Large Scale Applied Research Project (LSARP) Competition

The Large-Scale Applied Research Project (LSARP) Competition provides support to large-scale genomics research projects using genomic approaches to address challenges in Canada’s main economic sectors, as well as strategic initiative programs that address national and international opportunities.

Launched on May 17, 2010, the funding for this competition is targeted to projects focused on applying genomics research to create socio-economic benefits for Canada, to be realized or initiated before the end of the project

Funded Ontario Projects

2015 – Natural Resources and the Environment: Sector Challenges – Genomic Solutions
On December 8, 2016, Genome Canada announced the $110 million investment in the 2015 LSARP competition. The thirteen projects approved for funding use genomics to address the challenges and opportunities facing Canada’s natural resources and environment sectors to drive sustainability, growth, productivity, commercialization and global competitiveness. Three (3) research projects through Ontario Genomics – with one Genome British Columbia co-lead – were approved for funding:

2014 – Feeding the Future
On July 21, 2015, Genome Canada announced the $93 million investment in the 2014 LSARP competition. The eleven projects approved for funding applied genomics in the agri-food and fisheries/aquaculture sectors to address challenges and opportunities related to global food safety, security and sustainable production. Three (3) research projects received funding through Ontario Genomics:

2012 – Genomics and Personalized Health
On March 26, 2013, Genome Canada, in partnership with the Canadian Institutes of Health Research, announced the $149.8 million investment in the 2012 LSARP competition. The seventeen projects approved for funding were focused on the application of genomics to tailor patient treatments and therapies in fields as diverse as epilepsy, autism, HIV/AIDS, cancer, cardiovascular disease, rare neurological diseases, and stroke. Four (4) research projects received funding through Ontario Genomics, and one project was co-led with Genome Quebec:

2010 – Forestry and Environment; Multi-Sector
On May 9, 2011, Genome Canada announced the results of the 2010 LSARP competition. Three (3) projects received funding through Ontario Genomics, with a combined total investment of $23.8 million ($11.3 million from Genome Canada, $12.5 million from co-funding):


LSARP Descriptions:

SYNBIOMICS: Functional genomics and techno-economic models for advanced biopolymer synthesis (2015)

Project Leaders: Emma Master, Harry Brumer
Institutions: University of Toronto, University of British Columbia
Total Project Funding: $9.5 million

In a world that is requiring increasingly biological-based solutions to meet sustainably a growing need for materials, tree biomass remains one of the most abundant resources on earth. While there is general appreciation of the potential of microbial enzymes in expanding the range of products made from tree biomass, to date, biotechnology development has focused largely on the deconstruction of trees into sugars that can then be converted through fermentation to biofuels.
Drs. Emma Master of the University of Toronto and Harry Brumer of UBC are leading a team looking in the other direction. Their project, SYNBIOMICS, is focused on upgrading key biopolymers from trees using enzymes, to create materials that provide higher value than what otherwise might be realized. The project will harness the genetic potential of microorganisms to identify and develop new biocatalysts for this purpose. End users and stakeholders have helped to identify potential high-value products to target, including resins, coatings, bioplastics and adhesives.
To facilitate commercialization of the biocatalysts and bioprocesses the team develops, the project will establish roadmaps to foster small and medium-sized enterprises that will work together synergistically with nearby pulp mills. The results will expand Canada’s role in global bioproducts markets, creating lasting knowledge-based economic opportunities for Canada’s forest sector and rural communities.
The project’s GE3LS research activities include: coordinating an iterative bioproduct and biotechnology development cycle with End-users; developing techno-economic models for SME ecosystems in the forest sector; and analyzing anaerobic bioreactors to develop predictive tools for effluent treatment and energy recovery.
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Mine wastewater solutions: Next generation biological treatment through functional genomics (2015) 

Project Leaders: Lesley A. Warren, Jill Banfield
Institutions: University of Toronto, UC Berkeley
Total Project Funding: $3.7 million

The Canadian mining sector is a cross-country presence, with mines in every province and territory contributing more than $57 billion to the economy (3 per cent of Canada’s GDP) and employing over 375,000 people. As pressures on Canada’s freshwater water supplies grow, the sector as a whole, is seeking to develop the most sustainable approaches to mining possible. Mining wastewaters contain sulphur compounds, which can cause acidification and toxicity in receiving waters if not properly managed. Currently the industry lacks effective monitoring tools and innovative biological solutions to better controls these contaminants.
Dr. Lesley A. Warren of the University of Toronto, along with Dr. Jillian Banfield of University of California, Berkeley, is leading a project that will apply genomics, geochemistry and modeling to mining wastewaters to develop innovative biological monitoring, management and treatment tools. The integration of genomics will provide understanding of bacterial opportunities in these wastewaters for new flexible management and treatment options to safeguard the quality of wastewater. These new tools will enable the industry to better monitor, manage and reduce sulphur compounds in their wastewaters. Her international team will also generate new tools, to support science-informed, cost-benefit decision-making for the mining sector. This project is the first of its kind in Canada and possibly the world.
The involvement of three mining and two environmental consulting companies, provincial and national sector industry associations and government will ensure the project’s findings are applied, leading to lower management costs, decreased risk of environmental damage, reduced liabilities for the industry and better safeguards for Canada’s vital freshwater supplies.
The project’s GE3LS research component will develop a risk and options assessment for decision-making (ROAD). This process will enable translation of the team’s scientific knowledge into a nested set of decisions, to guide mining operational practices, corporate strategic planning and policy development.
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BEARWATCH: Monitoring impacts of Arctic climate change using polar bears, genomics and traditional ecological knowledge (2015) 

Project Leaders: Stephen C. Lougheed, Peter van Coeverden de Groot, Graham Whitelaw, Markus Dyck
Institutions: Queen’s University, Government of Nunavut
Total Project Funding: $9.5 million

Polar bears are the canary in the Arctic coalmine. Dependent on sea ice for hunting seals and land for denning, they are a sentinel of Arctic environmental change. Polar bears also play a central role in Inuit culture, spirituality and hunting practices and feature largely in their traditional knowledge system, called Inuit Qaujimajatuqangit (IQ). As sea ice quality and quantity decline, preferred food sources become less available. Polar bears’ numbers in Canada’s north – currently around 15,000, about two-thirds of the world’s population of them – are expected to decline. Canada must show international leadership in polar bear conservation, both to ensure polar bears’ persistence and to provide insight into the state of Arctic ecosystems.
BEARWATCH, led by Dr. Stephen C. Lougheed of Queen’s University, in collarboration with Drs. Peter van Coeverden de Groot and Graham Whitelaw from Queen’s University, and Markus Dyck, who is with the Government of Nunavut, will develop a non-invasive, fecal-based biomarker toolkit and a community-based monitoring program. The project will combine leading-edge genomics with comprehensive social science, developed and implemented within a framework of collaboration with northern communities, indigenous organizations and territorial and other levels of government. It will result in a database that combines IQ and other indigenous traditional ecological knowledge with polar bear genetic identity and ecological and physiological measures that permit assessment of bear health. The community-based monitoring program will provide ongoing data for tracking changes in polar bear populations, while also providing income to Arctic indigenous communities.
BEARWATCH will result in key insights for polar bear management and for tracking the changing ecosystems of the Canadian Arctic, situating Canada as a world leader in genomics-based, community-oriented research for wildlife management.
The project’s GE3LS research component will integrate polar bear Traditional Ecological Knowledge (TEK) and science as well as historical data, allowing the project team to compare insights from each knowledge system and translate findings into a community-based monitoring protocol that will track polar bear population responses to environmental change. It will also involve an evaluation of impacts of the research on Canadian polar bear management and policy, Environmental Assessments by northern resource industries, and Inuit Impact Benefit Agreements.
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Towards a sustainable fishery for Nunavummiut (2014)

Project Leaders: Virginia K. Walker, Stephen C. Lougheed, Peter Van Coeverden de Groot, Stephan Schott
Institutions: Queen’s University, Carleton University
Total Project Funding: $5.6 million

Affordable access to safe, nutritious and culturally relevant food is one of the biggest challenges facing the Nunavummiut, the people of Nunavut. Food costs are 140 per cent higher in Nunavut than in the rest of Canada with eight times more Inuit households facing moderate to severe food insecurity. 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, science-­based 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 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.
The Walker Project website is www.arcticfishery.ca
Download the Final Release
Download the Funded Projects Backgrounder
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Increasing feed efficiency and reducing methane emissions through genomics: A new promising goal for the Canadian dairy industry (2014)

Project Leaders: Filippo Miglior, Paul Stothard
Institutions: University of Guelph, University of Alberta
Total Project Funding: $10.3 million

The Canadian dairy industry adds $16.2 billion to Canadian GDP each year (2011 figures). That figure is forecast to increase as international demand for dairy products grows in the coming years, due to growing middle classes in emerging economies, demand for high-quality milk proteins in developing countries and world population expansion more generally. That figure can also grow (by an estimated $100 million annually) by improving two key traits in dairy cattle: their ability to convert feed into increased milk production and a reduction in their methane emissions (methane being a powerful greenhouse gas).
Dr. Filippo Miglior of the University of Guelph and Dr. Paul Stothard of the University of Alberta are leading a team that will use genomics-­based approaches to select for cattle with the genetic traits needed for more efficient feed conversion and lower methane emissions. To date, it has been both difficult and expensive to collect the data required for such selection. The latest genomic approaches and the award-winning phenotyping platform developed by Growsafe in Alberta offer an opportunity to address these problems and collect and assess the required data to carry out the selection.
The results of this project will assist dairy farmers and the industry more broadly to develop cattle that will carry these two important traits. Farmers will save money (as feed is the single largest expense in milk production), while the international competitiveness of Canada’s dairy industry will increase. The environmental footprint of the dairy industry will also be reduced, in part due to lower methane emissions, but also because more feed efficient animals produce less manure waste. Broad application of the project’s findings will be enhanced by the involvement of several industry organizations and international research partners in the project, not only benefiting Canada’s dairy industry, but also contributing to global food security and  sustainability.
Genome Alberta Press Release
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Sustaining and securing Canada’s honey bees using ‘omic tools (2014)

Project Leaders: Leonard Foster, Amro Zayed
Institutions: 
University of British Columbia, York University
Total Project Funding: $2.8 million

Honey bees play a critical role in Canadian agriculture. They produce 75 million pounds of honey each year and are responsible for pollinating many fruits and vegetable crops, nuts and oil seeds like canola. Through these activities, they contribute more than $4.6 billion to the Canadian economy each year.
Given this critical role, the high rate at which bee colonies are dying off is particularly alarming, posing a serious threat to the productivity of Canadian agri-­food industries and jeopardizing Canada’s food security. Canadian beekeepers have lost more than a quarter of their colonies each winter since 2006-­07 with certain provinces experiencing significantly higher death in some years. Replacing these losses by purchasing queen bees from offshore, as beekeepers have been doing, risks importing new diseases or invasive strains of honey bees (such as “killer” bees from  the US).
Dr. Leonard Foster of the University of British Columbia and Dr. Amro Zayed from York University are leading a project to guard the safety and sustainability of the beekeeping industry in Canada. The team will develop genomics and proteomics tools that will provide markers to selectively breed 12 economically valuable traits. This will enable beekeepers to quickly and cost­effectively breed healthy, disease-­resistant, productive bee colonies that are better able to survive harsh Canadian winters. While this will lessen, it will not eliminate, the need to import bees from other regions, so the team will also develop an accurate and cost-effective test to detect bees with Africanized genetics (“killer” bees). The team will work with beekeepers and other stakeholders and end users to ensure its tools are implemented and accessible to beekeepers by the end of the project. This will provide measurable economic benefits to Canada, including to beekeepers and the agri-­food industry and social benefits to the Canadian public. These benefits range in value from $8 million to $150 million per year.
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Enhanced CARE for RARE genetic diseases in Canada (2012)

Project Leaders: Kym Boycott, Alex MacKenzie
Institutions: Children’s Hospital of Eastern Ontario, University of Ottawa
Total Project Funding: $11.7 million

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 one to three 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 team will use powerful new gene 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. Once the disease-causing genes have been identified, researchers will test drugs that are currently on the market to identify those that might be effective against these rare diseases.
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Autism spectrum disorders: Genomes to outcomes (2012)

Project Leaders: Stephen Scherer, Peter Szatmari
Institution: The Hospital for Sick Children
Total Project Funding: $9.9 million

Genome Canada and CIHR-funded research has already led to some exciting breakthroughs in our understanding of autism spectrum disorder, a complex condition that affects normal brain development, social relationships, communication and behaviour. Among these breakthroughs is the identification of specific DNA anomalies associated with the illness. Now, Drs. Stephen Scherer, Peter Szatmari and team are going to the next level, aiming to identify the remaining genetic risk factors. This ground-breaking work will mark Canada’s contribution to an ambitious international initiative that aims to sequence and analyze the genomes of 10,000 people with autism spectrum disorder. With a more complete understanding of the genetic elements of autism, doctors will be able to make earlier diagnoses, provide better, more personalized care to patients and reduce the enormous cost autism imposes on our health care system.
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Early detection of patients at high risk of esophageal adenocarcinoma (2012)

Project Leaders: Lincoln Stein, Tony Godfrey
Institution: Ontario Institute for Cancer Research
Total Project Funding: $3.2 million

Chronic heartburn can damage the lining of the esophagus, leading to a condition known as “Barrett’s esophagus”. Patients with Barrett’s esophagus have a much higher chance of developing cancer of the esophagus. Until recently, the only way to diagnose Barrett’s esophagus was through endoscopy—an uncomfortable and time-consuming procedure. However, a swallowable sponge under development in the United Kingdom allows for quick and painless diagnosis of Barrett’s esophagus in a doctor’s office. The team led by Drs. Lincoln Stein and Tony Godfrey aim to supplement this test with genomic technologies, allowing doctors to follow patients over time to identify and treat those progressing to cancer. Early detection, treatment and even prevention of these cancers could save the healthcare system over $300 million a year.
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The microbiota at the intestinal mucosa-immune interface: A gateway for personalized health (2012)

Project Leaders: Alain Stintzi, David Mack
Institutions: Children’s Hospital of Eastern Ontario, University of Ottawa
Total Project Funding: $2.9 million

Inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis, are incurable debilitating lifelong diseases that can affect children. Early detection is critical to avoiding complications and improving their quality of life. At the moment, however, there is no single test to determine the presence or type of IBD and the tests that exist are very uncomfortable for children. Drs. Alain Stintzi, David Mack and team are developing a simple, non-invasive approach to detecting IBD that will also be more cost effective. Using cutting-edge technology, the scientists will examine intestinal bacteria to develop better ways of identifying IBD and determining its severity. This work could also lead to new treatment, enhancing the quality of life for children everywhere.
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Personalized medicine in the treatment of epilepsy (2012)

Project Leaders: Patrick Cossette, Berge Minassian, Jacques Michaud
Institution: Centre hospitalier universitaires de l’Université de Montréal
Total Project Funding: $10.8 million

Every time someone with epilepsy has a seizure there is a risk of brain damage. This is particularly true for children. Unfortunately, today’s anti-epileptic drugs simply don’t work on about one third of patients. The team led by Drs. Patrick Cossette, Berge Minassian and Jacques Michaud will identify genes that are associated with epilepsy and that are predictive of the response to various antiepileptic drugs. This will result in earlier and more effective care and potentially prevent cognitive decline in children.
This project is co-led with Genome Quebec.
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Biomonitoring 2.0: A high-throughput genomics approach to comprehensive biological assessment of environmental change (2010)

Project Leader: Mehrdad Hajibabaei
Institution: University of Guelph
Total Project Funding: $3.1 million

Sustainable development of the Canadian economy requires wise stewardship of our environment and natural resources; this is particularly true given the anticipated impacts of climate change. Biomonitoring seeks to describe and understand biological diversity at multiple ecological levels, both as a means to learn the typical mix of species that can be found in different habitats, and to establish “biological early-warning systems” that can tell us when environmental stresses are reaching a critical point. Canada is recognized as a world leader in biomonitoring, however, current practices have limitations.  They are personnel-intensive, which limit the frequency and intensity of sampling, particularly in remote areas. Also, present biomonitoring methodologies focus on a very limited subset of all species that can be found at a given location. Our project introduces ‘Biomonitoring 2.0’, a system based on cutting-edge DNA-sequencing technologies and state-of-the-art computational analysis, which will simultaneously reduce sample costs while dramatically increasing the knowledge gained from biological samples. Our test bed for this new system is Wood Buffalo National Park, a globally unique region spanning Alberta and the North West Territories that is under considerable threat from oil sands activities and other human impacts, in spite of its remoteness and protected status. By integrating our new genomics tools and technologies into a well-established Canadian biomonitoring framework, we will greatly increase our potential to manage our cherished national resources. The project team has been working closely with stakeholders including industry, government departments, First Nations and Métis, and environmental organizations. By developing a sophisticated, yet user-friendly Web-based portal, with client-based customized tools, we will be able to communicate much richer summaries of environmental health and impacts to society, through direct interactions with local stakeholders. www.biomonitoring2.org 
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NorCOMM2 – In vivo models for human disease & drug discovery (2010)

Project Leaders: Colin McKerlie, Steve Brown
Institution: Mount Sinai Hospital
Total Project Funding: $10.9 million

Identification of the genes associated with human disease is essential to the development of new prognostic, diagnostic, and treatment options. However, to understand what happens when genes go wrong, we need to understand the normal function of all our genes. This can’t be done using humans, so experimental models similar to humans in their development, physiology, and disease state that are easy to study and genetically manipulate are needed. The mouse meets these criteria so it is the most widely used animal model in biomedical research today. In fact, 99% of the coding genes (genes that make a protein) present in humans are also present in the mouse. Therefore, the mouse will help us with one of the greatest scientific challenges ahead; to understand the function of each of our 20,000 genes. This is an enormous task and the International Mouse Phenotyping Consortium has been formed by scientists in North America, Europe, and Asia to take on the challenge in a coordinated global effort.

The Project is made up of a team of Canadian and UK scientists who, over the next three years, will use publicly available resources to study the developmental problems and diseases that occur in 280 mouse models. Each of these models contains one mutated gene (different in each model) that no longer works or only partly works. The differences in the mutant models compared to normal mice will help us determine the function of that gene. This Project will represent a significant contribution by Canadian scientists to the international effort. We will use clinical tests like those used for humans (e.g. blood work, X-ray) to determine the effect of each mutation and whether the gene or the protein it produces could be a drug target or used in a diagnostic test. Our Canadian group brings specialized expertise to examine mutations in genes that cause embryonic death as well as world-leading experience in pathology screening for disease. Our team includes social scientists who will examine how this and other international research efforts can best be managed and share data and other resources to increase their real-world impacts. The global effort to understand the function of every gene is a huge project that will take the next 10 years to complete. Canada has a critical role to play. Like our UK partners, we have expertise and state-of-the-art facilities that have enabled us to establish a leadership position in this field. The knowledge generated and new discoveries made in this Project will enable the development of new drugs and new therapies by Canadian researchers in academia and the biopharmaceutical industry. Our Project has already partnered with drug discovery scientists at the Ontario Institute for Cancer Research and commercialization partners at MaRS Innovation in Toronto to create an opportunity to attract contract research to Canada and support Canadian companies that can capitalize on the mouse models that we generate. www.NorCOMM2.org
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Synthetic antibody program: Commercial reagents and novel therapeutics (2010)

Project Leaders: Sachdev Sidhu, Charles Boone
Institution: University of Toronto
Total Project Funding: $9.8 million

Cancer is now, or will shortly become, the number one cause of death in developed countries. Hence, there is an obvious and urgent need to accelerate the development and rational application of new therapies. The central premise of our program is that achieving this goal will require the identification of new therapeutic targets, the rapid development of specific and effective drugs directed against these targets, and the testing of these agents in relevant models of human cancer. Over the past decade, recombinant antibodies that target cancer-associated proteins have emerged as one of the most effective and major classes of targeted therapeutics in oncology. Moreover, while the production of small-molecule drugs remains a costly and slow process, technological advances have enabled the development of therapeutic grade antibodies in an academic setting, which now expands the cancer therapeutic domain beyond that of pharmaceutical companies.

To take advantage of these new developments, the Donnelly Centre at the University of Toronto has established the Toronto Recombinant Antibody Centre (TRAC), a state-of-the-art antibody platform that can be applied to the generation of therapeutic grade antibodies against hundreds of antigens in a high-throughput pipeline. In turn, the TRAC has partnered with the Centre for Drug Research and Development (CDRD) in Vancouver to leverage additional expertise in therapeutic antibody development. Importantly, we have assembled a consortium of leading cancer biologists from the Canadian research community, and together, we have compiled a panel of cancer related proteins that are high-value targets for next-generation cancer therapeutics. Taken together, our program represents a unique and complete platform for the development of antibody therapeutics in a Canadian academic environment. In a three-year framework, we will generate and validate hundreds of antibodies against a host of cancer-associated targets. These antibodies will be powerful tools for discovery research and a significant subset will be candidates for new therapeutic entities. In summary, the program will have major impact on basic research in cancer biology, on therapeutic options for cancer treatment, and on the development of commercial biotechnology in Canada.
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Stratifying and targeting pediatric medulloblastoma through genomics (2010)

Project Leaders: Michael Taylor, David Malkin, Marco Marra
Institution: The Hospital for Sick Children
Total Project Funding: $4.8 million

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. This results in a staggering burden of suffering for them and their families as well as economic costs of over $100 million annually to the health system. 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.

With support from Genome Canada, 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 tumors for treatment. Researchers are also identifying genetic changes that may reveal the risk factors that predispose children to this type of cancer. As they unravel the genetic basis of brain cancer, the research team is also working with families to determine what additional risks they are willing to assume in reducing therapy to improve quality of life. It is anticipated that the results of this research will lead to new ways to treat childhood brain cancers more effectively and to enhance the quality of life of children struck by this devastating disease.
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