$346M funding awarded for genomics research

Winnipeg, MB – Genome Canada has awarded a total of $346 million to support 33 new genomics and proteomics research projects. Of this, $167.2 million is provided by Genome Canada and $179.3 million by Canadian and international partners.

"These large-scale projects have tremendous potential to improve the health of Canadians and build the competitiveness and prosperity of the agricultural, forestry and fisheries sectors of our economy," says David Emerson, minister of industry and minister responsible for Genome Canada. "[The] funding announcement reinforces the important scientific advances that can be achieved for all Canadians and indeed the world through Genome Canada’s funding model."

The projects are intended to ensure Canada’s leadership in aquaculture and forestry research, bolstering the economic strength of these sectors. They will also provide Canada with new ways to fight against infectious diseases, including a nanotechnology-based system to diagnose infectious agents within minutes and at the location of the health care provider.

"All 33 projects were reviewed by an international panel of scientific experts and all of them were rigorously evaluated for scientific excellence," says Dr Cal Stiller, chairman of the board of Genome Canada. "The willingness of international experts to devote considerable time to reviewing the proposals speaks to the high regard in which Canadian genomics and proteomics researchers are held throughout the world."

With up to 50% of project funding being provided by the federal government, the remaining funds are leveraged from various sectors. More than 80% of leveraged funds are raised from the public sector in Canada, while another 9% comes from international public and private sector partners. Overall private-sector contributions amount to 11% in this competition. Given the scale of the projects being funded, Genome Canada says it has put in place a set of rigorous principles governing the accountability of funds provided by the public, private and not-for-profit sectors. Sound management practices are built into each project team.

All projects will take place at research institutions across Canada. Following is an outline of the projects involving laboratory-based research. They are divided into six groups: development of new technologies, agriculture, health, forestry, environment and fisheries. Title, value and Genome Canada funding plus project description and leaders are provided for each project.

1) DEVELOPMENT OF NEW TECHNOLOGIES

Quantum Dot Diagnostics: Simultaneous Genomic and Proteomic Profiling of Multiple Pathogens at Point-of-Care
Total value of project: $ 9,025,738
Genome Canada’s maximum contribution: $ 4,512,869
Description: Canada is developing cutting-edge expertise in the rapid and accurate diagnosis of infectious diseases, based on nanotechnology. Dr Kevin C Kain, director of the McLaughlin-Rotman Center for Global Health and Senior Scientist in the division of genomic medicine at the Toronto General Research Institute, and Dr Michael Greenberg, FIO Corp, are project leaders of Quantum dot diagnostics: simultaneous genomic and proteomic profiling of multiple pathogens at point-of-care.

Four-Dimensional Modelling of Genetic Disease Patterns
Total value of project: $ 3,468,113
Genome Canada’s maximum contribution: $ 1,734,057
Description: Prodigious masses of data are being generated by genomic technologies. Finding a way to visualize new data, and to model genetic disease patterns, is the goal of Dr Christoph Sensen and his team. Dr Sensen is professor of biochemistry and molecular biology at the University of Calgary and director of the Sun Center of Excellence for Visual Genomics.

2) AGRICULTURE

Use of Genomic Tools for Crop Improvements in Temperate Climates
Total value of project: $ 6,024,564
Genome Canada’s maximum contribution: $ 3,012,282
Description: A key to maintaining and improving Canada’s competitive position lies in crop improvement, a field of research that increasingly uses genomic approaches to identify genetic factors involved in the climatic adaptation of particular crops. Dr DB Fowler, a researcher on crop development at the University of Saskatchewan, is principal investigator.

Designing Oilseeds for Tomorrow’s Markets
Total value of project: $ 13,414,541
Genome Canada’s maximum contribution: $ 5,241,929
Description: Project aims to use genomic technologies to develop canola with desired seed coat characteristics and decreased levels of anti-nutritional factors. It is anticipated that the results of this research will enhance the overall usefulness of canola seed leading to improved meal for new food and feed applications, and increased seed oil content. Dr Randall J Weselake, Canada research chair in agricultural lipid biotechnology at the University of Alberta’s Agricultural Genomics and Proteomics Centre, and Dr Wilf Keller, research director at the National Research Council of Canada’s Plant Biotechnology Institute (NRC-PBI) in Saskatoon, are the project leaders.

The Pathogenomics of Innate Immunity (PI2)
Total value of project: $ 12,840,585
Genome Canada’s maximum contribution: $ 6,420,293
Description: Drawing on many of the findings of a previous Genome Canada project, the Functional Pathogenomics of Mucosal Immunity Program, this project will advance understanding of immune responses in humans and animals. Specific genes will be knocked out in mouse embryonic cells and in mice derived from these cells, and the cells and mice will then be challenged with the important human food-borne pathogen, Salmonella, which causes intestinal infections and diarrhea. A range of genes representing key pathways and decision points in innate immunity will be targetted for knocking out. Human and bovine cells will also be targetted using siRNA methods, which use a class of short (20-25 nucleotides long) RNA molecules that interfere with gene expression. By knocking out specific genes, the investigators will be able to determine their relevance in human and animal infections.

Dr Robert E.W.Hancock, Professor of Microbiology and Immunology at UBC, and Dr Lorne Babiuk, Professor of Veterinary Microbiology at the University of Saskatchewan, are project leaders of the Pathogenomics of Innate Immunity (or PI2 ).

3) HEALTH

Atlantic Medical Genetic and Genomics Initiative (AMGGI)
Total value of project: $ 6,563,458
Genome Canada’s maximum contribution: $ 3,281,729
Description: The project is an initiative to identify new genes with a major impact on health. AMGGI will utilize the Atlantic region’s unique population structure and history, as well as the high quality of the health care system to provide a streamlined discovery process. The project will generate tangible socio-economic benefits by improving health care and disease management for individuals, families and communities in Atlantic Canada burdened by devastating single gene disorders.

Dr Mark Samuels, a molecular geneticist at Dalhousie University in Nova Scotia, and Dr Terry-Lynn Young, a molecular geneticist at Memorial University of Newfoundland, are the project leaders of AMGGI.

Functional Annotation of Essential Alternatively Spliced Isoforms
Total value of project: $ 8,302,097
Genome Canada’s maximum contribution: $ 4,151,049
Description: In mammals, a single gene can produce numerous protein isoforms (multiple molecular forms of given proteins) through a process called alternative pre-mRNA splicing, or AS. Defects in AS are believed to account for several well-known diseases, such as cystic fibrosis, thalassemia, spinal muscular atrophy and several types of cancer. Little is known about the biological mechanisms that control AS.

Dr Sherif Abou Elela, a molecular biologist at the Universit de Sherbrooke’s Faculty of Medicine, is project leader.

An Integrated Genetic/Physical Genome Map for the Old World Monkey, Cercopithecus aethi
ops
Total value of project: $ 3,220,299
Genome Canada’s maximum contribution: $ 1,610,150
Description: Many species of old and new world monkeys serve as model organisms in biomedical research. Since nonhuman primate models are genetically close to humans, they can help elucidate complex human behaviours and diseases in ways not possible using mouse and rat models. The vervet monkey (Cercopithecus aethiops, also known as the African green monkey), is a non-endangered species native to southern Africa, and is a good model for studying neurological processes.

Dr Ken Dewar, a principal investigator at the McGill University and Genome Qubec Innovation Centre, and an assistant professor in the Department of Human Genetics at McGill University, is project leader.

Identification and Characterization of Genes Involved in Common Developmental Brain Diseases
Total value of project: $ 14,932,434
Genome Canada’s maximum contribution: $ 7,466,217
Description: The project leaders believe that genes causing schizophrenia and autism carry a high rate of mutations, and tend to be located at synapses, which are junctions between nerve cells (and other cells) in the brain where information is communicated and processed. Drawing on a collection of 5,000 blood samples collected from individuals affected by schizophrenia and autism (and their family members), the research team will analyse 1000 synpatic genes in 276 patients. This analysis will make it possible to perform the first direct chemical examination of the genes in humans coding for particular synapses, and subsequently to validate the biological effects of disease-related mutations of these synapse genes in different animal model systems.

Dr Guy A Rouleau, an authority on the genetic basis of human brain tumours, human neurodegenerative diseases and psychiatric illnesses at the University of Montreal, and Dr Pierre Drapeau, director of McGill’s Centre for Research in Neuroscience, are project leaders.

Pharmacogenomics of Drug Efficacy and Toxicity in the Treatment of Cardiovascular Disease
Montreal Heart Institute; Universit de Montral
Total value of project: $ 18,380,525
Genome Canada’s maximum contribution: $ 9,190,263
Description: No drug works well for all patients. Genetic differences among patients are believed to account for variations in drug responses. While genomics is opening the way to personalized, predictive and preventive medicine, pharmacogenomics in particular uses a patient’s genetic information to predict individual responses to medication. This international team of clinician-researchers and scientists will address drug response problems in the management of cardiovascular disease, which includes coronary heart disease, congestive heart failure, hypertension and stroke. The team will investigate the toxicity of lipid lowering drugs, especially statins, which are used to treat atherosclerosis, the concentration of lipids or fats, which narrow or block the arteries. The team will also study the efficacy of new anti-atherosclerotic agents.

Dr Jean Claude Tardif, an authority on atherosclerosis at the Montreal Heart Institute of the Universit de Montral, and Dr Michael S Phillips, from the Montreal Heart Institute, Universit de Montral and Director of Pharmacogenomics at Genome Qubec, are project leaders.

The GRID Project: Gene Regulators in Disease
Total value of project: $ 8,329,213
Genome Canada’s maximum contribution: $ 4,164,607
Description: Gene regulation is the process of DNA and protein interactions in a gene that determines where and how the gene will be activated. Small differences in gene regulation among individuals can lead to disease susceptibility or resistance. This project will clarify regulatory mechanisms in common diseases. The researchers will investigate gene regulation in a breed of transgenic mice developed at McGill University, in collaboration with Nucleis, a French company. Nucleis will set up a North American biotechnology laboratory in Montreal and train highly qualified personnel to work in this area. The project will also collaborate with other Canadian biomedical and pharmaceutical centres.

The project is being led by Dr Thomas J Hudson, geneticist, immunologist and allergist, and director of the McGill Genome Centre.

Identification of Genetic Pathways that Regulate the Survival and Development of Cancer and Cancer Stem Cells
Total value of project: $ 15,056,645
Genome Canada’s maximum contribution: $ 7,528,323
Description: The project focusses on the development of normal and leukemic immune cells. The team includes includes experts in leukemia, breast cancer, brain tumors, and cancer stem cells, and will study human tumours and mouse cancer models in order to address two crucial issues: what genetic alterations distinguish very aggressive from more benign tumours, and what genetic and biological malfunctions lead to the development of cancer stem cells.

Project leader is to Dr Cynthia Guidos, a senior scientist at the Hospital for Sick Children Research Institute in Toronto and a professor of immunology at the University of Toronto

Integrative Biology
Total value of project: $ 22,239,067
Genome Canada’s maximum contribution: $ 11,119,534
Description: The genomes of more than two hundred organisms have been sequenced, from microscopic earthworms to humans. The function of thousands of individual genes is attracting the attention of scientists. But integrative biology is revealing that genes work not individually but as physical or functional assemblies to perform their functions.

Project leader Dr Brenda Andrews is director of the Terrence Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto.

Genome-Environment Interactions in Type 1 Diabetes
Total value of project: $ 12,274,666
Genome Canada’s maximum contribution: $ 6,137,333
Description: This project is investigating the interactions of genetic risks and environmental factors underlying Type 1 Diabetes (T1D). It aims to understand the genetic control of T1D in humans and rodent models, and to study the role of exposure to common intestinal bacteria in regulating immune system development and how such exposures affect the probability that persons at genetic risk of T1D will develop the disease.

Dr Jayne Danska, senior scientist at Toronto’s Hospital for Sick Children and professor in the Faculty of Medicine at the University of Toronto, and Dr Andrew Macpherson, Canada research chair in mucosal immunology at McMaster University, are project leaders.

The Contribution of Genetic Modulators of Disease Severity in Cystic Fibrosis to other Diseases with Similarities of Clinical Phenotype
Total value of project: $ 5,787,662
Genome Canada’s maximum contribution: $ 2,893,831
Description: Canada is a world leader in research on cystic fibrosis (CF) and this project plans to build on this research strength, by investigating the genetics of other diseases with similar phenotypes – observable physical characteristics, which may be genetically determined. The project will apply knowledge about the genetic factors (so-called modifier genes) that influence the severity of CF to other diseases that are clinically similar to CF.

Dr Peter Durie, a pediatrician and senior scientist, and Dr Julian Zielenski, a geneticist at the Hospital for Sick Children’s Research Institute are project leaders.

Structural and Functional Annotation of the Human Genome for Disease Study
Total value of project: $ 15,435,809
Genome Canada’s maximum contribution: $ 6,946,114

Description: This project aims to bridge new biological knowledge with medical applications. Any two humans are 99.9% identical at the level of their DNA sequences. But recently, new forms of genomic variation have been appreciated above and beyond single nucleotide polymorphisms. These include large-scale variations, such as copy number changes, insertions, deletions, duplications and rearrangements, and they may
be much more widespread than was previously appreciated. In this project, collaborator Dr Steve Scherer of the Hospital for Sick Children will define and superimpose these large-scale genomic variations over top of the existing "first draft" of the human genome sequence map. In addition, collaborators Dr Ben Blencowe, Dr Tim Hughes and Dr Brendan Frey of the University of Toronto will define and integrate these new forms of genomic variation into the current human genome sequence map.

Project leader is Dr Robert Hegele, endocrinologist and scientific director of the London Regional Genomics Centre at the Robarts Research Institute.

The Dynactome: Mapping Spatio-Temporal Dynamic Systems in Humans
Total value of project: $ 21,432,032
Genome Canada’s maximum contribution: $ 10,716,016
Description: Canadian-led research over the last two decades has demonstrated that proteins interact with one another, and assemble pathways and networks within cells, which account for sophisticated cellular behaviour. The project will map protein interactions within human cells in order to determine whether diseases such as malignant cancers result not only from specific changes to individual genes and proteins, but also from changes in the entire cellular network.

Dr Tony Pawson, director of the Samuel Lunenfeld Research Institute at Toronto’s Mount Sinai Hospital, his colleague and fellow molecular biologist Dr Jeff Wrana, and University of Western Ontario biochemist Shawn Li, are project leaders.

Autism Genome Project
Total value of project: $ 13,749,710
Genome Canada’s maximum contribution: $ 6,874,855
Description: Autism, a severe neurodevelopmental disorder affecting thousands of Canadians, is characterized by impairments in social- communication and by a preference for repetitive activities. Although it is generally agreed that a strong genetic basis underlies the condition, the causes of autism are still unknown. This project will screen the genomes from over 6,000 members of 1,600 families to find where susceptibility genes reside along the chromosomes. Advanced genomic methods will then be used to assess the DNA in these chromosome regions in order to identify disease-associated genes.

Dr Stephen Scherer, senior scientist in the department of genetics and genomic biology at the Hospital for Sick Children is project leader. The project will bring together many of the leading geneticists, clinicians and genome scientists undertaking autism research in Canada, and link them to 170 other scientists from 10 other countries worldwide.

North American Conditional Mouse Mutagenesis Project: High Throughput Mammalian Functional Analysis for the Discovery of Novel Determinants of Human Disease
Total value of project: $ 20,244,725
Genome Canada’s maximum contribution: $ 6,305,777
Description: Knock-out mice are model organisms in which specific genes have been inactivated. This is a worldwide effort to generate knock-out mutations in every gene in the mouse genome, and is widely considered to be the next most important step following the Human Genome Project.

Dr Geoff Hicks, a cancer biologist at the Manitoba Institute of Cell Biology, and Dr Janet Rossant, a developmental biologist at the Hospital for Sick Children, are project leaders.

Functional Genomics for Emerging Infectious Diseases (PREPARE Project)
Total value of project: $ 5,700,748
Genome Canada’s maximum contribution: $ 2,850,374
Description: Infectious diseases are the leading cause of premature mortality around the world and the fifth leading cause of premature mortality in Canada. The world scientific community has the tools and expertise to address emerging and re-emerging infectious diseases (EID). This project has been set up to bring these research efforts together, to systematically investigate life-threatening pathogens and to find rapid scientific solutions.

Dr B Brett Finlay, a microbiologist and Peter Wall distinguished professor at the University of British Columbia, and UBC colleagues Dr Robert C. Burnham and Dr Neil Reiner are project leaders.

Dissecting Gene Expression Networks in Mammalian Organogenesis
Total value of project: $ 6,382,929
Genome Canada’s maximum contribution: $ 3,191,465
Description: Mammals develop from single cells to complex multi-cellular organisms in which each tissue and organ has a distinct architecture and function. But very little is currently known about organogenesis, the period during which the embryo as well as specific organs and organ systems are formed. In this project, the researchers plan to focus on the development of three organs in the mouse embryo – the heart, pancreas and liver. In particular, they will focus on tissues in the heart involved in valve formation and septation (division or partitioning), on the formation of islet cells that produce hormones in the pancreas and help control the level of sugar in the blood, and on hepatocytes or liver cells.

Dr Marco Marra, director of the Genome Sciences Centre of the BC Cancer Agency and Dr Pamela Hoodless, senior scientist at the Terry Fox Laboratory of the BC Cancer Agency, are project leaders.

Pleiades Promoter Project: Genetic Resource for CNS Regional & Cell Specific Molecular Delivery
Total value of project: $ 8,298,002
Genome Canada’s maximum contribution: $ 4,149,001
Description: Gene therapy has often been heralded as a new frontier in medicine, but gene transfer therapy has raised several safety issues. For example, more clinically relevant research is needed. Genes need to be delivered to specific cell types and also specific locations in the genome, so that therapy does not unintentionally alter healthy cells or mutate the genome. This project is designed to use the latest scientific techniques to address these safety concerns surrounding gene therapy.

Dr Elizabeth M Simpson, Canada research chair in genetics and behaviour, and senior scientist at UBC’s Centre for Molecular Medicine and Therapeutics within the Child and Family Research Institute, is project leader.

High Resolution Analysis of Follicular Lymphoma Genomes
Total value of project: $ 7,945,153
Genome Canada’s maximum contribution: $ 3,972,577
Description: One of the most common cancers of the immune system in Canada is follicular lymphoma, a disease in which the malignant cells have rearranged parts of chromosomes 14 and 18. This genomic rearrangement in turn leads to an accumulation of damaged cells. With time other genetic changes can occur in the follicular lymphoma cells that bring on a more aggressive form of the disease, diffuse large B cell lymphoma. The project aims to study the genomic rearrangements using new cutting-edge techniques.

The project is led by Dr Marco Marra, senior scientist at the Genome Sciences Centre of the BC Cancer Research Centre, Dr Joseph Connors, a professor at UBC and chair of the lymphoma tumor group at the British Columbia Cancer Agency, and Dr Randy Gascoyne, a hematopathologist at the BC Cancer Agency, who is also the sole Canadian member of the International Lymphoma Study Group (ILSG).

Efficient Identification and Cloning of Single Gene Deletions in the Nematode Caenorhabditis elegans
Total value of project: $ 9,040,032
Genome Canada’s maximum contribution: $ 4,520,016
Description: The nematode (Caenorhabditis elegans) is a small, about 1mm in length, roundworm used as a model organism in genetic research. Its genome was the first multicellular metazoan to be completely sequenced, in 1998, and almost half of its genes have homologs in humans with have comparable functions and common origins over evolutionary time.

Dr Donald Moerman, a professor of zoology at the University of British Columbia, is project leader of Efficient identification and cloning of single gene deletions in the nematode C elegans.

4) FORESTRY

Arborea II: Genomics for Molecular Breeding in Softwood trees. Discovery of Gene Markers to Enhance the Productivity and Value of Spruce
through Integrated Functional Genomics and Association Mapping
Total value of project: $ 11,804,085
Genome Canada’s maximum contribution: $ 5,902,043
Description: Spruce trees are the most widely used species in Canada’s forest plantations. Breeding new generations of spruce trees can be a slow process, so these forest genomics researchers are studying tree growth and yield as well as wood properties, at the molecular level. Genomics can be used to improve the productivity and competitiveness of Canada’s forest products industry.

Drs John MacKay and Jean Bousquet, forest biologists at Laval University, are project leaders.

Conifer Forest Health Genomics
Total value of project: $ 15,292,152
Genome Canada’s maximum contribution: $ 7,646,076
Description: The mainstay of Canada’s massive forest industry, our conifer forests are increasingly threatened by outbreaks of insect pests and the impacts of climate change. But what is the genomic and biological basis of conifer defence response to forest pests? And how do conifers adapt to abiotic stress associated with changing environments? This project draws on Treenomix, Canada’s first large-scale forestry genomics project, previously funded by Genome Canada, Genome BC and the Province of British Columbia, and applies existing and new knowledge to improve our understanding of spruce species (Picea spp.).

Dr Jrg Bohlmann and Dr Kermit Ritland of the University of British Columbia are project leaders.

5) ENVIRONMENT

Canadian Barcode of Life Network
Total value of project: $ 9,630,116
Genome Canada’s maximum contribution: $ 4,815,058
Description: DNA barcodes use a small fragment of an organism’s DNA a portion of a single gene to identify the species to which an organism belongs. They are powerful tools, which can be used to help catalogue biodiversity. DNA barcoding began in Canada, and Canadian scientists continue to lead international work aimed at developing a complete catalogue of the Earth’s life forms.

Dr Paul Hebert, an evolutionary biologist and director of the Biodiversity Institute of Ontario at the University of Guelph, is project leader.

6) FISHERIES

Atlantic Cod Genomics and Broodstock Development
Total value of project: $ 12,706,092
Genome Canada’s maximum contribution: $ 6,353,046
Description: The decline in Atlantic salmon stocks served as an incentive to develop today’s aquaculture sector. One approach towards maintaining growth and stability of the aquaculture industry is diversification into rearing other species such as Atlantic cod. Current estimates show that cod farming in Newfoundland alone could generate more than $100 million in new wealth while meeting consumer demand for a high quality food resource. This project encompasses cod broodstock development in New Brunswick and Newfoundland.

Dr Jane Symonds, director of aquaculture at the Huntsman Marine Science Centre (St Andrews, NB), and Dr Sharen Bowman, a specialist in genome sequencing and annotation at Genome Atlantic’s DNA Sequencing Centre (Halifax, NS) are project leaders.

Consortium for Genomic Research on All Salmonids Project (cGRASP)
Total value of project: $ 15,533,848
Genome Canada’s maximum contribution: $ 7,766,924
Description: Given the development and expansion of the salmonid aquaculture industry in Canada, the impact of farmed fish on wild fisheries needs to be minimized. Farmed fish need to be more resistant to disease and better adapted to their environment. Wild fish needed to be better understood and in some cases managed. This project follows up on the Genomics Research on Atlantic Salmon Project, previously funded by Genome Canada.

Dr Ben F Koop, director of the Centre for Biomedical Research at the University of Victoria, Dr William S Davidson, a molecularbiologist at Simon Fraser University specializing in molecular evolution, and Dr Stig Omholt, a professor at Norway’s Centre for Integrative Genetics, are project leaders.