May 7, 2021
The Canadian VirusSeq Data Portal is critical to sharing information to better understand the virus
Adaptation has been key to living and working during the COVID-19 pandemic. The agility of OICR’s software engineering team was recently on full display when they built a COVID-19 data portal in just four weeks – a record time for the group. The freshly launched Canadian VirusSeq Data Portal, part of Genome Canada’s CanCOGeN COVID-19 research initiative, provides a vital link between Canada’s public health units and researchers tracking the evolution of the virus and variants of concern.
“When you are building something this complex in such little time there really is no roadmap. Luckily our team was able to draw on our deep experience in building similar platforms, which helped us get this urgent project done on time,” says Dr. Christina Yung, Director, Genome Informatics, OICR. “This experience, incredible teamwork and a deep desire to assist in Canada’s response to the pandemic fueled our sprint to complete this project.”
Having created data portals for many major research projects, including the International Cancer Genome Consortium, Yung’s team was well prepared to meet the challenge and create this vital resource for Canada’s fight against COVID-19. Over the past several years the team has worked to package their software tools into a modular system called Overture.
“Overture provided us with a robust framework from which to start building the VirusSeq portal. From there we were able to customize the portal to meet the specific needs of users,” explains Yung. “By making it as easy to use as possible we hope to attract the participation of many public health units and researchers.”
The Canadian VirusSeq Data Portal allows public health units to easily submit genomic sequencing data of SARS-CoV-2 infections. The deidentified data is then validated and quickly released into the data portal where it can be used by experts such as virologists and epidemiologists. The data available through the portal will aid in better understanding the virus and provide increased surveillance for variants of concern.
“Our next steps will be to make updates and improvements to the portal as more users come onboard and provide feedback,” says Yung. “I encourage public health units and researchers to take advantage of this tool to deepen collaboration in our efforts against COVID-19.”
The following individuals at OICR contributed to the development of the Canadian VirusSeq Data Portal, which was led by Lincoln Stein and Christina Yung: Yelizar Alturmessov, Dusan Andric, Rosita Bajari, Jared Baker, Kim Cullion, Henrich Feher, Atul Kachru, Alexandru Lepsa, Justin Richardsson, Jaser Uddin, Linda Xiang.
April 8, 2021
Genome Canada has announced the launch of a new, Canadian SARS-CoV-2 Data Portal that will manage and facilitate data sharing of viral genome sequences among Canadian public health labs, researchers and other groups interested in accessing the data for research purposes.
McGill University’s, Dr. Guillaume Bourque and his team will lead the project in collaboration with the Canadian COVID Genomics Network (CanCOGeN) and a number of world-leading genomics scientists specializing in data science, including Dr. Christina Yung, Director of Genome Informatics, OICR, and Dr. Lincoln Stein, Head, Adaptive Oncology, OICR.
The team will also collaborate with DNA Stack, a CanCOGeN industry partner led by OICR Associate Dr. Marc Fiume. The Data Portal will make use of DNA Stack’s COVID Cloud platform to develop and provide real-time analytical dashboards, data exploration and standards-compliant data interfaces.
December 1, 2020
A national consortium including the Ontario Institute for Cancer Research will expand development of a software platform for genomics and health data and apply it to COVID-19. The $5.1 million project, called COVID Cloud, is co-funded by Canada’s Digital Technology Supercluster and aims to increase Canada’s capacity to harness exponentially growing volumes of genomics and biomedical data to advance precision health. The platform will be used by data scientists and domain experts to help understand, predict, and treat COVID-19 with molecular precision. With a global death count of over 1.4 million people and record numbers of cases nationally, solutions that can help Canada respond to ongoing challenges of the pandemic are urgently needed.
“We are proud to continue to support this consortium’s groundbreaking work through our COVID-19 program,” said Sue Paish, CEO of the Digital Technology Supercluster. “This project shows how Canadian partnerships across multiple organizations and sectors can drive innovation, help us address global health issues, showcase Canadian expertise, and position us well to rebuild and grow our economy.”
The project — a collaboration between BioSymetrics, Centre of Genomics and Policy at McGill University, DNAstack, FACIT, Genome BC, Mannin Research, McMaster University, Microsoft Canada, Ontario Genomics, Ontario Institute for Cancer Research, Roche Canada, Sunnybrook Research Institute, and Vector Institute — brings together Canadian leaders in software engineering, artificial intelligence, cloud computing, genomics, infectious disease, pharmaceuticals, commercialization, and policy. It leverages past work of partners to address needs of infectious disease research with guidance from domain experts.
“Tools that allow us to interrogate SARS-CoV-2 at a molecular level are essential to addressing this global health crisis, both now and in the future,” said Dr. Samira Mubareka, a microbiologist and infectious diseases physician at Sunnybrook, whose team was one of the first in Canada to isolate the novel coronavirus. “The insights we will learn by analysing integrated datasets using technology platforms like COVID Cloud can increase our preparedness for future waves and outbreaks.” Dr. Mubareka will co-chair the project’s translational science efforts along with Dr. Gabriel Musso, Chief Scientific Officer for BioSymetrics. “The infrastructure developed by this initiative will propel collaborative Canadian drug discovery efforts for COVID-19,” said Musso, whose team will lead bioinformatics and computational drug discovery for the project.
A major goal of the project is to make it easy for producers of genomic and health data to share data responsibly over industry standards, and for researchers to harness the collective power of information shared through them. The project deliverables include a suite of software products powered by enterprise-grade implementations of standards developed by Global Alliance for Genomics & Health (GA4GH), protocols that are being designed to facilitate the responsible sharing of genomic and health data, which will help advance precision medicine initiatives around the world.
“The platform is being built on a foundation of open standards that will allow for distributed networks of genomics and biomedical data to be built,” said Dr. Marc Fiume, CEO at DNAstack, whose team will lead software engineering for the project. “We are excited to see these technologies breaking down barriers to data sharing, access, and analysis and create new opportunities for genomics-based discoveries for our partners.”
This project is responding to global demand for highly specialized, scalable, distributed software infrastructure to support collaborative genomics research — a need that has surged since the onset of the COVID-19 pandemic. “COVID-19 has accelerated digital transformation of many industries, especially in healthcare,” said Kevin Peesker, President of Microsoft Canada. “The incredible power of Cloud applied to COVID at scale is expanding development of an information superhighway to securely connect scientists in Canada and around the world to the data and compute power they urgently need to help us overcome one of the greatest global health crises of our time.”
The platform will be used to support a series of projects in partnership with Canadian academic, clinical, and pharmaceutical collaborators, which are being coordinated by Canadian genome centres, Genome British Columbia and Ontario Genomics. These initial projects are being prioritized based on urgency and potential impact on Canada’s response to the COVID-19 pandemic.
“The COVID Cloud is an incredible platform that brings together resources and capacity to enable timely and comprehensive genomic analysis of SARS-CoV-2 for our province and our country,” said Bettina Hamelin, President and CEO of Ontario Genomics, whose team leads the ONCoV Genomics Coalition. “This made-in-Canada solution will immediately accelerate Canada’s response to COVID-19, while being a technological springboard for translating genomic data analysis into actionable medical insights across other disease areas in years to come.”
For more information, visit dnastack.com/solutions/covid-cloud.
November 5, 2020
Study finds that every month delay in cancer treatment can raise risk of death by around 10 per cent
Research led by Dr. Timothy Hanna suggests that minimizing delays to treatment could improve cancer survival rates
Many countries have needed to defer cancer surgeries, radiotherapy and other treatments through the COVID-19 pandemic, which has brought the impact of treatment delays into sharp focus. In a study published today in The BMJ, Dr. Timothy Hanna and collaborators report that people whose cancer treatment is delayed by even four weeks have in many cases a six to 13 per cent higher risk of dying – a risk that keeps rising the longer their treatment does not begin.
“We know that delay matters and now we understand how much it matters,” says Hanna, Radiation Oncologist at the Cancer Centre of Southeastern Ontario, Faculty of Queen’s Cancer Research Institute, OICR Clinician Scientists and lead of the study. “With these data, we can now quantify the impact of treatment delays – including those that we’re experiencing now throughout the COVID-19 pandemic.”
The research group reviewed and analyzed relevant studies from around the world that were published over the last two decades. They found that there was a significant impact on a person’s risk of death if their treatment was delayed, whether the treatment was surgical, chemotherapy or radiotherapy. They observed this impact across all seven types of cancer analyzed – breast, bladder, colon, rectum, lung, cervix and head and neck cancers.
For example, with cancer surgery, they saw a six to eight per cent increase in the risk of death for every four-week treatment delay, meaning that a three-month delay could increase the risk of death by about 25 per cent. The impact was even greater for specific treatments – such as bowel cancer chemotherapy – where a three-month delay could cause a 44 per cent increase in risk of death.
“As we move towards the second COVID-19 wave in many countries, the results emphasize the need to prioritize cancer services including surgery, drug treatments and radiotherapy as even a four-week delay can significantly increase the risk of cancer death,” says Dr. Ajay Aggarwal, co-lead of the study from King’s College London and the London School of Hygiene and Tropical Medicine.
Hanna hopes this study will help inform cancer treatment backlog management and prioritization. His prior work on prioritizing treatment during COVID-19, published in Nature Reviews Clinical Oncology, has been incorporated into health system planning and management in Ontario and around the world.
“The impact of cancer treatment delays will persist long after the threat of this pandemic subsides,” says Hanna. “As a clinician, a patient, an administrator or a decision-maker in our cancer care system, these results should encourage us all to put resources and efforts in place to minimize system level delays in cancer treatment.”
September 3, 2020
OICR-based PhD Candidate awarded University of Toronto COVID-19 Student Engagement Award
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.
“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.
“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.”
July 21, 2020
OICR researchers and collaborators awarded $520,000 in new funding for COVID-19 drug discovery project
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
The SUPPORT-Canada initiative will capture data and biospecimens in order to identify factors contributing to COVID-19 susceptibility, severity and outcomes.
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
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.
Dr. Laszlo Radvanyi
President and Scientific Director
April 16, 2020
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.
“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.