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Genome Alberta Portfolio
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Sector
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Projects |
Total Funding
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134 Genomics-Focused Initiatives
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Health |
39 projects
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$191M
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Over $573M Total Portfolio
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Agriculture/
Agri-Food
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57 projects
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$178M
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$221M of Genome Canada Funding
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Natural Resources
& Environment
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24 projects
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$160.1M
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Over $72M in Alberta Investments
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Platform/Other |
14 projects
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$44M
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If you would like more information about our project portfolio please
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Click Individual Title to Expand Project /
Principal Investigators
Project Lead -
- Stuart Turvey, BC Children's Hospital Research Institute
Project Co-Lead -
- Michael Kobor, BC Children's Hospital Research Institute
- Brett Finlay, Michael Smith Laboratories
- Padmaja Subbarao, Hospital for Sick Children
Alberta Researchers
- Tim Caulfield, University of Alberta
- Piush Mandhane, University of Alberta
Lead Centre
Lead Centre -
Co-Lead Centre
Participating Centre
Project Manager
Kate Del Bel
Diana Lefebvre
Notes
Project Summary
Asthma is now the most common chronic disease of childhood, affecting 1 in 7 Canadian children. It is also expensive with a total cost to treat estimated at over $2billion per year in Canada. This research program focusses on gut microbiome composition. Using new genomic technologies to analyse stool samples from babies, we may be able to predict which ones will go on to have asthma, and even better, our research will guide the ethical development of safe ways to replace these microbes to prevent asthma developing in the first place.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health funded initiative.
Principal Investigators
Project Lead -
- Francois Rousseau, Laval University
Project Co-Lead -
- Sylvie Langlois, University of British Columbia
Alberta Researchers -
- Christopher McCabe, University of Alberta
- Tim Caulfield, University of Alberta
Lead Centre
Lead Centre -
Co-Lead Centre -
Participating Centre -
Notes
Project Summary
Non-invasive prenatal screening (NIPS) genomics analysis of cell free DNA in maternal blood has the potential to perform well as a first-tier screening test for aneuploidies (T13, T18, T21). NIPS use as a first-tier screening test would simplify, streamline and enhance the safety of prenatal screening for fetal aneuploidies and could potentially detect other important fetal abnormalities. However, critical challenges must be tackled to offer NIPS to 450,000 pregnant women per year in Canada’s heterogeneous public health care system. This project aims to fill in evidence gaps related to 1) moving NIPS from a 2nd-tier screening test to a 1st-tier screening test; and 2) informing whether NIPS should also screen for other actionable chromosomal conditions.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health funded initiative.
Principal Investigators
Project Lead -
- Paul Keown, University of British Columbia
Project Co-Lead -
- Ruth Sapir-Pichhadze, McGill University
- Timothy Caulfield, University of Alberta
- Stirling Bryan, University of British Columbia
Alberta Researchers -
- Patricia Campbell, University of Alberta
- Michael Mengel, University of Alberta
- Banu Sis, University of Alberta
- Noureddine Berka, University of Calgary
- Lee Anne Tibbles, University of Calgary
- Scott Klarenbach - University of Alberta
Lead Centre
Lead Centre -
Co-Lead Centre -
Participating Centre -
Notes
Project Summary
Asthma is now the most common chronic disease of childhood, affecting 1 in 7 Canadian children. It is also expensive with a total cost to treat estimated at over $2billion per year in Canada. This research program focusses on gut microbiome composition. Using new genomic technologies to analyse stool samples from babies, we may be able to predict which ones will go on to have asthma, and even better, our research will guide the ethical development of safe ways to replace these microbes to prevent asthma developing in the first place.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health funded initiative.
Principal Investigators
Project Lead -
Project Co-Lead -
- Francois Bernier, University of Calgary
- Michael Brudno, University of Toronto
- Clara van Karnebeek, University of British Columbia
Notes
Project Summary
There are about 7,000 rare genetic diseases (RDs) that affect more than one million Canadians. RDs have a devastating impact on Canadians: two-thirds cause significant disability, three-quarters affect children, more than half lead to early death, and almost all have no treatment. The cause of more than one-third of the 7000 RDs is currently unknown. To understand the remaining unsolved RDs, C4R-SOLVE is exploring new sequencing technologies and improving data sharing world-wide, enabling the discovery of new causes of RDs. By achieving its goal, the C4R-SOLVE project will more than double our ability to diagnose this one third of RD patients, while building the infrastructure and tools needed to improve RD diagnosis around the world.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health funded initiative.
Principal Investigators
Project Lead -
- Rae Yeung, University of Toronto
Project Co-Lead -
- Susanne Benseler, Alberta Children's Hospital Research Institute, University of Calgary
Alberta Researchers -
- Deborah Marshall, University of Calgary
- Marvin Fritzler, University of Calgary
- Marinka Twilt, University of Calgary
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
Living with arthritis severely affects a child's ability to enjoy regular activities with friends and family and participate in school. Recently, effective drugs called "biologics" have become available for children with arthritis. They are expensive, however, causing a burden on public and private health care systems. In this project, we will allow doctors and families to quickly know: 1) who needs biologics, 2) which biologic works best for the individual child and 3) when can the biologic be safely stopped. Our research team will develop the first genomics-based, low-cost biomarker blood tests to rapidly identify the best treatment for each individual child, completely transforming the care of childhood arthritis. Project outcomes are expected to have immediate impact on treatment and quality of life for children with arthritis.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health
Principal Investigators
Project Lead -
- Ian Lewis, University of Calgary
Project Co-Lead -
- Hallgrimur Benediktsson, University of Calgary
Alberta Researchers -
- David Schriemer, University of Calgary
- Sergei Noskov, University of Calgary
- Chris Naugler, University of Calgary
- Bruce Dalton, Alberta Health Services
- Thach Lang, Alberta Health Services
- Fiona Clement, University of Calgary
Notes
Project Summary
The global rise in the prevalence of antibiotic resistant bacteria is a serious problem, threatening all modern medicine. A primary reason is the one-size-fits-all approach to treating infections, which encourages over use of drugs and results in unnecessary sickness and death. To address this problem, the project is using metabolomics to create an automated analytical system and database for predicting potential risks posed by each individual infection. It will implement a new Precisions Infection Management (PIM) strategy allowing clinicians to match patients to the exact level of antibiotic therapy necessary to cure infections without unnecessarily selecting for antibiotic resistant bacteria.
Genome Canada - 2017 Large-Scale Applied Research Project: Genomics and Precision Health funded initiative.
Principal Investigators
Project Lead -
- David Wishart, University of Alberta
Project Co-Lead -
- Christoph Borchers, University of British Columbia
Lead Centre
Lead Centre -
Co-Lead Centre
Notes
Project Summary
The Metabolomics Innovation Centre (TMIC) was launched in 2011 as a Genome Canada Science and Technology Innovation Centre. TMIC now serves as Canada’s national metabolomics laboratory and is mandated to provide Canadian scientists and trainees with access to comprehensive, cutting-edge metabolomic services and technologies. TMIC has nodes at Universities across Canada.
Genome Canada Genomics Technology Platform - GTP
Principal Investigators
Project Lead -
- Ian Lewis, University of Calgary
Project Co-Lead -
- Hallgrimur Benediktsson, Alberta Precision Laboratories
Alberta Researchers -
- Amir Sanati-Nezhad, University of Calgary
Notes
Project Summary
Currently, it takes 2-5 days to identify bloodstream infection (BSI) pathogens and perform antibiotic susceptibility testing. Patients who receive the wrong antibiotic over this time are ten times more likely to die. We are developing MicroSepDx™, a fully-integrated microbiology detection platform for identifying BSI pathogens and measuring antibiotic susceptibility decreasing the existing analytical timeframe to under 8 hours.
Genome Canada Genomic Applications Partnership Program - GAPP funded initiative.
Principal Investigators
Project Lead-
- Leonard Foster, University of British Columbia
Project Co-Lead -
- David Wishart, University of Alberta
Notes
Project Summary
The project will develop computational tools based on recent developments in advanced statistical algorithms, referred to as “deep learning,” to handle the “big data” generated by metabolomics. The first tool, DeepMet, will increase the number of molecules that can be identified in metabolomic experiments. The second, MetUnknown, will help assign chemical structures to molecules that are as of yet unknown. Together, these tools will help shine a light on the 98% of the metabolome that is overlooked by current methods.
Genome Canada - 2017 Bioinformatics and Computational Biology Competition
Principal Investigators
Project Lead
- Karen Goodman, University of Alberta - Alberta Public Laboratories
Project Co-Applicants
- Janis Geary, University of Alberta
- Jessica Dutton, Aurora College
Notes
Project Summary
Our proposed project seeks to address microbial genomics data management challenges by generating information required to develop data sharing processes that respect community values for H. pylori genomics research.
Specifically, we aim to: 1) Describe the current policies that govern sharing of microbial genomics data generated by Indigenous research partnerships; 2) Identify the potential impacts of H. pylori genomics data sharing on the Indigenous communities and groups whose members donate specimens.
Genome Canada and SSHRC - Societal Implications of Genomics Research
Principal Investigators
Project Lead -
- Ralf Paschke, University of Calgary
Project Co-Lead -
- Markus Eszlinger, University of Calgary
Project Co-Applicants -
- Douglas Demetrick, Alberta Precision Laboratories
- Martin Sommerville, University of Alberta
Notes
Project Summary
Clinicians in Canada are faced with a lack of tools needed to appropriately stratify patients that present with thyroid nodules. Thus, many patients undergoing screening for suspicion of thyroid cancer are exposed to invasive and often unnecessary diagnostic procedures. The project team has developed the ThyroSPEC™ assay, a highly accurate, cost-efficient mass spectrometry based mutation detection panel that allows for the identification of the most prevalent mutations associated with thyroid cancer. This project aims to clinically validate and implement the current version of the ThyroSPEC™ assay in a routine diagnostic setting in Alberta.
Genome Alberta Strategic Initiatives Program (SIP)
Principal Investigators
Project Lead
- Quan Long - University of Calgary
Project Co-Applicants
- Paul Gordon - University of Calgary
- Guido van Marle - University of Calgary
Notes
Project Summary
Third-Generation Sequencing (TGS) technology offers an exciting breakthrough opportunity for virology researchers. However, TGS faces technical challenges including a relatively high base calling error rate that is hard to distinguish from the high mutation rate of viruses. This project will develop novel tools for TGS by taking advantages of existing development focusing on base calling of TGS, viral evolution and viral transmission. We aim to develop tools characterizing viral transmissions and viral evolution in the presence of sequencing errors; and to validate the tools by analyzing HIV epidemiology, evolution and pathogenesis. These tools will enhance our understanding of HIV, and will be widely applicable to study other viral evolution, epidemiology and pathogenesis questions.
Funded under the Enabling Bioinformatics Solutions competition.
Principal Investigators
Project Lead
- Tarah Lynch, University of Calgary
Project Co-Lead
- Matthew Croxen, Alberta Public Laboratories
Project Co-Applicants
- Gregory Tyrrell, University of Alberta
- Tanis Dingle, Alberta Public Laboratories
- Daniel Gregson, Alberta Public Laboratories
- Johann Pitout, Alberta Public Laboratories
- Tom Griener, Alberta Public Laboratories
Notes
Project Summary
The goal of this proposal is to generate a portable and flexible platform that generates results from routine bioinformatics workflows, and adds the output to an accessible, database which can be integrated with additional data as needed. This goal will be achieved by the following three objectives: (1) develop a flexible database architecture to manage HTS data and capture analytical output; (2) establish exemplar bioinformatics workflows to analyze pertinent organisms; (3) generate a user-friendly interface to access the data. This platform will be compatible with Alberta Precision Laboratories (APL) server infrastructure and current APL database schemas.
Funded under the Enabling Bioinformatics Solutions competition.
Principal Investigators
Project Lead
- Ian Lewis - University of Cagary
Project Co-Lead
- Daniel Gregson - Alberta Public Laboratories
Project Co-Applicants
- Brian Yipp - University of Calgary
- Lorne Tyrell- University of Alberta
- Sergei Noskov - University of Calgary
- Andre Buret - University of Calgary
- Yonatan Grad - Harvard T.H. Chan School of Public Health
Notes
Project Summary
The COVID-19 pandemic has created a global medical and economic crisis. Laboratory testing capacity has played pivotal role in our national response to this emergency. The shift from targeted, clinically oriented testing, to widespread high-throughput community testing may dramatically increase the need for affordable COVID19 tests. Although many new assays are coming online, most of the existing and emerging diagnostic tests work by detecting the SARS-CoV-2 genetic material and ultimately will suffer from the same supply chain limitations. To address this, our research team is developing an alternative proteomics-based assay for detecting the virus directly from nasal swabs. Our proteomics strategy does not require any specialized supplies and could enable up to 1,000 tests per day per instrument.
Funded under the Alberta COVID-19 Rapid Response Program competition.
Principal Investigators
Project Lead -
- Francois Bernier, University of Calgary
Project Co-Leads -
- Carolyn O'Hara, Alberta Public Laboratories
- Dennis Bulman, Alberta Children's Hospital Research Institute, University of Calgary
Notes
Project Summary
Alberta patients with or suspected of having rare genetic diseases continue to face lengthy diagnostic odysseys, and clinical genome wide sequencing has emerged as a rapid and cost effective approach to diagnosis. Large scale clinical genomics are not available in Alberta, and APL has relied mainly on US commercial labs to provide clinical GWS at significant, and increasing, cost. This project proposes to address whether all or most costs could be offset by implementation of clinical GWS in Alberta, as well as addressing concerns associated with reliance of non-Canadian providers (i.e. availability of data for re-analysis and secondary uses, privacy and legal concerns).
Funded under the Genome Canada Genomics Applications Partnership Program.
Principal Investigators
Project Lead
- Jason de Koning, University of Calgary
Project End-Users
- Francois Bernier, University of Calgary
- Paul Gordon, University of Calgary
- Billie Au, University of Calgary
- Gerald Pfeffer, University of Calgary
Notes
Project Summary
Rare genetic diseases are individually rare but collectively quite common, affecting approximately 3 million Canadians. Unlike common diseases, genetic causes for rare diseases must often be hypothesized from plausibility criteria, and identified through progressive exclusion of candidate variants in a single case or a small number of heterogeneous cases. Few integrated software systems exist to aide geneticists, and commercially products available are often expensive, based on closed-source algorithms, and have diagnostics criteria that depend strongly on well characterized disorders. We aim to improve this by putting more powerful, open source tools for reproducible causal-gene discovery in the hands of Alberta geneticists, meeting a significant unmet need in the Alberta health genomic community.
Funded under the Enabling Bioinformatics Solutions competition.
Principal Investigators
Project Lead
- Matthew Croxen - Alberta Public Laboratories
Project Co-Lead
- Linda Chui - University of Alberta
Project Co-Applicants
- Amanda Melin - University of Calgary
- Paul Gordon - University of Calgary
- Nathan Zelyas - University of Alberfta
- Byron Berenger - Alberta Health Services
- Francois Bernier - University of Calgary
- Guido van Marle - University of Calgary
- Bonita Lee - University of Alberta
Notes
Project Summary
Mutations are common and expected in coronaviruses genomes. We can take advantage of these mutations to track the spread of the viruses in the community, providing vital public health information on the movement and potential sources of disease. To improve on the speed in generating this genetic information, we will rapidly generate genetic sequences of over 1,900 of these viruses . We will also validate automated methods to rapidly sequence viral genomes at the Public Health Laboratory on an ongoing basis. This information will help public health better understand the dynamics of viral spread in Alberta, so that policies to stop disease spread can be used more effectively, as well as provide important information for diagnostics, therapeutics, and vaccine development.
Funded under the Alberta COVID-19 Rapid Response Program
Principal Investigators
Project Lead
- Francois Bernier, University of Calgary
Project Co-Lead
- Jim Kellner, University of Calgary
Project Co-Applicants
- Marvin Fritzler, University of Calgary
- Michael Esser, University of Calgary
- Graham Thompson, University of Calgary
- Matthew Croxen, Alberta Public Laboratories
- Nils Forkert, University of Calgary
Notes
Project Summary
Working in concert with Alberta Health Services Public Health Officers, leading clinicians and Alberta Public Laboratories, the team will recruit the Alberta Childhood COVID-19 Cohort (ABCCC), consisting of all children under the age of 18 who undergo testing for the SARS-COV2 virus. Specifically the project will 1) assess the role of children’s immune response as well as their genetic makeup in order to determine risk factors for severe illness and gain insight into targeted treatments, and 2) study the epidemiology of pediatric COVID-19 infections by reading the viral genome to determine the origin and transmission patterns in Alberta of pediatric COVID-19 infections.
Genome Canada COVID-19 Regional Genomics Initiative - Alberta COVID-19 Rapid Response Program
Principal Investigators
Project Lead
- Dylan Pillai - University of Calgary
Project Co-Lead
- Charles Chiu - University of California, San Francisco
Project Co-Applicants
- Byron Berenger - Alberta Health Services
- Guido van Marle - University of Calgary
Project Collaborator
- Xian Ding Deng - University of California, San Francisco
Notes
Project Summary
Our group has developed an approach called "Metagenomic sequencing with spiked primer enrichment" (MSSPE) which allows for highly sensitive detection of viral genomes in complex matrices such as respiratory specimens. We seek here to validate MSSPE in clinical samples infected with human coronaviruses including 2019 novel coronavirus in collaboration with our public health partners. Once optimized, we then will use viral genome sequences to develop isothermal nucleic acid amplification tests (NAAT) assays that requires at most a lithium ion battery for point of care testing (POCT) .By coupling MSSPE and POCT methodology we hope to develop a paradigm for rapid deployment of novel viral diagnostic POCT for any viral pandemic threat leading to public health containment.
Funded under the CIHR COVID-19 program.
Principal Investigators
Project Lead -
- Casey Hubert - University of Calgary
Project Co-Lead -
- Alex Alexander - Alberta Health
Notes
Project Summary
The COVID-19 pandemic has demonstrated the urgent need for early warning surveillance systems that can provide information to public health authorities on emerging COVID-19 variants and other infectious diseases. Wastewater-based epidemiology (WBE) is a non-invasive, comprehensive and cost-effective early warning system that enables population-level monitoring independent of clinical testing. The research team has already developed an innovative platform for field-based sampling of wastewater followed by optimized nucleic acid purification in the lab. They have partnered with Alberta Health and municipal end-users to demonstrate that COVID-19 case numbers can be predicted with a six-day lead time, mirroring results from other teams globally. This project will leverage existing wastewater surveillance activities to analyze other high priority disease targets in Alberta municipalities and First Nations communities. As well as mitigating infection transmission and supporting the early detection of outbreaks, WBE can potentially create economic benefits by minimizing indirect effects of increased disease burden on employment, family structure, mental health, and education.
Genome Canada Genomic Applications Partnership Program (GAPP)
Principal Investigators
Project Lead -
- Pere Santamaria - University of Calgary
Project Co-Lead -
- Jord Cowan - Parvus Therapeutics
Notes
Project Summary
More than 100 autoimmune diseases have complex immune responses to autoantigens. Nanoparticles coated with autoimmune-disease-relevant peptide-major histocompatibility complexes (Navacims) have the potential to halt and cure autoimmune disease by restoring immune tolerance without compromising normal immunity to infections and cancer. They are currently the only technology that can activate internal generation of disease-specific regulatory T cells within the host. This project aims to understand the types of changes in the structure of the nuclear DNA of the cells that are re-programmed by Navacims, to expand the commercial and clinical potential of Parvus Therapeutics’ proprietary platform. It seeks to precisely define the cellular identity of the initial, transitional and final T cell types of this cellular re-programming process, and to identify biomarkers to monitor effectiveness and efficacy of treatment. This information will then be used to define, validate and develop a clinical/biomarker strategy for Phase 2 and Phase 3 trials, potentially revolutionizing the treatment of autoimmune diseases, many of which are multi-billion dollar per year markets.
Genome Canada Genomic Applications Partnership Program (GAPP)
Principal Investigators
Project Lead -
- Barb Thomas, University of Alberta
Project Co-Leads -
- Nadir Erbilgin, University of Alberta
- Yousry El-Kassaby, University of British Columbia
Alberta Researchers -
- Debra Davidson, University of Alberta
- David Wishart, University of Alberta
- Uwe Hacke, University of Alberta
- Andreas Hamann, University of Alberta
- Gwendolyn Blue, University of Calgary
- Henry An, University of Alberta
- Andy Benowicz, Alberta Agriculture and Forestry
- Deogratias Rweyongeza, Alberta Agriculture and Forestry
- Barry White, Alberta Agriculture and Forestry
- Lee Charleson, Alberta Agriculture and Forestry
Lead Centre
Lead Centre
Co-Lead Centre
Notes
Project Summary
The goal of the RES-FOR project is to integrate genomic, metabolomic and phenotypic data into selection models that will reduce the selection time and therefore the breeding cycles in lodgepole pine and white spruce tree improvement programs in Alberta. These new integrated models will help us produce healthy, productive, and resilient forests while informing policy, determining the economic value of genomic selection and identifying social/political factors influencing the use of these cutting-edge selection strategies.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment funded initiative
Principal Investigators
Project Lead -
- Sally Aitken, University of British Columbia
Project Co-Leads -
- Sam Yeamen, University of Calgary
- Richard Hamelin, University of British Columbia
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
Climate change is impacting forest health and productivity. We will use genomic tools combined with experiments testing trees’ resistance to heat, cold, drought stress, and disease to develop better reforestation options for Douglas-fir, lodgepole pine, western larch and jack pine. The results will help tree breeders and foresters select and plant trees that will be healthy in new climates in western Canada.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment funded initiative
Principal Investigators
Project Lead -
- Joerg Bohlmann, University of British Columbia
Project Co-Lead -
- Jean Bousquet, Universite Laval
Alberta Researchers -
- Janice Cooke, University of Alberta
Lead Centre
Lead Centre -
Co-Lead Centre -
Participating Centre -
Notes
Project Summary
Climate change affects Canada’s forests with increased frequency and severity of biotic (e.g., insects) and abiotic (e.g., drought) disturbances. Changing forest products markets demand improved wood quality and productivity to maintain Canada’s industry competitiveness. This project will deliver leading knowledge, socioeconomic decision support tools and applied genomic tools to significantly enhance conventional breeding programs and accelerate the development and deployment of genomics-improved spruce stock.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment
Principal Investigators
Project Lead
- Janice Cooke, University of Alberta
Project Co-Lead
- Catherine Cullingham, Carleton University
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
Over the past two decades, mountain pine beetle (MPB) has killed more than 20 M hectares of mainly lodgepole pine forests in western Canada. In the wake of this MPB epidemic, decision makers seek reforestation strategies that increase forest resiliency to future outbreaks. Simultaneously, the uncertain risk that MPB poses to jack pine challenges decision makers east and north of the epidemic to develop effective risk management plans that are commensurate with the risk posed to their jurisdiction. TRIA-FoR proposes an interdisciplinary and integrative approach to develop knowledge, tools and application frameworks that mitigate risk for the present MPB epidemic and improve resiliency in future epidemics. Risk and resiliency will be investigated in the context of MPB-pine-climate interactions that we believe affect MPB population dynamics, human dimensions in forest resource management, and impacts on diverse communities connected to forests at risk.
Genome Canada - 2020 Large-Scale Applied Research Project funded initiative.
Principal Investigators
Project Lead -
- Debbie McKenzie, University of Alberta
Project co-Lead -
- David Wishart, University of Alberta
Alberta Researchers -
- Ellen Goddard, University of Alberta
- Judd Aiken, University of Alberta
- David Coltman, University of Alberta
- Sabine Gilch, University of Calgary
- Evelyn Merrill, University of Alberta
- Hermann Schaetzl, University of Calgary
- Valerie Sim, University of Alberta
- Paul Stothard, University of Alberta
- David Westaway, University of Alberta
- Holger Wille, University of Alberta
Notes
Project Summary
Chronic wasting disease (CWD) is a fatal, transmissible, incurable disease affecting deer, moose, and elk in western Canada. The CWD project aims to advance our understanding of the biology of this disease. Together with managers, hunters, and First Nations they will develop new inclusive strategies to rapidly identify disease, allow early detection, and reduce disease spread risk.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment funded initiative.
Principal Investigators
Project Lead
- Douglas Muench, University of Calgary
Project Co-Lead
- Christine Marineau, Natural Resources Canada
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
Constructed wetland treatment systems (CWTS) are one of very few scalable and cost-effective technologies for remediating large volumes of wastewaters. An in-depth understanding of how these nature-based, passive, low energy systems operate to treat industrial waste is needed to enhance treatment efficacy in cold weather, particularly in northern environments that are challenged by short summers and cold winters. The surface mining of oil sands in the Athabasca region of northern Alberta, while contributing extensively to Canada’s gross domestic product and economic development, produces enormous volumes of toxic oil sands process-affected water (OSPW) that has accumulated on-site in storage facilities (currently exceeding 1 billion m3). This project is aimed at reducing OSPW toxicity through biodegradation processes that take place in CWTS. The goal of this project is to apply genomics-based methods and incorporate public preferences derived from Experimental Decision Laboratories (EDL) and artistic approaches to inform and enhance the efficacy of CWTS for the treatment of OSPW and to guide policy making.
Genome Canada - 2020 Large-Scale Applied Research Project funded initiative.
Principal Investigators
Project Lead -
- Steven Jones, Canada's Michael Smith Genome Sciences Centre, BC Cancer
Project Co-Lead -
- Maribeth Murray, University of Calgary
Notes
Project Summary
The richness of Canada's biodiversity is under threat today due to climate change, habitat destruction and novel emerging diseases. Now more than ever there is an increasing need for active human intervention to prevent further loss in biodiversity. A common thread across conservation strategies is the need for genomic tools to address knowledge gaps related to species evolution, adaption, viability and genetic diversity. A reference-quality whole genome sequence is the foundation for such genetic analysis and the subsequent development of these management tools. The Canadian BioGenome Project will lead Canada’s contribution to these efforts and will raise Canada’s profile in the field of conservation genomics. The goals of the project are to identify species (ca. 400) that are of specific relevance to Canada where genomic information and tools will be important to generate and develop policy recommendations for application of genomics to conservation and monitoring.
Genome Canada - 2020 Large-Scale Applied Research Project funded initiative.
Principal Investigators
Project Lead
- Maribeth Murray - University of Calgary
Project Co-Lead
- Peter Pulsifer - Carleton University
Project Co-Applicants
- Anna-Maria Hubert - University of Calgary
- Jennifer Parrott - Inuvialuit Regional Corporation
- Eric Solomon - Ocean Wise - Ikaarvik
Lead Centre
Lead Centre
Co-Lead Centre
Notes
Project Summary
Wildlife genome information is extremely valuable for environmental decision making, yet much remains unused for this purpose. This project draws together partners to co-develop a suite of genomics knowledge-mobilization tools that will support environmental decision making. Project activities and outcomes will support conservation, natural resource management, and the sustainability of Arctic wildlife. Outcomes will also support Canada’s efforts to protect Arctic species, and ensure food security for Arctic Peoples.
Instagram @ Arctic.Genomics
Genome Canada - Genomics in Society Interdisciplinary Research Teams competition.
Principal Investigators
Project Lead
- Elizabeth Edwards - University of Toronto
Project Co-Lead
Project Co-Applicants
- Ania Ulrich - University of Alberta
- Neil Thompson -University of Waterloo
- Michaye McMaster -SiREM
- Kris Bradshaw -Federated Co-Operative Limited
- Dan Kraemer -Imperial Oil
Project Collaborator
- Karen Budwill - Alberta Research Council
Project End-Users
- Sandra Dworatzek - SiREM
- Michaye McMaster - SiREM
- Kris Bradshaw -Federated Co-Operative Limited
- Dan Kraemer - Imperial Oil
Lead Centre
Lead Centre
Participating Centre
Notes
Project Summary
Genomics-based modeling of the microbial populations associated with BTEX biodegradation will allow for the development of additional bioremediation culture formulations and associated genomics monitoring tools, that can function in complex site-specific geochemical conditions present at many contaminated sites.
Funded under Genome Canada Genomics Application Partnership Program.
Principal Investigators
Project Lead -
- Lisa Gieg, University of Calgary
Project Co-Lead -
- Faisil Khan, Memorial University
- John Wolodko, University of Alberta
Notes
Project Summary
The geno-MIC project has 4 main goals: (1) Identify the microbial actors and pathways, chemical species, and MIC mechanisms that lead to facility failures; (2) Develop -omics and chemical-based monitoring tools to detect and measure MIC and associated chemical end-products; (3) Devise better predictive modelling and risk assessment tools to help improve materials design and maintenance/ operating practices. (4) Improve corrosion control strategies to reduce potential failures by developing standards and guidelines.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment funded initiative
Principal Investigators
Project Lead -
-
Casey Hubert, University of Calgary)
Project Co-Lead -
- Gary Stern, University of Manitoba
Alberta Researchers -
- Marc Strous, University of Calgary
- Maribeth Murray, University of Calgary
- Stephen Larter, University of Calgary
- Thomas Oldenburg, University of Calgary
Lead Centre
Lead Centre -
Co-Lead Centre -
Participating Centre -
Notes
Project Summary
Using genomics approaches to understand microbial communities within the Canadian Arctic environment, and who in the community degrades hydrocarbons under these conditions, is the goal of GENICE. This is being done by integrating knowledge from Arctic community and spill-response organizations into GENICE research, then putting project outcomes to practical use within existing spill response approaches.
Genome Canada - 2015 Large Scale Applied Research Project: Natural Resources and the Environment funded initiative
Principal Investigators
Project Lead -
- Casey Hubert, University of Calgary
Project Co-Leads -
- Adam MacDonald, Nova Scotia Department of Energy
- Todd Ventura, Saint Mary's University
Project Co-Applicants -
- Martin Fowler Applied Petroleum Technology AS
- Calvin Campbell, Natural Resources Canada
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
This project focuses on de-risking exploration and development in offshore Nova Scotia (NS) by the validation and integration of new genomics-based technologies with traditional exploration approaches. Promising bioassay strategies currently being developed will undergo rigorous validation testing towards commercial readiness, and new bioassay strategies based on state of the art lipidomics and metabolomics will be developed. The main deliverable for the project will be integration of different omics data layers with geochemistry and other geoscience into an easily accessible and marketable database for mapping target sites to enumerate the existence and type of reservoir leakage at prospective target sites.
Genome Canada Genomic Applications Partnership Program (GAPP)
Principal Investigators
Project Lead -
- Michael Dyck, University of Alberta
Project Co-Leads -
- John Harding, University of Saskatoon
- Bob Kemp, PigGen Canada
Project Co-Applicants
- Paul Stothard - University of Alberta
- Ellen Goddard - University of Alberta
- Ben Willing - University of Alberta
- Graham Plastow - University of Alberta
- Matthew Loewen - University of Saskatchewan
- Janet Hill - University of Saskatchewan
- Claire Rogel-Gaillard - INRA- The Jouy-en-Josas Research Centre
- Jack Dekkers - Iowa State University
- Bonnie Mallard - University of Guelph
- Claude Robert - University Laval
Project Collaborator
Lead Centre
Lead Centre
Co-Lead Centre
Notes
Project Summary
Genomics is being used to investigate how pigs respond to infection to minimize the impact of disease; an attribute referred to as disease resilience. The role of the microbiome, immune response, maternal effects, feed management, and producer decision-making behaviours are also being examined. The goal – to support the integration of resilience strategies into the pork industry.
Funded under Genome Canada 2014 Large Scale Applied Research Project: Genomics and Feeding the Future
Principal Investigators
Project Lead -
- Flavio Schenkel, University of Guelph
Project Co-Lead -
- Paul Stothard, University of Alberta
Project Co-Applicants
- Ellen Goddard, University of Alberta
- Jennie Pryce
- Erin Connor, United States Department of Agriculture
- Eileen Wall, Scotland's Rural College
- Mike Coffey, Scotland's Rural College
- Birgit Gredler, Qualitas AG
- Christine Baes, University of Guelph
- Angela Canovas, University of Guelph
- Mehdi Sargolzaei, University of Guelph
- Getu Hailu, University of Guelph
- Vern Osborne, University of Guelph
- Yuri Montanholi, Dalhousie University
- Zhiquan Wang, Unversity of Alberta
Project End-Users
- Daniel Lefebvre, Valacta
- Camiel Huisman, GrowSafe Systems
- Patti Beaumont, Lactanet
- Gerrit Kistemaker, Lactanet
- Janusz Jamrozik, University of Guelph
- Jarmila Johnston
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
The Efficient Dairy Genome Project is an international project whose research objectives will allow genomic selection of more feed efficient animals, which produce more milk with fewer inputs, while also producing less methane, a powerful greenhouse gas. Analyses will reveal the socio-economic and environmental benefits of selecting for these two traits and factors that may impact adoption of the technology.
Funded under Genome Canada 2014 Large Scale Applied Research Project: Genomics and Feeding the Future funded initiative.
Principal Investigators
Project Lead -
- Graham Plastow, University of Alberta
Project Co-Lead -
- Bob Kemp, Genesus Genetics
Notes
Project Summary
The objective of this project is to develop and validate genomic breeding values for crossbred pigs in order to maximize profitability for commercial producers. This will be achieved by collecting and integrating pedigree, genotype, and phenotype data of purebred nucleus and crossbred commercial pigs in order to select purebred lines that are proven to advance crossbred performance in commercial herds.
Genome Canada Genomic Applications Partnership Program - GAPP funded initiative
Principal Investigators
Project Lead -
- Eduardo Taboada, Public Health Agency of Canada
Project Co-Lead
- G. Douglase Inglis, Agriculture and Agri-Food Canada, Lethbridge
Project Co-Applicants
- Catherine Carrillo, Canadian Food Inspection Agency
- Linda Chui, University of Alberta
- Valerie Boras, Alberta Health Services
- Rita Finley, Public Health Agency of Canada
- Alex Wong, Carleton University
Notes
Project Summary
Campylobacterios is an acute intestinal illness caused by infection by bacteria within the genus, Campylobacter; it is the most commonly reported bacterial foodborne infection in Alberta and in Canada. Most cases of campylobacteriosis are caused by Campylobacter jejuni (Cj), with a significant proportion of Cj infections associated with the consumption of contaminated chicken products. Data from the chicken supply chain and human clinical cases shows that Canadian strains in circulation are extremely diverse and fewer that 5% of strains are responsible for >50% of human infections. The goal of this project is to use whole genome sequencing to identify molecular signatures for rapid, sensitive and accurate detection of high risk Cj strains relevant to the poultry sector.
Funded under the Alberta Applied Agriculture Genomics Program (A3GP).
Principal Investigators
Project Lead -
- Marcus Samuel, University of Calgary
Project Co-Applicants -
- Douglas Muench, University of Calgary
- Gordon Chua, University of Calgary
- Sateesh Kagale, National Research Council
- Raju Soolanayakanahally, Agriculture and Agri-Food Canada (AAFC)
Notes
Project Summary
This project will harness proprietary genetic technologies that aim to manipulate hormonal signaling in wheat to develop new, improved, abiotic stress-resistant wheat varieties. This will be followed by further incorporation of this genetic improvement into elite Canadian wheat varieties (e.g. both bread and durum) based on conventional breeding schemes.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Changxi Li, Agriculture and Agri-Food Canada
Project Co-Lead -
- John Basarab, Alberta Agriculture and Rural Development
Project Co-Applicants -
- Paul Stothard, University of Alberta
- Graham Plastow, University of Alberta
- Carolyn Fitzsimmons, University of Alberta
- Michelle Miller, Delta Genomics
- Sinead Waters, Teagasc - Agriculture and Food Development Authority
Notes
Project Summary
To promote wider application of genomic tools in the industry, the project aims to refine genomic prediction tools to improve prediction accuracy by increasing genotype and phenotype data from multiple beef breeds and by analyzing multiple layers of beef cattle “omics” data. The project will also develop a user-friendly platform, which will be a web-based portal with multiple, relevant modules. The genomic prediction platform with improved accuracy will help service providers to deliver genomic decision support tools to their customers, which will allow the beef industry to improve beef production efficiency and quality via selection and management of genetics in their herd.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Athan Zovoilis, University of Lethbridge
Project Co-Leads -
- Jason de Koning, University of Calgary
- Paul Stothard, University of Alberta
Notes
Project Summary
In response to stakeholder consultations across the province, recommendations from post-secondary institutions, and support from the broader research and end-user community, Genome Alberta has developed BioNet Alberta for Genome Canada’s Regional Priorities Partnership Program (RP3). BioNet Alberta is a diverse network-based approach to building provincial capacity in the area of B/CB. The Network is structured around 4 key Pillars: (1) Network Management, Outreach, and Knowledge Exchange; (2) Training and Development; (3) Computational Solutions and Tool Development, and (4) Implementation of Pan-Alberta Service Platform. This multi-tiered approach will provide a distributed platform to develop a more cohesive genomics and B/CB community that is expected to enhance research and development capacity.
Twitter: @AlbertaBioNet
Genome Canada Regional Priorities Partnership Program (RP3)
Principal Investigators
Project Lead -
- Peter Facchini, University of Calgary
Project Co-lead -
Project Co-Applicant -
- Jillian Hagel, Willow Biosciences Inc
Notes
Project Summary
Opiates are the primary drugs used in Western medicine for pain management and palliative care. Cultivation of opium poppy crops outside of North America remains the sole source for essential medicines including codeine, morphine and thebaine. Continued reliance on opium poppy cultivation is problematic owing to uncertain crop yields due to environmental factors, climate change, disease and pests. To circumvent these issues, we are using plant-based genomics resources to establish an alternative bioproduction system for high-value opiates in a reliable, environmentally benign, scalable, and cost-effective yeast fermentation platform. An overarching goal is the establishment of a high-titer opiate bioproduction platform in baker’s yeast from thebaine feedstock using plant and microbial genes.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
Project Co-Applicants-
- Kelly Turkington, AAFC
- Wen Chen, AAFC
- Richard Hamelin, University of British Columbia
Notes
Project Summary
Many of the most devastating crop diseases are caused by airborne microorganisms: late blight in potato, rusts in wheat, white mould in bean, and Sclerotinia stem rot in canola. NGS technologies could allow us to detect, quantify and forecast all these organisms – and more – at the same time, thereby increasing the efficiency of currently used methods. The goals of the current research are to characterize the airborne microbial diversity in agricultural fields across Alberta using NGS technologies and to benchmark the performance of these technologies against other validated methods (microscopy and other molecular methods).
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Paul Stothard, University of Alberta
Project Co-Lead -
- Graham Plastow, University of Alberta
Project Co-Applicants -
- Russell Greiner, University of Alberta
- Benjamin Willing, University of Alberta
- Kirill Krivushin, University of Alberta
Notes
Project Summary
Overall goal is to develop a tool for selection of pigs that are resilient in the face of multiple natural infections. To achieve this, detailed data characterizing the physiology, genomics, and health status of pigs will be analyzed by applying a variety of algorithms from the field of machine learning to find patterns that accurately predict which animals remain healthy despite being exposed to a variety of bacterial and viral pathogens. Once patterns are discovered, they can be used to inform breeding decisions.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Graham Plastow, University of Alberta
Project Co-Lead -
- John Harding, University of Saskatchewan
Notes
Project Summary
Understanding of reproductive PRRS, as well as creating data to validate genomic results from previous studies are essential to develop new tools to combat PRRS. Previous research identified a single genetic marker (SNP) on chromosome 7 (DRGA) associated with a substantial improvement in fetal viability following PRRSV infection of pregnant dams. This region includes a gene associated with metabolism of a hormone associated with growth and other biological processes. Levels of this hormone in fetal and maternal serum decrease following PRRSV infection, which is likely to have a negative impact on fetal growth and development, and such levels during late gestation may also induce a critical endocrine state responsible for a significant portion of virus-induced fetal death. The goal of this project is to determine if DRGA is causally associated with PRRSV fetal viability. Confirmation of DRGA’s association with fetal viability will facilitate the natural selection for PRRS resilient fetuses, potentially providing an alternative means to control reproductive PRRS that is not reliant on genetic modification or editing.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Graham Plastow, University of Alberta
Project Co-Lead -
- Andrea Doeschl-Wilson, The Roslin Institute, University of Edinburgh
Notes
Project Summary
The primary aim of this pilot project is to develop the experimental protocol and generate preliminary data and statistical tools for future efforts to identify, validate, and demonstrate the efficacy of genomics-based tools to select for resilience in pig production systems. Ultimately, this will improve animal welfare and decrease cost of production, as well as help reduce the environmental impact and the threat of antimicrobial resistance from pig production.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Jeroen De Buck, University of Calgary
Project Co-Lead
- Herman Barkema, University of Calgary
Notes
Project Summary
We propose to use state-of-the-art genomics and metagenomics approaches to identify influential members of the mammary gland microbiota with central roles in maintaining udder health and modulating mastitis susceptibility. An innovative approach will be used for targeted isolation and characterization of these beneficial "foundation species" from the native microbial community of the udder. A combination of foundation species will help develop a synthetic mini-microbial community to be tested against major mastitis pathogens. In addition, to bridge the gap between basic laboratory science and translational research, both safety and efficacy of our microbiome-based therapeutic will be further assessed in controlled experiments involving lactating cows.
Alberta Applied Agriculture Genomics Program (A3GP)
Principal Investigators
Project Lead -
- Paul Stothard, University of Alberta
Project Co-Lead -
- Gary Van Domselaar, Public Health Agency of Canada
Lead Centre
Lead Centre -
Co-Lead Centre -
Notes
Project Summary
The goal of this project is to provide a suite of analytical tools that can accurately put together the jumbled collection of sequence fragments coming out of current genome sequencing instruments, to identify the genes and other embedded “instructions”, and then to illustrate them in ways that are familiar to researchers, and in ways that are useful for conveying important genomic information that may provide new insights and aid in making scientific discoveries that benefit Canada’s bioeconomy.
Genome Canada - 2017 Bioinformatics and Computational Biology Competition
Principal Investigators
Project Lead
- Rodrigo Ortega-Polo, AAFC Lethbridge Research and Development Centre
Project Co-Lead
- Marc Robinson-Rechavi, Université de Lausanne
Project End-Users
- Agriculture and Agri-Food Canada
- ShelleyHoover, Alberta Agriculture and Rural Development
- Patricia - Wolf Veiga, National Bee Diagnostic Centre/Grande Prairie Regional College
- RenataBorba, Alberta Beekeepers Commission
Project Co-Applicants
- Athan Zovoilis, University of Lethbridge
- Amro Zayed, York University
- Benjamin Dainat, Swiss Bee Research Centre
- Philipp Engel, University of Lausanne
- Vicent Doublet, University of Ulm
- Jacques Dainat, National Bioinformatics Infrastructure Sweden, SciLifeLab, Uppsala University
Notes
Project Summary
The recent advent of sequencing technologies has enabled the generation of a large amount of bee microbiome data from different sources. There is an urgent need for those bee microbiome datasets to be made more accessible so that information can be applied for scientific discoveries and can be translated for stakeholder use. The goal of this project is to advance the development of the BeeBiome Data Portal, which was initiated by the international Bee Microbiome consortium (http://beebiome.org/). The portal will maximize the value of the complex and diverse bee microbiome datasets by enabling analysis and dissemination of information on the microorganisms and viruses associated with bees.
Funded under the Enabling Bioinformatics Solutions Competition
Principal Investigators
Project Lead
- Michael Dyck, University of Alberta
Project Co-Lead
- Bob Kemp, Genesus Genetics
Project Co-Applicants
- John Harding, University of Saskatchewan
- Graham Plastow, University of Alberta
- Jack Dekkers, Iowa State University
- Bonnie Mallard, University of Guelph
Project End-Users
- Bob Kemp, Genesus Genetics
- Tim Nelson, PigGen Canada
Notes
Project Summary
The project goal is to validate and deliver genomics-based selection tools that will increase the rate of genetic improvement for disease resilience in pigs by 30%. Objectives are to: (1) fully validate promising disease resilience indicator traits and genomic tests in a health-challenged environment; (2) validate and implement the genomic tests and indicator traits of disease resilience in high-health breeding herds; (3) develop a genomic data and evaluation pipeline for use in high-health breeding herds, and (4) assess the impact of incorporating disease resilience into existing genetic improvement programs.
Funded under Genome Canada Genomics Applications Partnership Program
Principal Investigators
Project Lead
- Graham Plastow, University of Alberta
Project End-User
- Jack Behan, Alpha Phenomics
Notes
Project Summary
The goal of this project is to develop a powerful and efficient computing algorithm for whole-genome sequence association and prediction analyses. This project will provide the Alberta beef industry and research institutions with a powerful tool for fast integration of sequence information into genomic research and applications. Specifically, the newly developed algorithm and platform are expected to facilitate the identification of the causal mutations for complex traits due to the simultaneous modelling of sequence variants and their annotation information. It is also expected to improve the accuracy of genomic prediction compared to the current array-based methods from using the whole genome sequence variants and their genome annotation information in the prediction.
Funded under the Enabling Bioinformatics Solutions competition.
Principal Investigators
Project Lead
- Christine Baes - University of Guelph
Project Co-Leads
- Marc-Andre Sirard - University Laval
- Paul Stothard - University of Alberta
- Ronaldo Cerri - University of British Columbia
Project Co-Applicants
- Ellen Goddard - University of Alberta
- Flavio Schenkel - University of Guelph
- Jennie Pryce - Agriculture Victoria
- Ezequiel Nicolazzi - The Council on Dairy Cattle Breeding (US)
- John Cole - United States Department of Agriculture - Agriculture Research Services
- Oscar Gonzalez-Recio - Universiad Politecnica de Madrid
- Silvia Wegmann - Qualitas AG
- Beat Bapst - Qualita AG
- Angela Canovas - University of Guelph
- Jan Lassen - Aarhus University
- Vern Osborne - University of Guelph
- Getu Hailu - University of Guelph
- Dan Tulpan - University of Guelph
- John Parkins - University of Alberta
- Claude Robert - Universite Laval
- Roger Cue - McGill University
- Marcos Colazo - Alberta Agriculture and Forestry
- Nathalie Bisonnette - Agriculture and Agri-Food Canada
- J.T. McClure - University of Prince Edward Island
- Javier Sanchez - University of Prince Edward Island
Project End-Users
- Daniel Lefebvre - Lactanet
- Francesca Malchiodi - University of Guelph
- Gerrit Kistemaker - Lactanet
- Jose Antonio Jimenez - Confederacion de Asociaciones de Frisona Espanloa
- Janusz Jamrozik - University of Guelph
- Allison Fleming - Canadian Dairy Network
- Michael Lohuis - Semex
- Rene Lacroix - Valacta
Project Collaborators
- Herman Barkema - University of Calgary
- Graham Plastow - University of Alberta
- Peter Amer -Abacus Bio
- Wolfgang Heuwieser - Freie Universitat Berlin
- Jose Vasconcelos - Sao Paulo State University
- Jose Santos - University of Florida
- David Kelton - University of Guelph
- Luiz Brito - Purdue University
- Daniela A.. Lourenco - University of Georgia
- Nicolas Friggens - H2020 GenTORE Project
- Niel Karrow - University of Guelph
Lead Centre
Lead Centre
Co-Lead Centre
Project Manager
Project Manager
- Nienke Van Staaveren - University of Guelph
Project Co-Manager
- Mary De Pauw - University of Alberta
Notes
Project Summary
This project looks ensure the global competitiveness of Canada’s dairy cattle industry both on-farm and in exporting Canadian dairy genetics, while ensuring overall sustainability. To address these needs, new datasets and genomic tools will be developed to deliver a more ‘resilient’ cow. New genomic breeding tools for the dairy producers and the AI industry will be implemented based on a novel selection index for resilience, which will include novel traits related to fertility, health and environmental efficiency (i.e. feed efficiency and methane emission). The new index for resilience will allow farmers to reduce costs related to poor cow fertility, diseases and animal feed, which represent the largest expenses in milk production, resulting in an estimated annual net savings for the dairy industry of $200M.
Funded under the Genome Canada 2018 Large-Scale Applied Research Project Competition
Principal Investigators
Project Lead
- Tim McAllister, AAFC Lethbridge Research and Development Centre
Project Co-Lead
- Leluo Guan, University of Alberta
Project Co-Applicants
- Trevor Alexander, AAFC Lethbridge Research and Development Centre
- Graham Plastow, University of Alberta
- Arun Kommadath, University of Saskatchewan
- Karen Schwartzkoph-Genswein, AAFC Lethbridge Research and Development Centre
- Rahat Zaheer, AAFC Lethbridge Research and Development Centre
- Greg Penner, University of Saskatchewan
- Devin Holman, AAFC Lethbridge Research and Development Centre
- Rodrigo Ortega-Polo, AAFC Lethbridge Research and Development Centre
- Gabriel Ribeiro, University of Saskatchewan
Notes
Project Summary
Liver abscesses and bovine respiratory disease (BRD) cause the greatest disease associated economic losses in the Canadian Beef Industry. As these conditions are mainly caused by Gram-negative bacteria, this combined with antimicrobial resistance (AMR) may account for the limited efficacy of current antimicrobials. This study will use “omic” technologies to characterize the interaction between these disease-causing microbiomes and the host in a relationship we have defined as the “microactome”.
Funded under the Genome Alberta Strategic Initiatives Program.
Principal Investigators
Project Lead
- Cheryl Waldner - University of Saskatchewan
Project Co-Lead
Project Co-Applicants
- Anatoliy Trokhymchuk -
- Matthew Links - University of Saskatchewan
- Tim McAllister -
- Janet Hill - University of Saskatchewan
- John Campbell - University of Saskatchewan
- Paul Stothard - University of Alberta
- Henry An - University of Alberta
- Xiaoli Fan - University of Alberta
- Rahat Zaheer - AAFC Lethbridge Research and Development Centre
- Yanyun Huang - Prairie Diagnostic Services
- Nathan Erickson - University of Saskatchewan
- Murray Jelinski - University of Saskatchewan
- Sheryl Gow - Public Health Agency of Canada
Project End-Users
- Anatoliy Trokhymchuk - Prairie Diagnostic Services
- John Campbell - University of Saskatchewan
- Rahat Zaheer - AAFC Lethbridge Research and Development Centre
- Yanyun Huang - Prairie Diagnostic Services
- Murray Jelinski - University of Saskatchewan
- Nathan Erickson - University of Saskatchewan
- Sheryl Gow - Public Health Agency of Canada
Lead Centre
Lead Centre
Co-Lead Centre
Notes
Project Summary
This research supports large-scale uptake of genomic tools and strategies to rapidly field-test groups of calves for disease and antibiotic resistance. We will develop a diagnostic support network and cutting-edge computing tools for the livestock industry to manage genomic test data, assess risk and inform therapy decisions. The result will be precision use of antibiotics—quick and accessible information for veterinarians to tailor antibiotic therapy for individual pens of calves. Viruses and bacteria identified in calves arriving at feedlots can also pinpoint vaccine gaps for cow-calf producers.
Funded under Genome Canada 2018 Large-Scale Applied Research Project competition.
Total Budget for All Projects: $
