Genomics: Your Solution?

ANNUAL REPORT 2014-2015

Future Solutions

Messages from the President & CEO and Chair of the Board of Directors

Genomics Solutions In Ontario

How is genomics providing solutions in these industry sectors?

Health >

Annual Report 2014-2015

Genomics for Personalized Treatment of Heart Failure (HF)

Heart failure (HF) is the most costly chronic disease in developed and developing countries. More than 26 million people worldwide are suffering from HF, placing great stresses on patients, caregivers and healthcare systems.

The number of patients will be increasing in the next decades due to ageing populations, therefore improved diagnosis and therapy of HF are important goals of major healthcare organizations. In keeping with its mission to address areas of unmet medical needs and develop innovative health care solutions, Roche Diagnostics is partnering with the University of Ottawa Heart Institute (UOHI) to develop a better way to identify and classify HF, based on testing novel biomarkers for the disease.

The aim of this collaboration is to assist physicians in earlier identification and classification of HF and support personalized HF treatment that might result in more effective therapies and better outcomes for HF patients. These are important aspects in view of patient burden and costs associated with HF, with particular focus on minimizing length of hospitalization, re-admissions, unnecessary treatments and adverse events. The project aims at promoting Canadian leadership in medical innovation and attracts additional partnerships and investments from major leaders in the global biotech industry.

Identifying Rare Disease Genes

Gene mutations cause not only well-recognized rare diseases such as muscular dystrophy and cystic fibrosis, but also thousands of other rare disorders. While individually rare, these disorders are collectively common, affecting 1 to 3 percent of the population. It is estimated that as many as half of Canadians with rare disorders are undiagnosed.

Drs. Kym Boycott, Alex MacKenzie and the team are using next generation sequencing technologies to identify the genes implicated in many of these rare diseases. Besides providing important new understanding into human disease, this project will yield other benefits, including avoiding invasive procedures, stopping ineffective treatments, developing earlier and better diagnoses, devising more appropriate treatment, and predicting the chances that one of these rare diseases could be passed on to offspring.

Learn about genomics solutions and innovations in health and contact Kathryn Deuchars, Director, Ontario Personalized Medicine Network & Senior Manager, Business Development & Research.

Agriculture >

Annual Report 2014-2015

Genomics Solutions in Agriculture

OGI supported Ontario Beekeepers' Association (OBA) and Dr Amro Zayed at York University to lead to the development of biological markers that will provide a powerful tool to assist bee keepers in healthy bee colonies. Identifying genetic traits that improve pest resistance in honeybees could address the issue of colony collapse disorder, a serious problem threatening the health of honeybees and the economic stability of commercial beekeeping and pollination operations worldwide.
OGI collaborated with the Canadian Dairy Network in a research project to genotype 1500 cows for genetic evaluation. Current genetic evaluation is primarily done on data from sires and this data will expand the information available and account for the variability seen when the cows are not taken into account.
A project led by Genome Alberta and the Ontario Genomics Institute will help industry growth by using genomics-based approaches to select for dairy cattle with the genetic traits needed for more efficient feed conversion and to lower methane emissions. To date, it has been both difficult and expensive to collect the data required for such selection. The research team led by Dr. Filippo Miglior of the University of Guelph and Dr. Paul Stothard from Livestock Gentec at the University of Alberta want to change that by using the latest genomic approaches and the award-winning phenotyping platform developed by Growsafe in Alberta, to collect and assess the required data to carry out the selection.

Learn about genomics solutions in agriculture and contact Elaine Corbett, Manager, Business Development & Research.

Mining >

Annual Report 2014-2015

Tapping into the potential of genomics in mining

Lesley Warren, McMaster University, and Stephanie Marshall, Glencore, discuss how their collaboration can help better understand the role of microbes and how genomics information can be used to meet the goals of environmental stewardship, efficiency and sustainability in the mining industry.

Phytoremediation of nickel-copper mine tailings

Ambiotek (página web en español) is an emerging company developing environmental solutions including a phytostabilization technology for use towards mine tailings reclamation. This technology was initially developed for tailings in Chile. OGI helped Ambiotek partner with researchers at the Vale Living with Lakes Centre at Laurentian University (Drs Daniel Campbell, Nathan Basiliko and Nadia Mykytczuk) to characterize the rhizosphere microbial communities of plants that grow on tailings near Sudbury, Ontario with the long term aim of further developing the phytostabilization technology for colder environments.

Learn more about the potential of genomics in mining and contact Helen Petropoulos, Director, Business Development & Research.

Water >

Annual Report 2014-2015

Genomics has the potential to help develop and optimize tools and technologies for the water sector

OGI catalyzed a collaboration between the Walkerton Clean Water Centre and Dr. Trevor Charles from the University of Waterloo. OGI provided seed funding to help improve the efficiency and improve quality operations of slow sand filtration systems for drinking water treatment in small and remote communities.

OGI’s Pre-commercialization Business Development Fund (PBDF) supported Dr. Bernie Kraatz from the University of Toronto and ENDETEC, a global company focused on innovative sensor solutions for water safety, in their work towards developing a biosensor for simple, low-cost, rapid, on-site detection of bacteria in water samples.

OGI introduced Bishop Water Technologies (BWT) to the power of genomics and to Dr. Christopher Weisener from the University of Windsor. Together they are using metagenomics to help improve and optimize BWT’s “BioCord” technology for municipal and industrial wastewater treatment.

Learn about the potential of genomics for the water sector and contact Sugy Kodeeswaran, Senior Manager, Business Development & Research.

Forestry >

Bioproducts >

Fisheries >

Annual Report 2014-2015

Fisheries: A Genomics Solution

Accelerated melting of Arctic sea ice due to climate change is increasing access to arguably the last remaining under-exploited fishery in the Northern Hemisphere.

Dr. Virginia K. Walker of Queen’s University and colleagues together with Nunavut communities will integrate Traditional Ecological Knowledge (TEK) with leading-edge genomic science and bioinformatics to gain an understanding of fish stock demographics and structure. This will allow monitoring of their migration, characteristics and adaptation and inform strategies to maintain genetically diverse and healthy stocks.

Increased accessibility, primarily to Arctic char, but also to Arctic cod and Northern shrimp, coupled with a developed, sustainable, science-based fishing plan will offer opportunities for employment and economic benefits for Nunavut communities as well as greater food security.

The Walker Project website is www.arcticfishery.ca.

To learn more about the potential of genomics in fisheries, contact Kim Flock, Manager, Research & Business Development.

“Arctic cod from multi-mesh gill nets” (top right) photo credit: Peter Van Coeverden de Groot

Personalized Medicine >

Annual Report 2014-2015

Personalized Medicine and Mental Health: A Genomics Solution

One in five Canadians will experience some form of mental illness in their lifetime. Treatments are available but each person responds differently to them, in part because of their genes. A clinically proven genetic test analyzes an individual’s genes and recommends the optimal drugs for that person along with dose adjustments among the 33 most commonly prescribed antidepressant and antipsychotic drugs.

Clinical testing in the United States has shown that this test doubles the odds of a patient responding to antidepressant medication. More than 200,000 patients have received these tests in the United States. Assurex Health, the company that developed this test, is partnering with Dr. James Kennedy and his team at Toronto’s Centre for Addiction and Mental Health (CAMH) to develop an enhanced genomic test. Assurex Canada has been set up to bring this test to Canadians. The test will incorporate new genomic markers discovered at CAMH that influence how some patients respond to psychiatric medications.

Assurex Canada and CAMH will together validate these markers for their ability to predict efficacy and side effects of psychiatric medications; the most predictive markers will be integrated into the test. When launched in 2017, the test is anticipated to reduce the need for “trial-and-error” approaches to prescribing and increase the likelihood that people will respond optimally to the medications prescribed for them, while reducing side effects. This will increase the proportion of patients who stay on their medications and improve their quality of life. It will also save the Canadian healthcare system an estimated $4,000 per year per treatment-resistant patient and will generate royalty revenues for CAMH as the test is marketed internationally.

Learn more about The Ontario Personalized Medicine Network (OPMN), and contact Kathryn Deuchars, Director, Ontario Personalized Medicine Network & Senior Manager, Business Development & Research.

Highlights of the Year

0

publications

*Genome Canada supported research

OGI successfully managed research to provide solutions to projects with budgets over

50.5M

0

Full-time jobs created

*Genome Canada supported projects

Total Genome Canada contribution for research competitions was

11.6M

Catalyzed flow of

47.5M

of private R&D into Ontario

Sparking new Solutions

In 2014-2015 OGI strategically cultivated, funded, and managed large-scale genomics projects and the genomics resources they created, as well as technology development associated with these projects.

Genomics Innovation Network (GIN)

Annual Report 2014-2015

Genomics Innovation Network (GIN)

Genome Canada supports 10 “Nodes” that together form Canada’s Genomics Innovation Network (GIN). Each Node provides researchers across Canada and internationally with access to leading-edge technologies used in genomics, metabolomics, proteomics and other related areas of research. They also assist researchers in the development of research proposals by providing advice on appropriate technologies, study design, data analysis, and bioinformatics that improve the quality of the research. As a Network, the Nodes collaborate and harness their collective power for the advancement of genomics research.

Three of these GINs were funded or co-funded in Ontario. Two Nodes in Quebec were co-led by Ontario Genomics Institute:

Toronto Centre for Phenogenomics

Node leader: Colin McKerlie
The Toronto Centre for Phenogenomics is the largest research facility in Canada designing, producing, and studying more than 250 mouse models each year with specific genetic mutations that allow researchers to learn more about the causes of disease and develop improved treatments.

Network Biology Collaborative Centre

Node leaders: Jeff Wrana, Anne-Claude Gingras
The Network Biology Collaborative Centre provides services to Canadian scientists with a focus on functional understanding of the role of genes and gene products in human health and the impact of their alteration on the initiation and progression of disease.

The Centre for Applied Genomics

Node leaders: Stephen Scherer, Lisa Strug
The Centre for Applied Genomics provides genome sequencing and analysis, and other genomics services, to the Canadian and international research communities. Its development of new algorithms and methods for the analysis of whole genome sequence data underpin major, international research collaborations.

View a map of all Nodes in Canada.

Sharing Big Data for Health Care Innovation

Towards a Sustainable Fishery for Nunavummiut

Annual Report 2014-2015

Towards a Sustainable Fishery for Nunavummiut

Affordable access to safe, nutritious and culturally relevant food is one of the biggest challenges facing the Nunavummiut, the people of Nunavut. This lack of affordable, nutritious foods is linked to growing health problems, including diabetes and childhood rickets.

Accelerated melting of Arctic sea ice due to climate change is increasing access to arguably the last remaining under-exploited fishery in the Northern Hemisphere. This increased accessibility, primarily to Arctic char, but also to Arctic cod and Northern shrimp, coupled with a developed, sustainable, sciencebased fishing plan will offer opportunities for employment and economic benefits for Nunavut communities as well as greater food security. It is the Nunavummiut that should be the beneficiaries of these resources, rather than foreign fishing fleets.

Understanding the genetic differences among these fish populations is key to developing that plan. Dr. Virginia K. Walker of Queen’s University and colleagues together with the Nunavut communities will integrate traditional and local knowledge with leading-edge genomic science and bioinformatics to gain an understanding of the genomes of these fish populations. This will allow monitoring of their migration, characteristics and adaptation and inform strategies to maintain genetically diverse and healthy stocks.

The project with a total funding of $5.6 million for Genome Canada's 2014 Large-Scale Applied Research Program (LSARP), will work toward strengthening Nunavut fisheries, augment sovereignty claims in the Canadian Arctic, increase employment and economic development opportunities, ensure access to a healthy food source, and improve food security for the people of Nunavut.

Project leaders are: Virginia K. Walker, Stephen C. Lougheed, and Peter Van Coeverden de Groot, Queen’s University; Stephan Schott, Carleton University.

“Arctic cod from multi-mesh gill nets” (top right) photo credit: Peter Van Coeverden de Groot

The Genomic Applications Partnership Program (GAPP)

Annual Report 2014-2015

Funded by Genome Canada, The Genomic Applications Partnership Program (GAPP) represents a key element in Genome Canada’s strategic plan towards funding downstream research and development (R&D) projects that address real world challenges and opportunities as identified by industry, government, not-for-profits and other “Users” of genomics research. These projects were led by the Ontario Genomics Institute in Round 3 of this competition.

Toward a national framework for clinical cancer genome profiling in Canadian hospitals

Project Leaders: Suzanne Kamel-Reid, Princess Margaret Cancer Centre (University Health Network); Jeff Sumner, LifeLabs Medical Laboratory Services Lead Genome Centre: Ontario Genomics Institute

Total project funding: $6 million

Approximately 200,000 Canadians are diagnosed with cancer each year. More than one in four of these patients can benefit from targeted treatment based on a genomic analysis of their tumours. Indeed, genome-based tumour profiling helps treat patients with the right drug at the right time, improving outcomes and saving lives. However, at present this breakthrough testing is not widely available and is currently only being used in a clinical trial setting for patients with advanced cancers at one Toronto Hospital, and its collaborators. This genomics project between Dr. Suzanne Kamel-Reid of Princess Margaret Cancer Centre (University Health Network) and LifeLabs Medical Laboratory Services, Canada’s leading diagnostic lab company, is the first step in providing national market access to this potentially vital information. In addition to saving lives, personalized cancer medicine data can reduce healthcare costs significantly, as the cost of treatment can be up to 10 times more than the cost of laboratory genomic cancer testing. Projected to total Canadian healthcare expenditures, genomic tumour profiling is expected to save the healthcare system hundreds of millions of dollars annually. 2 The genomics project aims to develop a cloud-based cancer genome analysis infrastructure and shared interfaces between Princess Margaret and LifeLabs that will make this vital information available to all Canadians.

Novel Rapid Diagnostic Tools for Lung Transplantation: Bringing Omics to the Bedside

Project Leaders: Shaf Keshavjee, University of Toronto; Thomas Hartnett, United Therapeutics (Lung Bioengineering Inc.) Lead Genome Centre: Ontario Genomics Institute

Total project funding: $6 million

A considerable number of patients needing a lung transplant die due to a lack of donor organs deemed suitable for transplant. Now, a proposed genomics approach to assessing donor lungs has the potential to save thousands of lives while reducing healthcare costs. The project, led by Dr. Shaf Keshavjee of Toronto’s University Health Network (UHN) in collaboration with the U.S. biotech firm Lung Bioengineering Inc., a subsidiary of United Therapeutics Corp., intends to develop a genomics-based diagnostic test to determine whether a donor lung meets transplant requirements. At present, such evaluations are based on physiological assessments alone. As a result, less than 15 per cent of lungs, the healthiest, are deemed suitable for transplant, leaving unused countless “marginal” lungs that also could save lives. A genomics-based analysis could increase the number of transplant-acceptable lungs to nearly 50 per cent, resulting in a greater number of patients receiving this life-saving intervention. Using diagnostic test kits, donor lung conditions would be precisely monitored through biomarker analyses. Under Dr. Keshavjee’s research leadership, some biomarkers have already been isolated that can predict lung quality. Building on these findings, this new initiative will result in the creation of rapid diagnostic tools that could be used in transplant centres around the world. The world’s first successful clinical lung transplant took place at Toronto General Hospital in 1983. Today’s genome project has the potential to further cement Canada’s global leadership in this high-tech medical sector. This initiative may also reduce the economic burden on the Canadian healthcare system while improving overall quality of life for lung-transplant patients.

Applying a Solution

Spark

OGI supports investment into high risk early stage idea development and commercialization. Investment through the SPARK program was designed to help fund very early stage, highly innovative ideas.

In 2014-2015, three OGI-funded projects in Ontario each received $30,000:

Methane to Bioplastics: Bacterial strains for production of high value bioplastics on methane feedstock >

Methane to Bioplastics: Bacterial strains for production of high value bioplastics on methane feedstockLed by Trevor Charles, University of Waterloo, this project will focus on using bacterial genomics and synthetic biology approaches to create bioplastics. The use of plastics is widespread in society. However, the detrimental environmental consequences of plastic pollution have raised the need for alternatives. This work, using waste methane as feedstock, could lead to the production of valuable renewable materials from a potent greenhouse gas that is a key waste product of landfills and wastewater treatment systems.

Genomic Ancestry in a non-model wildlife species at risk, the Eastern Wolf >

Genomic Ancestry in a non-model wildlife species at risk, the Eastern WolfLed by Brent Patterson and Linda Rutledge, Trent University and the Ontario Ministry of Natural Resources & Forestry (OMNRF), this project aims to improve wolf conservation in Ontario. The research team will be collaborating with scientists at Princeton University to validate and optimize a rapid and efficient genetic mapping approach on the Eastern Wolf, which has the potential to make genomics more accessible to labs with limited resources and provide researchers with an effective, low-cost methodology for genomic analysis of fish and wildlife populations.

Forestry: Is genomics a solution? >

Forestry: Is genomics a solution?

Creating a Non-Invasive Norway Maple

Led by Travis Banks and Darby McGrath of Vineland Research and Innovation Centre, this project will initiate work to develop a Norway maple tree that is no longer invasive, in an effort to keep our cities green. Pests and disease are destroying city trees and there are no alternatives suitable to survive the extreme conditions of Ontario urban environments. Having fallen out of favour because of invasiveness, Norway maple was used extensively as an urban tree, which thrives in polluted and compact soils, withstands hot summers and cold winters, and suffers few diseases. SPARK funding will enable DNA sequencing of the Norway maple genome and update methods to identify new Norway maple plants that are unable to create fertile seeds.

Pre-commercialization Business Development Fund (PBDF)

OGI's Pre-commercialization Business Development Fund (PBDF) is a unique early stage investment fund that helps companies to test a proof of principle in order to drive the economic impact of outcomes of genomics and proteomics research and technology development. Specifically, it aims to provide early-stage funding as researchers move towards commercial applications and to speed up transfer of products from lab to marketplace. The fund invests up to $100K per project.

Water Safety >

Water Safety

ENDETEC, a global company focused on innovative sensor solutions for water safety, in collaboration with Drs. Heinz-Bernhard Kraatz (University of Toronto) and R. Stephen Brown (Queen's University), will develop a DNA biosensor for simple, low-cost, fast, on-site detection of bacteria in water samples. Current culture-based techniques for water monitoring are time-consuming and expensive, which can lead to delayed results and decision making for users that manage water resources. The PBDF funding will support proof-of-concept experiments validating the performance of the DNA biosensors with environmental samples. The first applications will be for recreational water (including beaches) and treated wastewater. "DNA biosensor technology can potentially be a game-changer for water monitoring, providing truly rapid monitoring and expanding the range of organisms that can be detected," said Mr. Doug Wilton, VP Operations for ENDETEC.

Cancer Treatment >

Cancer Treatment

Formation Biologics Inc. (formerly AvidBiologics) is an oncology drug development company dedicated to anti-cancer biologics. Through PBDF funding, the company aims to develop AVID200, a novel anticancer agent targeting a protein expressed by a variety of solid tumours including lung, breast, and head and neck. Specifically, Formation Biologics is developing antibodies that are linked to highly toxic chemotherapeutic drugs, and these antibody-drug conjugates (ADCs) target a specific cell surface receptor known to contribute to the etiology of various cancers. ADCs can selectively recognize specific proteins in cancer cells without damaging most normal tissues. This type of cancer therapeutic has the potential for superior safety and efficacy compared to older generation treatments. Using the PBDF investment, the company will perform a pilot safety study of this ADC to accelerate their drug development process for AVID200. "We are very grateful to have received an investment from the Ontario Genomics Institute to further development of this important anti-cancer therapeutic," said Ilia Tikhomirov, President and CEO of Formation Biologics. "Programs like OGI's Pre-commercialization Business Development Fund are crucial to the success of early stage biotechnology companies in Ontario," he continued.

Safe Crops >

Safe CropsGlobal soybean production is threatened by an aggressive fungus responsible for Asian Soybean Rust (ASR), which can cause yield losses of up to 80percent. ASR is currently controlled by fungicides. However, resistance to these chemicals can be seen. Dr. Charles Després (Brock University) is identifying activators designed to stimulate soybean plant immunity, an alternative mode of action to protect the crop. These chemicals can be used alongside traditional fungicides to ensure long-term global food security. With the help of the PBDF and support from Syngenta, Dr. Després will validate his product. Potentially, his technology platform will allow the agriculture industry to identify new chemicals that will optimize production and safety from ASR and support precision agriculture for better decision making, and high yields.

Policy as a Solution

Ontario Personalized Medicine Network (OPMN)

In 2014, in support of the Ontario Personalized Medicine Network, the Ontario Genomics Institute has conducted stakeholder consultations across the province to identify potential gaps and opportunities in the application of “personalized medicine” in Ontario. To that end, the OPMN released the following findings:

Financials

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Independent Auditors' Report

To the Board of Directors of Ontario Genomics Institute

We have audited the accompanying consolidated financial statements of Ontario Genomics Institute, which comprise the consolidated statement of financial position as at March 31, 2015, the consolidated statements of operations, changes in net assets and cash flows for the year then ended, and notes, comprising a summary of significant accounting policies and other explanatory information.

Management's Responsibility for the Consolidated Financial Statements

Management is responsible for the preparation and fair presentation of these consolidated financial statements in accordance with Canadian accounting standards for not-for-profit organizations, and for such internal control as management determines is necessary to enable the preparation of consolidated financial statements that are free from material misstatement, whether due to fraud or error.

Auditors' Responsibility

Our responsibility is to express an opinion on these consolidated financial statements based on our audit. We conducted our audit in accordance with Canadian generally accepted auditing standards. Those standards require that we comply with ethical requirements and plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements are free from material misstatement.

An audit involves performing procedures to obtain audit evidence about the amounts and disclosures in the consolidated financial statements. The procedures selected depend on our judgment, including the assessment of the risks of material misstatement of the consolidated financial statements, whether due to fraud or error. In making those risk assessments, we consider internal control relevant to the entity's preparation and fair presentation of the consolidated financial statements in order to design audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the entity's internal control. An audit also includes evaluating the appropriateness of accounting policies used and the reasonableness of accounting estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements.

We believe that the audit evidence we have obtained is sufficient and appropriate to provide a basis for our audit opinion.

Opinion

In our opinion, the consolidated financial statements present fairly, in all material respects, the consolidated financial position of Ontario Genomics Institute as at March 31, 2015, and its consolidated results of operations and its consolidated cash flows for the year then ended in accordance with Canadian accounting standards for not-for-profit organizations.

Chartered Professional Accountants, Licensed Public Accountants

July 28, 2015
Toronto, Canada

Our Team

Corporate information

Ontario Genomics Institute

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Toronto, ON M5G 1M1

CANADA

E-mail: info@ontariogenomics.ca

Website: www.ontariogenomics.ca