$56M supports genomic projects across Canada

Wallenstein, ON – Genome Canada today announced the first 12 projects selected for funding under its Genomic Applications Partnership Program (GAPP).

The 12 projects will receive total funding of $56 million. Genome Canada is contributing $15 million, with the balance (about $41 million) provided by co-funding partners including the genomics end-user. These projects comprise the first two rounds of multiple rounds of projects that will be funded under GAPP. GAPP is designed to move genomics-based solutions to the marketplace through academic partnerships with industry and other “users” of genomics. It is also intended to stimulate investment from private and public partners to fund projects that address real world challenges and opportunities in the field of genomics.

GAPP projects partner academic researchers with “users” of genomics (e.g. industry, provincial governments, non-profits, or other organizations). In addition, GAPP projects will support training the next generation of graduate students and post-doctoral fellows, thanks to a new partnership between Genome Canada and Mitacs, which will create research internships for future projects.

“These first two rounds have proven that there is a high degree of interest and engagement from a whole range of industry sectors that see Canada’s genomics research enterprise as a valuable source of ideas and innovation.,” said Dr. Pierre Meulien, president, Genome Canada.

The following 12 projects have been awarded funding:

SALMON and CHIPS – Commercial Application of Genomics to Maximize Genetic Improvement of Farmed Atlantic Salmon:

• Project Leaders: Elizabeth G. Boulding, University of Guelph; Keng Pee Ang, Cooke Aquaculture Inc. and Kelly Cove Salmon Ltd.
• Lead Genome Centres: Genome Atlantic and Ontario Genomics Institute
• Description: Aquaculture companies are increasingly incorporating genomics technology into their breeding programs to develop desirable stock traits for improved growth and disease resistance. Cooke Aquaculture/Kelly Cove Salmon will partner with Dr. Boulding and her academic group from the University of Guelph to incorporate genomics marker technology into Kelly Cove Salmon’s current breeding program.

A Metagenomic Approach to Evaluate the Impact of Cheesemaking Technologies and Ripening Conditions on the Microbial Ecosystem of Premium Washed Rind Cheeses:

• Project Leaders: Steve Labrie, Université Laval; Manon Duquenne, Agropur Cooperative
• Lead Genome Centre: Génome Québec.
• Description: Agropur will partner with Dr. Labrie, whose genomics-based techniques to monitor microbiota composition will have a direct impact in the production of high quality cheeses. This project will use next-generation sequencing to monitor the ripening process of premium washed rind cheeses. It will also lead to the development of a new genetic tool that will allow Agropur to improve production control, limit losses and produce high quality cheese with increased shelf life and reduced returns. In addition, the project will lead to the creation of a set of standardized genomic profiles that will allow for the development of optimal cheese culture.

Development of low cost diagnostic platform for infectious disease testing:

• Project Leaders: Shana Kelley, University of Toronto; Graham Jack, Xagenic Canada Inc.
• Lead Genome Centre: Ontario Genomics Institute.
• Description: Conventiona llab testing for infectious diseases such as Hepatitis C, malaria and tuberculosis is inefficient and not cost-effective, particularly in developing countries. The development o f fast and accurate point-of-care testing for these infections would significantly improve the clinical management of infectious disease s. For this research, Xagenic will partner with Dr. Kelley to leverage expertise in viral assay development, sensor technology and plastic chip fabrication. This project will lead to a single affordable and accurate genotyping test to screen for infectious pathogens, and will provide a new solution for rapid disease diagnosis. The low-cost, disposable, battery-powered testing device will identify pathogens in human blood in minutes.

Genomics for a Competitive Greenhouse Vegetable Industry:

• Project Leaders: Keiko Yoshioka, University of Toronto; Daryl J. Somers, Vineland Research and Innovation Centre
• Lead Genome Centre: Ontario Genomics Institute
• Description: Greenhouse vegetables tomatoes, peppers and cucumbers are susceptible to a number of diseases. Vineland Research and Innovation Centre will partner with Dr. Keiko Yoshioka, who has discovered a key gene involved in plant disease resistance. Using gene technologies to enhance disease resistance in greenhouse vegetables, this project aims to develop new commercial traits and varieties.

Augmenting the Plant Microbiome to Improve Crop Yield and Stress Resilience Project:

• Co-Leaders: Vladimir Vujanovic and Jim Germida, University of Saskatchewan; Geoffrey von Maltzahn, Symbiota, LLC.
• Lead Genome Centre: Genome Prairie
• Description: Symbiota is partnering with Drs. Vujanovic and Germida, who have discovered a new class of natural microbes that can dramatically improve crop yield and stress resistance. The project will use genomic tools to systematically evaluate and field test a number of crop-microbe combinations with high commercialization potential. It aims to develop breakthrough microbial products that will address the significant need for improved yield, water use efficiency and heat-stress tolerance in major crops in Canada and around the world including wheat, maize, soybean, canola, barley, and pulses.

Better Feed for Better Fish: Biomarker Platform for Commercial Aquaculture Feed Development:

• Project Leaders: Matthew Rise, Memorial University; Richard Taylor, EWOS Innovation
• Lead Genome Centre: Genome Atlantic
• Description: This project seeks to develop tools to better assess the health of farmed salmon from their genes. Scientists at Memorial University and EWOS Innovation will jointly develop a platform to quantify the expression of multiple genes related to health and performance, using a single biological sample. This will allow aquafeed producer EWOS to develop novel, high-quality feeds. New feeds will be commercialized within the life of the project and continue for three to five years following the project’s completion. Some of these feeds will focus on growth, while others – clinical feeds – will focus on combatting the infections that are currently reducing salmon numbers.

Making Feed Go Further: Development and Commercialization of Next Generation Enzymes Supplement for Pork and Poultry:

• Project Leaders: Adrian Tsang, Concordia University; Paul Matzat, Elanco Animal Health, a division of Eli Lilly & Co
• Lead Genome Centre: Génome Québec
• Description: Pork and poultry lack the enzymes to digest up to one-quarter of the feed they are given. Animal health company Elanco is partnering with Concordia University to develop new enzyme combinations for pork and poultry producers. The project will screen proprietary enzymes for digestibility of common ingredients found in Canadian pork and poultry feed that are expected to result in significant improvements in feed conversion and thus improve producer profit margins.

Matching the Drug to the Patient: Safer and More Effective Drug Therap
y for Mental Health Patients:

• Project Leaders: James Kennedy, Centre for Addiction and Mental Health; C. Anthony Altar, Assurex Health.
• Lead Genome Centre: Ontario Genomics Institute
• Description: Treatments for mental illness are available but each person responds differently, in part due to their genes. A clinically proven genetic test, called GeneSight, analyzes an individual’s genes and recommends the optimal drugs for that person along with dose adjustments among the 33 most commonly prescribed antidepressant and antipsychotic drugs. Assurex Health, the company that developed GeneSight, is partnering with scientists at Toronto’s Centre for Addiction and Mental Health (CAMH) to develop the Enhanced GeneSight (E-GeneSight) genomic test. E-GeneSight will incorporate new genomic markers that scientists at CAMH have identified and characterized for their association with patient responses to psychiatric medications. Assurex Canada and CAMH will together validate these markers for their ability to predict efficacy and side effects of psychiatric medications; the most predictive markers will be integrated into E-GeneSight.

Healthy Veins, Healthy Kidneys: Developing Vasculotide, a Genomic/Proteomic – Derived Treatment to Target Vascular Inflammation and Destabilization:

• Project Leaders: Dan Dumont, Sunnybrook Research Institute; Parimal Nathwani & Paul Van Slyke, Vasomune Therapeutics
• Lead Genome Centre: Ontario Genomics Institute
• Description: More than one million cardiac surgeries are carried out each year, usually successful. Nearly one-third of high-risk patients, however, will experience a rapid loss of kidney function after surgery, known as Acute Kidney Injury, or AKI. AKI is the result of short-term interruptions in blood flow during surgery; 11 percent of patients who develop AKI after bypass surgery will die, compared to 2 percent of those who do not. Those who survive AKI are at risk of developing longer-term kidney complications. Drs Dumont and Van Slyke conceptualized and designed a drug called Vasculotide (VT) that binds to the Tie2 receptor, which is responsible f or maintaining vascular health (and thus blood flow). Vasomune Therapeutics, the company developing and commercializing the drug, is partnering with these researchers to develop VT to the point where it is ready for human clinical trials.

Fighting Heart Failure: Cardiovascular Biomarker Translation Program:

• Project Leaders: Peter Liu, University of Ottawa Heart Institute; Gabriela Bucklar – Suchankova, Roche Diagnostics International Ltd.
• Lead Genome Centre: Ontario Genomics Institute
• Description: Heart failure (HF) is the most costly chronic disease in developed and developing countries. Roche Diagnostics is partnering with the University of Ottawa Heart Institute (UOHI) to develop a better way to identify and classify HF, based on testing novel biomarkers for the disease. To date, with previous Genome Canada funding, UHOI, University of Toronto and Roche Diagnostics have identified eight novel biomarker candidates for HF characterization and have filed for global patents for these candidates. Now the partners will conduct further clinical evaluation of the biomarkers, with the intent of developing a HF biomarker panel and an accompanying clinical development program to translate the findings from basic research to clinical benefit of patients.

Delving into Mouse Proteins: Development of Disease Biomarker Assessment Assays and Kits for Targeted Quantitative Proteomics of Mouse Plasma by Mass Spectrometry:

• Project Leaders: Christoph Borchers, University of Victoria; Gary Kruppa, MRM Proteomics, Inc.
• Lead Genome Centre: Genome British Columbia
• Description: It is currently extremely difficult to carry out proteomic research on mouse models, the mainstay of most other forms of biomedical research, due to the small volumes of blood that can be sampled from live animals. MRM Proteomics, Inc., and the University of Victoria – Genome BC Proteomics Centre are developing new tools that will enable researchers to use mouse models for proteomics research. The tools are based on multiple reaction monitoring mass spectrometry (MRM – MS) and consist of assays that allow researchers to measure the concentration of individual proteins in mouse plasma. Three new products will be developed: a complete assay to quantify the 500 most abundant proteins in mouse plasma as a service offering; three kits for disease biomarker proteins, one each for discovery research, oncology and cardiovascular diseases; and two kits for quality control of mouse plasma proteomics experiments.

Getting at Pests Early: Protecting Canada’s Forests against Invasive Alien Species by Next Generation Biosurveillance:

• Project Leaders: Richard Hamelin, University of British Columbia; Cameron Duff, Canadian Food Inspection Agency
• Lead Genome Centres: Genome British Columbia and Génome Québec
• Description: The Canadian Food Inspection Agency (CFIA) is partnering with scientists at the University of British Columbia and a network of academics from Université Laval in Québec and Natural Resources Canada to develop, validate and deploy genome-based biosurveillance tools aimed at two invasive species – the Asian gypsy moth and Phytophthora ramorum. The tools will use DNA detection arrays that target unique genome regions in the pests, improving CFIA’s ability to better detect and identify these two species. The project will take approximately three years, after which CFIA laboratories will use the tools to enhance and complement their current procedures. The benefits will be significant. Knowing more about the sources of infestations will decrease the resources needed for inspection and surveillance and reduce treatment costs.