformatics, statistical analyses, and the interpretation and reporting of results. GMEL is currently involved with multiple epidemiological studies and clinical trials, including CURE, ACTIVE, COMPASS, NAVIGATE ESUS, INTERSTROKE, ORIGIN, and PURE, among others.

While GMEL provides services in all areas of life sciences research, the laboratory has a particular focus on using the most cutting-edge genetic techniques to assess whether the promise of personalized medicine can be realized. The team explores the genetic risk of stroke, diabetes, obesity, and the response to some of the most widely prescribed drugs for those diseases.

Among GMEL’s key achievements was their description that clinical context is important when determining the effectiveness of clopidogrel treatment in patients with acute coronary syndromes or atrial fibrillation. Clopidogrel is used globally to reduce the risk of heart attack and stroke; however, studies by others showed that individuals carrying a CYP2C19 loss-of-function allele have an attenuated benefit from clopidogrel treatment, leading to an FDA black box warning. GMEL’s studies of acute coronary syndrome and atrial fibrillation added context to such findings and showed that the negative effects of loss-of-function alleles do not apply to all patient populations, and that the CYP2C19 gain-of-function allele may be equally or more important than the loss-of-function allele in specific populations. GMEL research also described a pharmacogenetic association between CES1 and the risk of bleed with the novel anticoagulant, dabigatran, and described an association between a COX-2 variant and its effect on aspirin. Research and collaborations from GMEL also identified genetic determinants of lipoprotein concentrations, glucose metabolism, homocysteine concentrations, as well as markers of inflammation, coronary artery disease, stroke, and atrial fibrillation.

Recent studies also resulted in the development of statistical methodologies and bioinformatics tools to identify gene-gene and gene-environment interactions, which have been adopted by multiple other research laboratories. GMEL developed a novel approach to test regional genetic associations, which has recently been expanded to include machine-learning approaches to determine polygenic risk scores. GMEL pioneered the use of Mendelian randomization (MR) to show that diabetes is causally involved in coronary heart disease, and that bile acid sequestrants reduce the risk of heart disease. The team also used MR to show that HER2 is a causal mediator of the protective effect of ACE inhibitors on kidney function.

GMEL has established a broad array of instrumentation for genomic and proteomic analyses. Among such instrumentation is the QIAsymphony instrumentation suite, BioAnalyzer, Fragment Analyzer, Gene Titan Array Scanner, Illumina iScan, Two Ion Torrent Series platforms for exome sequencing, BioNano Genomics Irys System, Thermofisher ViiA7 RT-PCR System, QuantStudio 3D Digital PCR System, Pyromark Q24 instrument, BioMark HD System, Bio-Plex Luminex Multiplex assays, Olink panel assays, and the SomaLogic SOMAscan technology, among others.

GMEL also has the necessary bioinformatics infrastructure (10 dedicated servers) to process large genomics projects at reasonable turnaround times. Among such infrastructure, GMEL uses Cisco Systems platforms, including a Quad Cisco UCSB-B200 bladed system, with combined Intel Xeon based 128 core CPU and 512 GB RAM, running within a VMware ESXi 5.5 environment. GMEL also uses a dedicated Cisco UCS C240 M4 rack application server, with Intel Xeon based 28 core CPU and 384 GB RAM, 3.2 TB Fusion-ion SX300 PCIe SSD and internal 8TB SAS 7.2K SFF HDD, running Linux based distribution.

From start to finish, GMEL provides a full-service analytical platform for researchers’ genomic and proteomic needs. Whether your project includes tens of samples or tens of thousands, GMEL is always willing to establish new collaborations and assist with your research. For more information about GMEL services, please contact Sue McMillan at 905-527-4322 ext. 40377, or smcmill@mcmaster.ca.

StemCore Laboratories: Catalyzing genomics projects in the Nation’s Capital

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StemCore Laboratories is one of Canada’s most advanced genomics facilities, fueling breakthroughs in stem cell research and regenerative medicine, as well as other health-related areas such as cancer, heart disease, and diabetes.

Located at the General Campus of the Ottawa Hospital, StemCore is a core facility of the Ottawa Hospital Research Institute (OHRI) and the University of Ottawa. Founded in 2002 by stem cell pioneers Drs. Michael Rudnicki and Ronald Worton, StemCore supports the research community in Ottawa and beyond to facilitate small, medium, and large-scale high-throughput genomics projects.

Initial major investments from Genome Canada and the Stem Cell Network provided infrastructure funding for StemCore’s startup and facilitated the Stem Cell Genomics Project. Ongoing funding has been provided by the Government of Ontario, The Ottawa Hospital Foundation, the University of Ottawa, Genome Canada, Ontario Genomics, the Canada Foundation for Innovation, and the Stem Cell Network.

Since it’s inception, StemCore has offered a wide array of technologies to support the research community and help researchers answer basic questions about human health and disease. The services currently provided by StemCore include Sanger DNA Sequencing, Next Generation Sequencing (NGS), Single Cell Analysis, and Flow Cytometry.

The DNA Sequencing Facility is equipped with a 3730 DNA Analyzer, the first such instrument in Canada. The 3730 remains a veritable workhorse, supporting numerous applications including DNA sequencing, fragment analysis, and bisulfite sequencing.

NGS services are supported by Illumina’s MiniSeq and NextSeq 500. StemCore’s burgeoning Single Cell Analysis Facility is equipped with 10X Genomics Chromium and Fluidigm C1 platforms. Ancillary instrumentation is available for sample QA/QC (Qubit, AATI Fragment Analyzer, Countess II) and data validation (qPCR, digital droplet PCR). Cell sorting services using the MoFlo XDP are provided as a front-end workflow for downstream genomic analyses.

StemCore’s five-member team has a combined seventy-three years of experience. Working closely with OHRI’s Bioinformatics Core Facility, this expert, dedicated staff is able to provide end-to-end genomics services. Available services include, experimental design, statistical calculations, proof of concept studies, grant-writing support, assay development, and manuscript preparation. Our goal is to assist researchers to ensure project success.

StemCore supports basic, translational, and clinical research projects from multiple disciplines including stem cells and regenerative medicine, personalized medicine, cancer, agriculture and agri-food, public health, environmental genomics, and bio-pharma. A few of the notable research projects facilitated by StemCore include:

The Stem Cell Genomics Project
Led by Dr. Michael Rudnicki, this groundbreaking initiative is providing crucial insight into the genes guiding stem cell identity. During the five-year lifespan of this project, StemCore interacted with twenty-five world-renowned stem cell biologists throughout Canada in this Genome Canada and Stem Cell Network supported endeavour. Five-hundred well characterized embryonic and adult stem cell populations were prepared and profiled. This project resulted in the construction of StemBase, which continues to be an important resource for stem cell researchers around the world.

The Ovarian Cancer Atlas
This innovative project, led by Dr. Barbara Vanderhyden, aims to perform single cell transcriptome analysis of ovarian cancer samples. This data will allow her team to identify and characterize the hierarchy of cancerous and normal cells contained within the tumor.  The data obtained will be correlated with therapeutic response and will provide crucial insight into treatment of this disease.

Duchenne Muscular Dystrophy Identified as a Disease of Stem Cells
For nearly 20 years, researchers thought that muscle weakness observed in people with Duchenne muscular dystrophy (DMD) was primarily due to problems in muscle fibres. But Dr. Michael Rudnicki and his team showed that it is also due to problems inside muscle stem cells, which give rise to muscle fibers. This completely changed the understanding of DMD and could eventually lead to far more effective treatments. Experiments at StemCore played a key role in this discovery by revealing that muscle stem cells express the DMD gene, something that had never before been observed.

Bringing Personalized Medicine to People with Lung Cancer
This project will develop a method to test for multiple genetic mutations all at once in small tumour samples from people with non-small cell lung cancer. These mutations can determine which drug will best work for a given patient. This is particularly important in light of the increasing number of clinically relevant mutations and the limited number of patient cells available for analysis. This project will develop improved protocols that permit rapid, multiplexed testing to allow patients to fully benefit from personalized therapy. This project is funded by Genome Canada and is a partnership between the Ottawa Hospital Research Institute and the Eastern Ontario Regional Laboratory Association. It is led by Dr. David Stewart and Craig Ivany.

For more information about our services please see the StemCore website or contact StemCore’s Director, Dr. Pearl Campbell, at (613) 737-8899 x73110 or pcampbell@ohri.ca. We would be happy to assist you with your project.

Ontario Agriculture & Agri-food Sector to benefit from Regional Priorities Partnership Program

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October 3, 2018, Ontario, Canada – Putting genomics innovations in the hands of those who use them leads to increased competitiveness, economic growth and job creation.

Today, Ontario Genomics (OG), The Agricultural Adaptation Council (AAC) and Genome Canada (GC) announced the launch of the Ontario Regional Priorities Partnership program (ON-RP3) – a new, industry-pull funding program to support the application of genomics innovations aimed at advancing Ontario’s agriculture and agri-food sector.

Ontario’s diverse agriculture and agri-food sector is critically important.  One in every eight jobs in Ontario currently comes from the agriculture and agri-food sector. At over $37B, it accounts for approximately one third of the total GDP generated by the sector in Ontario. While Ontario’s agriculture and agri-food sector is strong and growing, the demands and challenges the sector is faced with are also growing. In the context of enhancing a socially and environmentally responsible industry, genomics-based innovations and technologies provide significant opportunities to advance Ontario’s agriculture and agri-food sector.

ON-RP3 will provide a total of $2 million to support co-led industry-academic, proof-of-concept stage projects that will deliver genomics/genomics-derived tools, products or processes for industry-identified challenges and opportunities within Ontario’s Agriculture and Agri-food Sector.

Through ON-RP3, projects will apply genomic innovations to advance Ontario’s agriculture and agri-food sector and prepare them for industry implementation within two years or less of project completion. To ensure maximum impact, eligible research topics will be focused on the strategic priority areas identified in the sector strategy report, Genomics for Agriculture & Agri-Food: Ontario’s Strategic Opportunity

The ON-RP3 Request for Applications and Program guide and application forms can be found on the OG website and AAC website. Registrations are due to Ontario Genomics by 9 a.m. EST on November 12, 2018.

QUOTES

“Our agriculture and agri-food sector is critically important to Ontario’s economy and genomics technologies, tools and processes hold great promise to accelerate its success. By investing in industry-pull partnership programs, we are enabling the application of innovative genomics-based solutions that will strengthen this sector, create new jobs and drive economic growth for our province.”
–  Dr. Bettina Hamelin, President & CEO, Ontario Genomics

“This priority partnership program will help provide Ontario’s agriculture and agri-food sector with the innovative tools, products and processes it needs to seize new opportunities and efficiently respond and adapt to challenges in our ever-changing and increasingly competitive marketplace.”
– Terry Thompson, Executive Director, Agricultural Adaptation Council

“We are thrilled to support Ontario’s focus on agriculture and agri-food as a key driver of the economy. This novel partnership program deepens the use of and benefits from genomics innovations by building a pathway from proof-of-concept through to application by Ontario’s agriculture industry.”
– Marc LePage, President and CEO, Genome Canada

Media
For further information, please contact us at info@ontariogenomics.ca and info@adaptcouncil.org

New applied genomics projects to spur innovative technologies and job creation in agri-food, health and the environment

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August 16, 2018, Lincoln, Ontario – The application of genomics-based research and development is strengthening Ontario’s economy. It is leading to much needed advancements in farming practices, health care, and environmental stewardship. Bringing together academic researchers with companies to accelerate technology development lays the foundation for increased competitiveness, economic growth and job creation.

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Today, the Minister of Science and Minister of Sport and Persons with Disabilities, the Honourable Kirsty Duncan, announced federal funding for seven new projects under Genome Canada’s Genomic Applications Partnership Program (GAPP).  Three of these projects are based in Ontario – driving $2.9 million of federal funding into the province, and an additional $5.9 million in investments by industry, the Ontario government and other funding partners, for a total of $8.8 million to support the application of genomics innovations in Ontario.  These projects are designed for significant economic and social impacts in the near-term, spurring innovation and commercialization and creating jobs in Ontario.

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The Minister made the announcement at Vineland Research and Innovation Centre. Vineland is partnering with a team of University of Toronto researchers to develop genomics-based technologies that will induce broad-spectrum disease resistance in greenhouse vegetables, allowing new varieties of vegetables to thrive and reducing waste. This will give growers across Ontario and Canada a competitive advantage in a national industry that already generates more than $1 billion annually from retail sales and exports.

In another GAPP project, researchers at McMaster University are partnered with Hamilton-based start-up Adapsyn Bioscience Inc. to use its proprietary technology platform that combines genomic and metabolomic data with artificial intelligence and machine learning to redefine and accelerate drug discovery for novel treatments of a wide spectrum of diseases.  This partnership secured significant foreign and domestic investment and is creating new high-tech jobs in Ontario.

The third Ontario-based GAPP project announced today brings together researchers at the Sunnybrook Research Institute and University of Toronto with Canadian start-up Fusion Genomics to further develop novel infectious disease surveillance tools. Their technology is unique in its ability to detect and genetically characterize infectious viral pathogens through bioaerosols to serve as early warning for disease outbreaks in both humans and agricultural animals. The development of this pre-emergence environmental detection technology will drive a paradigm shift in public health and animal welfare by offering complete genomic data to anticipate outbreaks, inform disease transmission dynamics and enable vaccine design and production.

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Quick facts

  • GAPP is a program that partners researchers with companies and other end-users who will apply their innovations with the goal of increasing and accelerating the positive social and economic impact of Ontario’s and Canada’s genomics R&D capacity.
  • Genome Canada launched GAPP in 2013. To date, approximately $86.1 million, including co-funding has been invested in 23 Ontario-based GAPP projects, fuelling innovations, spurring job creation and attracting foreign investment in Ontario’s health, agriculture & agri-food, fisheries, environment and natural resource sectors.
  • A Genome Canada partnership with Mitacs provides placements and funding for graduate students and post-doctoral fellows to work on GAPP projects within industry partners’ operations. Three post-doctoral fellows will be working with the Ontario-based McMaster/Adapsyn team. The partnership prepares Canada’s next generation of innovators to advance the field of genomics by allowing candidates to apply their knowledge and skills in a real-world setting. Companies, meanwhile, benefit from the high-quality research expertise.

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“Through these collaborative investments, we are enabling the development of real-world genomics-based solutions that will positively impact the health and well-being of Ontarians, the strength of our province, and the growth of our economy.”
– Dr. Bettina Hamelin, President and CEO, Ontario Genomics

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Cracking the code

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As published on the July/August 2018 Water Canada Magazine
By Britney Hess

Ontario unlocks genomic information to propel the circular economy.

News_20180808_01Understanding the genomics of our biological planet is key to addressing the grand challenges facing our world today, from climate change and global population growth to increasing food and energy demands, health issues, and protection of our natural resources.
Every living organism has DNA—a code that directs its biological functions and influences how it grows and interacts with the environment. Genomics is the science of understanding, interpreting, and harnessing this genetic code. In addition to innovations in healthcare, agriculture, and advanced manufacturing, the insights gleaned from genomics are resulting in the creation of environmentally-friendly solutions that are allowing us to improve the water we drink, the air we breathe, and the way we extract minerals and energy from the earth.
Ontario Genomics is a not-for-profit organization focused entirely on stimulating, enabling, and nurturing genomics innovations across all sectors of the bio-economy. Connecting scientists, ideas, and partner organizations from across the province and around the world, Ontario Genomics works with project teams to develop plans and secure funding to enable the development and application of solutions for our circular economy. Several of these projects are developing innovative genomics-based techniques for water monitoring, treatment, and re-use—three of which are highlighted here.

Real-time water toxin detectionNews_20180808_02


Harmful algal blooms (HABs) are a major environmental problem and a growing concern in Canadian waters. Harmful bloom events are caused by cyanobacteria, which has negative impacts on other organisms through production of toxins and oxygen deprivation and severe impacts on human health, aquatic ecosystems, and the economy. Climate change, nutrient imbalances from phosphorus, and warming water temperatures provide optimal conditions for growth of harmful bacteria.
Environmental Bio-Detection Products Inc. (EBPI) is an Ontariobased biotechnology company working with researchers at the University of Guelph and the University of Waterloo to develop a rapid on-site detection platform for water contaminants produced by bacteria found in HABs. The most prevalent of these toxins is Microcystin-LR (MC-LR). The team developed a portable hand-held detector that employs DNA aptamers, which are short DNA strands, to detect and signal the presence of MC-LR contaminants in real-time with sufficient sensitivity to meet World Health Organization drinking water guidelines. The platform has also shown promise for detection of other small molecule contaminants in water samples.

Responsible solutions for wastewater treatment


With recurring droughts and increasing water shortages, wastewater is becoming an ever-more valuable resource. The main objectives of wastewater treatment are to protect the planet from harmful toxins and to restore our water supply.
Based in Renfrew, Ontario, Bishop Water Technologies (BWT) has partnered with Dr. Chris Weisener at the University of Windsor to understand and improve their environmentally-friendly treatment solution for wastewater. By characterizing the microbial ecosystem through genomic sampling, the team is working together to identify and quantify the microbes and to determine their activities in relation to nutrient removal from wastewater. BWT manufactures a novel microbe-based solution called BioCord which is a man-made, inert, polymer scaffold. It provides more surface area for nutrient cycling biofilm to develop, enabling the removal of nitrates and phosphates from wastewater, and reducing point source nutrient loads to the Great Lakes at a fraction of the cost and without any chemicals.

Reducing sulphur contamination in mining wastewaters


Sulfur-contaminated wastewater is a large global mining-related environmental liability. Bacteria drive the key sulfur compound transformations responsible for water contamination, however little is known about how these bacteria affect the sulfur geochemistry in mining wastewater impoundments.
Consequently, these impoundments are viewed as a “black box.” With mines in every province and territory, and as pressures on Canada’s freshwater water supplies grow, there is an urgent need to gain greater understanding and develop sustainable approaches to the treatment of mining wastewaters.
An international team led by Dr. Lesley Warren at the University of Toronto and Dr. Jillian Banfield at the University of California, Berkeley is working to apply genomics, geochemistry, and modelling to mining wastewaters with the objective of developing innovative biological monitoring, management, and treatment tools for sulphur compounds in their wastewaters, as well as support science-informed, cost-benefit decision-making for the mining sector. This project, the first of its kind in Canada and possibly the world, involves three mining and two environmental consulting companies, as well as provincial and national sector industry associations and government.

Genomics is the most transformative technology of the 21st century. Recent advancements are accelerating our knowledge and the opportunity to develop sustainable solutions to protect and treat our waters, as well as innovative applications across all sectors of our bioeconomy to help move Canada towards a circular economy.