September 3, 2020

Analyzing SARS-CoV-2: A cancer researcher trainee’s perspective

OICR-based PhD Candidate awarded University of Toronto COVID-19 Student Engagement Award

This scanning electron microscope image shows SARS-CoV-2 (round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2, also known as 2019-nCoV, is the virus that causes COVID-19. The virus shown was isolated from a patient in the U.S. Credit: NIAID-RML
This scanning electron microscope image shows SARS-CoV-2 (round blue objects) emerging from the surface of cells cultured in the lab. SARS-CoV-2, also known as 2019-nCoV, is the virus that causes COVID-19. The virus shown was isolated from a patient in the U.S. Credit: NIAID-RML

When the COVID-19 pandemic shut down labs across Canada, cancer research trainees looked for ways to help respond to the pandemic. PhD candidates Tom Ouellette and Jim Shaw saw an opportunity to combine their skills and contribute to the cause.

Ouellette and Shaw were recently awarded a University of Toronto COVID-19 Student Engagement Award for their project titled Network and evolutionary analysis of SARS-CoV-2: A vaccine perspective. Together, they will develop new machine learning tools to analyze the SARS-CoV-2 genome and how it evolves. 

Tom Ouellette, PhD Candidate in Dr. Philip Awadalla’s lab at OICR.

“We’re two like-minded individuals with complementary skillsets who enjoy coding, math and solving problems, which – fortunately – can be done remotely,” says Ouellette, who is a PhD Candidate in Dr. Philip Awadalla’s lab at OICR. “We saw the opportunity to help with COVID-19 research and we’re happy to apply our skills to help advance research towards new solutions for this pressing problem.”

Ouellette specializes in evolution and population genetics and Shaw specializes in network analysis and algorithm development. Through this award, they will investigate how SARS-CoV-2 is evolving by looking into specific regions of the virus’ genetic code from samples around the world, using mathematical modelling, machine learning, and evolutionary simulations. They are specifically interested in how these changes in the genetic code may alter the virulence, or severity, of the virus.

Jim Shaw, PhD Candidate in mathematics at the University of Toronto.

“Just like cancer, different pressures or stresses can make viruses evolve,” says Shaw, who is a PhD Candidate in mathematics at the University of Toronto. “Understanding these changes can have an impact on how we build vaccines. Furthermore, better understanding of the virus’ evolution may shed light on viral reinfection, which is an important issue as we move into the later stages of the pandemic.”

Ouellette and Shaw plan to publicly release the code that they develop through this initiative for other researchers to build upon.

“SARS-CoV-2 has a much simpler genome than a cancer genome, so it can serve as a simplified model to test out new analytical techniques,” says Ouellette. “Ultimately, I hope to bring the tools and technology we create back into my research on cancer so we can better understand how cancer evolves and becomes resistant to treatment.”

Read more on how OICR researchers are helping understand and overcome COVID-19

July 21, 2020

OICR Drug Discovery awarded for COVID-19 research

OICR researchers and collaborators awarded $520,000 in new funding for COVID-19 drug discovery project

Dr. Gennady Poda
Dr. Gennady Poda, OICR Scientific Advisor and Group Leader

OICR Scientific Advisor and Group Leader, Dr. Gennady Poda, and collaborators at Sunnybrook Research Institute have been awarded $520,000 to identify new therapeutics and existing drugs that could be repurposed for the treatment of COVID-19. This award, which was announced on July 17 by Premier Doug Ford, is part of the Government of Ontario’s $20 million COVID-19 Rapid Research Fund.

Using OICR supercomputers and advanced computational chemistry techniques, Poda and collaborators aim to identify drugs that can stop the virus from replicating in the body by targeting the virus’ key polymerase enzyme, RdRP.

“We’ll be looking for new potential drugs to treat the COVID-19 infections by rapidly identifying approved drugs and compounds that are in clinical trials that could inhibit RdRP,” says Poda. “We will advance the most promising compounds into preclinical animal models and, if the data is promising, into patients.”

Continue reading – OICR Drug Discovery awarded for COVID-19 research

June 25, 2020

CanPath Awarded $2.1 million CIHR Grant for SUPPORT-Canada COVID-19 Initiative

The SUPPORT-Canada initiative will capture data and biospecimens in order to identify factors contributing to COVID-19 susceptibility, severity and outcomes.

Dr. Philip Awadalla

CanPath (the Canadian Partnership for Tomorrow’s Health), co-led by OICR Investigator Dr. Philip Awadalla, has been awarded a $2.1 million grant from the Canadian Institutes of Health Research (CIHR) through their COVID-19 Rapid Research Funding competition. The initiative, titled SUrveying Prospective Population cOhorts for COVID-19 pRevalence and ouTcomes in Canada (SUPPORT-Canada),aims to capture data and biospecimens to enable population-level surveillance. SUPPORT-Canada will enable researchers and clinicians to find factors contributing to COVID-19 susceptibility, severity and outcomes, thus identifying factors predisposing individuals or communities across Canada to a high risk of infection.

“The integration of clinical programs with our broader existing population cohort infrastructure creates the opportunity to rapidly assess patterns across Canada, while discovering and tracking critical biological and environmental determinants of disease susceptibility and severity for COVID-19,” says Awadalla, who is the lead Principal Investigator for the SUPPORT-Canada Initiative and National Scientific Director of CanPath.

Continue reading – CanPath Awarded $2.1 million CIHR Grant for SUPPORT-Canada COVID-19 Initiative

May 6, 2020

A message from OICR’s President and Scientific Director, Dr. Laszlo Radvanyi

Dr. Laszlo Radvanyi

I hope that everyone has continued to stay safe and healthy as the world continues to grapple with the risks and challenges presented by COVID-19. The impacts of the pandemic have been felt by individuals and organizations across society, including cancer patients and Ontario’s cancer research community.

While things are obviously not business as usual, I am happy to see OICR’s people rise to the challenge and find solutions to allow us to continue to focus on cancer research while working remotely. My thanks go to OICR’s staff, Board and Scientific Advisory Boards, collaborators and others who have quickly adapted to continue our work as best we can. A big thank you also to our funders at the Ministry of Colleges and Universities for their continued support. We will gradually restore our onsite cancer research activities in a manner that will ensure a safe work environment for all our onsite staff. Our priority remains to improve the lives of those with cancer through research.

OICR’s leadership recognizes that the pandemic has resulted in unprecedented challenges for cancer researchers across Ontario. We have taken steps to ease this burden and are working with OICR-funded researchers and partner organizations to overcome these challenges together. More information about how we are assisting our funded researchers can be found on our website.

Due to our collaborative, cross-disciplinary research strengths, OICR is well-situated to contribute to COVID-19 research. OICR researchers are engaged in numerous projects with others in Ontario and abroad. It has been heartening to see such a swell of collaborative spirit and to see the research community doing what we can to help overcome COVID-19. I invite you to visit our website to learn more about how OICR is doing its part. We are especially cognizant on how these research activities impact cancer patients, as they are an especially vulnerable population at this time.

COVID-19 has disrupted cancer research on a global scale. I look forward to a time when we can resume all of our research activities and once again contribute to the international campaign against cancer at full capacity. During the pandemic, cancer has not and will not cease to be a reality for the thousands of Ontarians living with this disease and their families. Everyone at OICR remains steadfast in our commitment to improve the lives of those facing cancer.

In closing, I offer my deepest appreciation to all those working on the front lines of this crisis and thank all off the members of Ontario’s cancer research community for their continued dedication during this difficult time. All our thoughts also go out to any families that have been affected during this crisis.

Sincerely,
Dr. Laszlo Radvanyi
President and Scientific Director
OICR

April 16, 2020

University students step up to flatten the COVID curve

Former OICR intern leads the development of a COVID-tracking site used by more than 400,000 people in Canada to date

Flatten is quickly becoming a go-to source of information about how COVID-19 is spreading across Canada.

In less than a month, more than 400,000 people have submitted data on their symptoms, travel history, age and medical conditions, making Flatten the country’s leading crowdsourced COVID data repository.

Behind the project is a team of first- and second-year university students who are determined to help.

Yifei Zhang, Vice President of Flatten.

“We just wanted to put our technical skills to good use during this time,” says Vice President of Flatten, Yifei Zhang, in a University of Waterloo story. “It’s been great working together with everybody trying to build a platform that will be useful for Canadians across the country.”

As a web-based, data-gathering platform, Flatten provides a real-time heat map of self-reported confirmed and potential COVID-19 cases across the country. The platform helps increase awareness and flatten the curve of COVID-19 cases.

Over the last four weeks, Flatten has rapidly evolved from an idea into an incorporated non-profit organization, with support from advisors such as Dr. Geoffrey Hinton and sponsors such as Google Cloud, the Vector Institute and CIFAR.

The team behind Flatten has established collaborations with health authorities across Canada, such as in Montreal, and plans to work with other municipal governments and provinces..

“We work with leading advisors and collaborators to make sure we’re surveying the right questions and providing the right information for Canadians today to help flatten the curve,” says Zhang.

Zhang, who is completing his second year as a software engineering student at the University of Waterloo and leads Flatten’s website development, attributes his website development knowledge to his internship with OICR’s WebDev team.

“My time at OICR reinforced my interest in working in health and biology, giving me the motivation and drive to pursue this initiative,” says Zhang. “At OICR, I gained experience working with a high volume of data using robust techniques and I was able to bring that knowledge into developing Flatten.ca. A lot of the fundamentals we used to build this site came from best practices that I learned from my term at OICR.”

Learn more at flatten.ca.