Genomic research projects receive $60M in funding

Ottawa, ON – Genome Canada has announced a total of $60 million in funding for 16 genome-research projects across the country.

Each of the projects will focus on important questions and challenges faced in their respective sector and involve end-users of the technology. In addition, each project will see researchers participate in an international partnership that is working to understand the function of each one of the 20,000 genes found in the human genome.

“This competition is part of Genome Canada’s mandate to fund a wide range of large-scale genomics research projects through a competitive process,” said Dr Pierre Meulien, president and CEO of Genome Canada. “We are proud of the process and the results which are a testament to the high level of excellent applied research being carried out in this country.”

The project are as follows:

Project Leaders: Patrick Tang and Judith Isaac-Renton. Lead Genome Centre: Genome British Columbia. Project title: Maintenance of Canada’s precious fresh water supplies. Scientists will use the new field of metagenomics (the study of microbial communities) to compare microbes of healthy watersheds with those that have been affected by pressures from industry, population growth, environmental degradation or changing land uses. Changes in the microbial population will help to serve as an early warning of problems in a watershed. They will also develop tools to match the microbial fingerprint of contaminated watersheds to the specific source of pollution. An ongoing GE3LS-based consultation will be undertaken with stakeholders to facilitate wider adoption of this new approach to monitoring the health of watersheds, engaging with the potential polluters in a proactive manner to avert polluting events.

Project Leader: Richard Hamelin. Lead Genome Centre: Genome British Columbia. Project title: Keeping our forests healthy. The scientists are developing DNA-based diagnostic tests to identify and monitor pathogens. This will generate a number of important benefits, including preventing invasive pathogens from harming our forests, assisting the forest and nursery industries with plant and product certification and creating a competitive advantage for Canadian companies in international markets. It will also produce annual economic benefits in the tens of millions of dollars by reducing losses from disease. There are significant commercialization opportunities through the sale of these diagnostic tools on world markets. The project will undertake the largest forest pathogen sequencing effort in the world, helping to fill in gaps in our understanding of these threats. An integrated GE3LS component will generate insights into the commercialization of these tools and examine the public policy issues and social acceptance of using genomics technologies in the current forestry management framework.

Project Leaders: Leonard Foster and Stephen Pernal. Lead Genome Centre: Genome British Columbia. Project title: Saving endangered bee populations. Researchers are developing new tools to identify disease-resistant bees as well as new treatments tailored to bee pathogens. This marks the first, industry-wide step to reverse the decline in honey bees. Successful implementation will potentially generate benefits of over $200 million annually by increasing the bees available for pollination and boosting honey production.

Project Leaders: Lindsay Eltis and William Mohn. Lead Genome Centre: Genome British Columbia. Project title: Towards a new range of bioproducts from forest biomass. The scientists are exploring the microorganisms found in soil that naturally degrade biomass. Unlocking the potential of forest biomass will lead to better forest management practices and improve the economics of lignin-based products. To expedite the wider use of these innovations, an integrated GE3LS component is investigating key technological, commercial organizational, environmental and societal issues.

Project Leaders: Carl Douglas and Shawn Mansfield. Lead Genome Centre: Genome British Columbia. Project title: Clean energy from the poplar tree. The scientists are studying the genetic underpinnings of tree growth as well as the traits associated with biofuel suitability in two species of poplar. Their overall aim is to develop short-rotation, fast-growing trees that can grow in a variety of climates across Canada with wood that can be more readily converted to biofuel while minimizing the ecological footprint. A social research component is working with scientists to examine the social and economic issues associated with establishing breeding programs for fast-rotation poplar plantations.

Project Leaders: Sally Aitken and Andreas Hamann. Lead Genome Centre: Genome British Columbia. Project title: Adapting to climate change. Climate change is causing a mismatch between the natural genetics of trees and the locations where they grow. Seedlings that were once well adapted to a specific region are now poorly adapted to their environment due to changes caused by climate change. The scientists are applying state-of-the-art technologies from genomics as well as geospatial analysis and climate modeling to two of the most important western Canadian trees – lodgepole pine and spruce. Scientists are sequencing seedlings to better understand what genes are involved in adaptation to local climate conditions. This will lead to ensuring that the right trees get planted in the right climactic areas, improve the long-term health of forests and generate economic benefits of hundreds of millions of dollars every year.

Project Leaders: Michael Taylor, Marco Marra, and David Malkin. Lead Genome Centres: Genome British Columbia and Ontario Genomics Institute. Project title: Understanding childhood brain cancer. Brain cancer is the leading cause of pediatric cancer deaths. Children who survive have a much poorer quality of life due to the aggressive treatment used to fight the disease. Studies indicate that children with a good prognosis are often over-treated and could be spared complications by reducing the amount of treatment they receive. At the same time, children with a poor prognosis are often subjected to painful treatments which may, in fact, be futile. The scientists are using genome wide approaches to study medulloblastomas, the most common form of childhood brain cancer, to develop markers that will more accurately classify the tumours for treatment. Researchers are also identifying genetic changes that may reveal the risk factors that predispose children to this type of cancer.

Project Leaders: Graham Plastow, John Harding, and Bob Kemp. Lead Genome Centre: Genome Alberta. Project title: Maintaining healthy and more profitable pig production. With the mapping of the pig genome, scientists now have an opportunity to apply genomic-based tools to the pork industry. The researchers are applying genomics to help reduce the impact of two of the most common diseases in commercial pig production – Porcine Circovirus Associated Disease and Porcine Respiratory and Reproductive Syndrome. Scientists are studying mechanisms in pigs that make them genetically less susceptible to these diseases, providing important new diagnostic tools for breeders and expanding our understanding of disease control mechanisms. This work will lead to new strategies for disease control in addition to new drugs, improved vaccines, and a safer food chain by reducing the use of antibiotics.

Project Leaders: Stephen Moore and Stephen Miller. Lead Genome Centre: Genome Alberta. Project title: Improving
the Canadian cattle herd. The scientists are developing genomic selection techniques to boost genetic improvement in cattle. Specifically, they are targeting traits that are difficult to improve through conventional means. Low-cost tests are being developed that will allow an animal’s entire genome to be inferred from a relatively small number of genetic markers, giving valuable information about its breeding value at a very early age. This will bring immediate benefits to breeders, enhance product traceability and lay the foundation for the next generation of technologies aimed at environmentally sustainable production. It is estimated that this research will generate benefits in excess of $300 million over the next ten years.

Project Leaders: Curtis J Pozniak and Pierre Hucl. Lead Genome Centre: Genome Prairie. Project title: Maintaining the breadbasket of Canada. Wheat is a major Canadian crop, generating over $11 billion annually in value-added food. Current breeding programs use some genomic tools, but the full potential of genomics is not being realized. Remarkably, the wheat genome is five times the size of the human genome and is being coordinated by the International Wheat Genome Sequencing Consortium. The scientists in this project are playing a key role in the consortium, sequencing chromosome 6D which is itself larger than the genome of rice. Together with its international partners, Canada is identifying the genes that wheat breeders can use to develop the next generation of wheat cultivars. GEL3S researchers are examining the role of public-private partnerships in wheat genomics and breeding research and will recommend strategies to maximize return on investment.

Project Leader: Mehrdad Hajibabaei. Lead Genome Centre: Ontario Genomics Institute. Project title: Early Warning System. Canada is an international leader in biomonitoring – analyzing the biological diversity of plant and animal life in a particular region. This allows scientists to establish early warning systems to alert us to environmental stresses before there is a catastrophic loss of habitat. Previous research funded by Genome Canada developed new protocols besed on the next generation of sequencing tools that enable genomic analysis of biomonitoring samples and enable a thorough assessment of ecosystem health. Now, Canadian scientists are applying these tools in a natural environment, Wood Buffalo National Park, which is threatened by encroaching industrial development. The researchers will use DNA sequencing technologies as well as computational analysis to create a biomonitoring approach covering the entire spectrum of life in an ecosystem. This will reduce monitoring costs while greatly increasing the quantity and scope of derived data derived..

Project Leaders: Colin McKerlie and Steve Brown. Lead Genome Centre: Ontario Genomics Institute. Project title: Understanding the function and dysfunction of our genes. The scientists are taking part in an ambitious international project to understand the function of every one of our 20,000 genes. By studying the developmental problems and diseases in 280 mouse models each with a different abnormal or mutated gene, scientists are determining the effect of each mutation. This will determine whether the gene or the protein it produces could be a target for drugs or be used to diagnose disease. Discoveries from the project will feed the Canadian biopharmaceutical pipeline and transform the human genome from a list of genes to a living blueprint.

Project Leaders: Sachdev Sidhu and Charles Boone. Lead Genome Centre: Ontario Genomics Institute. Project title: Targeting cancer. Over the past decade, human antibodies have emerged as prime candidates for fighting cancer and other major diseases. With funding from Genome Canada, scientists are using cutting edge technology to develop antibodies targeted at proteins that have been associated with cancer. Scientists from the Donnelly Centre’s Toronto Recombinant Antibody Technology Centre are working together with researchers from the Ontario Institute for Cancer Research’s Selective Therapies Program to develop a program of large scale antibody production

Project Leaders: B Franz Lang and Mohamed Hijri. Lead Genome Centre: Genome Québec. Project title: Reclaiming polluted land sites. Mining activities, oil and gas extraction, agriculture and industrial processes can all contaminate soil, creating a significant world-wide problem. Efforts are underway to reduce the production of industrial and agricultural pollutants at their source, but this does not address the enormous legacy sites containing trace metals that can remain in the soil for millennia. Genome Canada is funding research into phytoremediation – a promising new biotechnology that uses plants to clean up pollutants in the soil. Part of the research involves sequencing selected microbes that are most effective in soil detoxification, which will place important new data in the public domain. The project will also develop a step-by-step methodology for sustainability assessments for site rehabilitation, including a toolkit for boards of directors and legal guidelines for governments and corporations.

Project Leaders: John MacKay and Jörg Bohlmann. Lead Genome Centres: Genome Quebec & Genome British Columbia. Project title: Sprucing up the forestry industry. The scientists will develop marker technologies to identify spruce seedlings that have superior growth and wood properties, or superior insect resistance. Genetic marker systems and biomarkers will be developed and applied to Canadian forestry programs. It is estimated that by applying “Marker Aided Selection” (MAS) to just 20% of Canadian spruce plantations, wood yield could increase by 1.5 million cubic meters per year, boosting GDP by $300 million. Using methods such as MAS also allows wood production to be concentrated on a smaller land area, allowing more forest to be set aside for conservation.

Project Leaders: Christopher McMaster and Conrad Fernandez. Lead Genome Centre: Genome Atlantic. Project title: Understanding the cause of genetic diseases. One in twelve Canadians suffers from an “orphan disease”. The discovery of effective treatment for these conditions is often hampered by inadequate scientific understanding of the condition, limited resource allocation to study these diseases and the cost of new drug development. Building on the successful Atlantic Medical Genetics and Genomics Initiative, scientists are developing new therapies to orphan disease patients in a shorter time, at reduced costs. The researchers are working to: discover genes responsible for these diseases; locate therapeutic targets; and identify small molecules and drug leads that could lessen the impact of these diseases. Researchers are also focusing on using or converting existing drugs to more rapidly address unmet medical needs.