October 29, 2020
Dr. Trevor Pugh, OICR Senior Investigator, OICR Director of Genomics and Senior Scientist, Princess Margaret Cancer Centre has been named a Recipient of Canada’s Top 40 Under 40 for 2020.
The annual award was founded by Caldwell and recognizes 40 exceptional Canadian leaders who are visionaries, creative problem-solvers, inspire others, give back to the community and are under the age of 40.
Pugh and his fellow awardees were selected from over 900 nominees by an independent advisory board, comprising more than 25 business leaders from across Canada. Honourees were chosen on four key criteria: vision and innovation, leadership, impact and influence, and social responsibility.
When told that he had won, Dr. Pugh was elated.
“I could not believe it,” he said. “I’m tremendously excited. I really look forward to connecting with the Top 40 Under 40 community. It is very gratifying to see genome science and translational science – which has a direct impact on patient care – be recognized as an important field along with business luminaries.”
Pugh is a world-leading cancer genomics researcher and molecular geneticist whose mission is to use comprehensive genomic profiling and molecular technologies to guide the treatment of patients.
After receiving a PhD in medical genetics from the University of British Columbia, he did further postdoctoral work at Harvard Medical School, Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), as well as the Dana-Farber Cancer Institute.
He leads a multidisciplinary lab with 24 staff and trainees, and oversees 55 research staff at one of the largest genomics facilities in Canada at OICR and the Princess Margaret Cancer Centre. He is also an Associate Professor in the Department of Medical Biophysics at the University of Toronto.
Pugh is listed on the 2019 Highly Cited Researchers List by Clarivate Analytics. This list recognizes researchers whose published work has ranked in the top 1 per cent by citations of other researchers the world over.
He has also developed novel genomics technologies, including a new method which assesses and monitors if immune cells have been activated to fight cancer cells.
“I congratulate Trevor on being named to the prestigious Canada’s Top 40 Under 40. Through his cutting-edge research and leadership, Trevor is creating a future in which genomics are a routine part of cancer detection and precision treatment,” says Dr. Laszlo Radvanyi, President and Scientific Director, OICR. “Through his work at OICR I have seen firsthand Trevor’s outstanding commitment to his field, the collaborative and transparent spirit in his work, and his heartfelt desire to improve the lives of those with cancer.”
As a clinical molecular geneticist, genome scientist, and computational biologist, Pugh’s goal is to bring cutting-edge genomic technologies into routine use in cancer clinics – especially vital as the latest cancer treatments are increasingly based on genetic information.
Known widely for his leadership of numerous cancer genome research projects, Pugh’s expertise in clinical genomics has been foundational to the launch of the national Terry Fox Marathon of Hope Cancer Centres Network, which has become the nation-wide focal point to accelerate precision medicine for cancer. The Network will unite top-tier researchers and clinicians to test cutting-edge technologies in the clinic, share data and results for each cancer patient in Canada and provide access to any clinical trial – no matter where patients live.
This will give us a true and accurate representation of cancer as it occurs in populations across Canada, says Pugh, and will help us get answers to questions such as:
“How often does this genetic change occur in the population? What treatments did cancer patients get that worked best for specific or rare molecular cancer subtypes?
“We have no way of knowing or asking for that information now.”
Pugh’s research is also focused on detecting cancer as early as possible – even before it is diagnosed.
While screening tests exist for some cancers – such as mammography, colonoscopy and prostate specific antigen – most cancers do not have a non-invasive, early screening option.
“That is worrisome for people, especially those at high-risk for less frequent but lethal cancers,” says Pugh. “We want to change that using annual blood tests. The vision is early cancer screening for everybody, for every cancer type.”
With OICR’s support, Pugh and co-lead Dr. Raymond Kim of the Princess Margaret Cancer Centre are leading CHARM, a study that will test the blood samples of people without cancer to look for early traces of the disease. Data from this study will help scientists track how blood and immune systems change as people develop cancer, and how different environments and stressors affect the cancer risk.
“If we want to increase the speed at which patients can benefit from new treatments, we have to promote cross-training between everyone in healthcare: clinicians, scientists, computer whizzes, lab technologists, patients,” says Pugh. “We urge everyone to step outside their comfort zones, work together on a science project, learn a new skill and to collaborate!”
Adapted from an original post by the University Health Network.
October 23, 2020
This year, more than 5,700 people with cancer received innovative treatments or interventions through participating in clinical trials supported by the Canadian Cancer Clinical Trials Network (3CTN). Today, 3CTN has published their 2019-2020 Annual Report, highlighting their progress made towards enhancing the impact of academic cancer clinical trials across Canada. The report marks the midpoint of their strategic plan for 2018-2022.
Highlights of the report include feature articles on:
- How 3CTN has boosted recruitment for their supported trials by nearly 130 per cent, surpassing all expectations and targets;
- New Network initiatives such as improving trial options for children and people outside of urban areas;
- The tools and technologies that are streamlining and standardizing clinical trial management;
- The patient representatives who play a key role in the success of the Network.
October 15, 2020
OICR team awarded $300,000 to expand cancer research software tools for more researchers, new disease applications and greater impact
OICR’s Genome Informatics team receives federal funding from Canada’s National Research and Education Network to expand Overture, an open-source software suite for big data genomic research
Software tools are key to turning big data into discoveries in science and medicine. Reusing existing software accelerates the pace of discovery and can maximize the impact of public funding for research but only if the software is accessible and useable.
Today, Canada’s National Research and Education Network, CANARIE, announced their support of 12 teams across Canada as they adapt their existing research platforms for re-use by other research teams. With this funding, the OICR Genome Informatics team will evolve the accessibility and functionality of Overture, their software suite for big data genomic research.
“Our team has a longstanding commitment to the community,” says Dr. Christina Yung, Director of Genome Informatics. “We want to maximize the impact with the resources we have, which means focusing on key challenges and making our tools the most useful for the research community. This funding will allow us to do just that.”
Overture is a software suite of customizable and extendable tools for big data genomic research. One of Overture’s key products allows research teams to store and distribute genomic datasets while providing an authentication and authorization system for secure and safe data sharing. Overture also provides user-friendly portals for browsing and querying data, which was developed as part of the International Cancer Genome Consortium (ICGC) and the European-Canadian Cancer Network (EUCANCan).
CANARIE’s support will allow OICR’s team to simplify Overture installation and configuration, provide additional authentication functionality and improve the customizability of the data portal.
“With this support, we will add new features to increase adoption by new research teams,” says Yung. “The hope is to enable research teams from across Canada and around the world to re-use the software that we developed and accelerate their own discoveries. We’re grateful for how the community has contributed to our research through sharing open-source software and we’re proud to give back.”
“The ability to connect, share data and work collaboratively with researchers from across Canada and the world is a priority for our government,” said the Honourable Navdeep Bains, Minister of Innovation, Science and Industry [link to release]. “Today’s funding will help accelerate Canadian discoveries by making it easier for our researchers to find, access, and reuse data with collaborators across the country and around the world.”
October 15, 2020
Morgan Taschuk reflects on a decade of supporting critical cancer research and on her new role as OICR’s Director of Genome Sequence Informatics
Cancer genomics research depends on infrastructure and analysis tools that collect, process, analyze and annotate vast quantities of valuable sequencing data. Behind these systems at OICR is a team of individuals dedicated to enabling cancer research discoveries. OICR is proud to announce that Morgan Taschuk will now lead this essential team as Director of Genome Sequence Informatics (GSI).
Here, she reflects on her new role and her outlook on the next few years.
Your behind-the-scenes work is essential to the cancer research we do at OICR. How would you describe your work?
Our team makes sequencing data analysis and management easier for researchers and clinicians in several different ways. We create and maintain the infrastructure and computational tools that researchers need to process, analyze and annotate sequencing data, so they can spend their time working on other challenging research questions.
GSI also offers expert bioinformatics support services directly to researchers to collaborate on challenging research projects. In addition, OICR Genomics is pursuing clinical accreditation this year and so we have a team of clinical genome interpreters who can issue reports on a patient’s unique genome. There’s a lot going on!
How has your work evolved since you’ve been at OICR?
I began at OICR nearly a decade ago, when most of our bioinformatics work was custom for every project, and our sequencing instruments produced a fraction of the data of instruments today. Any kind of automation was quite limited and the amount of analysis we could scale up was limited by the number of people we could hire. Back then, the biggest projects were analyzing human whole genomes for research and participating in international consortia.
In the last nine years, I’ve seen us scale up our sequencing and analysis capabilities, expand a fantastic team of highly educated experts from computer science through data analysts to clinical genome interpreters, and reinforce our reputation of excellence in bioinformatics and computational biology. We’re doing everything we were doing a decade ago plus much more. We sequence single cells, cell free and circulating tumour DNA, analyze immune profiles, participate in international consortia like ICGC-ARGO, contribute to SARS-CoV-2 projects, and will soon produce clinically accredited genome reports, all while still sequencing whole genomes for research.
Today, our team oversees around two petabytes of data, and runs about 3,000 workflows and about 1.8 terabytes of analysis, per day. Genome Sequence Informatics is a team of about 20 people, including bioinformaticians, software developers and engineers, currently supporting 155 research projects – and their resulting research discoveries – each year.
As the Director of Genome Sequence Informatics, what are you most looking forward to?
This new role allows me to focus on the bigger picture rather than on technical challenges. I see this as an opportunity to unify efforts across teams, departments, and across the institution. For example, if one team that we support is doing a task differently than another, I can help bring them together to work towards a common solution for everyone so we can learn from each other, maintain more consistent quality control, and make the best use of the resources and funds we have. I’m looking forward to more productive interactions with the phenomenal teams at OICR and with other organizations around the country and world.
What are your top priorities over the next couple of years?
My goal over the next few years is to share what we’ve created with the community while growing our network. We’ll continue to create solutions to fulfill the evolving needs of researchers and clinicians. We’ll continue to publish our code so other bioinformaticians can confirm what we’ve done and start their own analysis pipelines. We’ll publish protocols and guidelines that we’ve created for our clinically accredited analysis as well as our core assays. And we’ll share our challenges and solutions with the community so we can build on our collective expertise. In addition, we’ll reach out to other teams and organizations to collaborate and learn from them. The bioinformatics, software development, and clinical genomics communities have vast knowledge that we want to take advantage of, improve and share.
The next couple of years for GSI are going to be about collaborative, open science so the scientific and clinical communities can all benefit from the progress made by Genome Sequence Informatics and OICR as a whole.
October 7, 2020
Vivian talks about the research that OICR is doing during COVID-19 and the kinds of safety precautions that OICR is taking.
September 24, 2020
OICR-supported researchers discover new way to match advanced pancreatic cancer patients with the most appropriate treatment for their disease
Over the next 10 years, it is expected that pancreatic ductal adenocarcinoma (PDAC) will become the second leading cause of cancer-related deaths in North America. Precision medicine for PDAC is dependent on understanding which cancers will respond to treatment and which will not, but progress in this space has been limited by challenges including the complexity and severity of the disease. With more than 10 years of clinical and genomic data from the COMPASS trial, OICR-supported researchers have recently discovered a new, simplified way to match patients with the most appropriate treatment for their disease by measuring the expression of two genes, GATA6 and Keratin 5. Their discovery was recently published in Clinical Cancer Research.
“Even with current chemotherapies, patients diagnosed with PDAC have a median survival of one year,” says first author Dr. Grainne O’Kane, Medical Oncologist at the Princess Margaret Cancer Centre. “This work is dedicated to extending the lives of these individuals.”
The study group discovered that by measuring the expression of GATA6 and Keratin 5 in a patient’s tumour sample, they can differentiate subtypes of advanced pancreatic cancer. The different subtypes of the disease tend to respond to treatments differently, so clinicians and patients could potentially use this information to help guide treatment selection.
More specifically, the group showed cancers with low GATA6 expression and high Keratin 5 expression tend to be resistant to mFFX, one of the usual chemotherapy regimens. The study highlights the need for new, effective treatments for these patients.
“To discover these specific genes, we used sophisticated sequencing and in-depth analyses, but what we’ve found is that this classification can be done using simpler, widespread pathology techniques,” says senior author Dr. Sandra Fischer, Staff Pathologist at University Health Network. “This is promising because these discoveries can be easily applied in the clinic, and translated into patient care.”
The article was selected by Clinical Cancer Research to be highlighted on the front cover of the September 2020 issue and featured as one of the Issue Highlights.
Through the COMPASS trial, the researchers plan to further evaluate and validate this classification technique.
“I’m proud to be part of this team,” says Fischer. “Every step we take is a stride forward towards more precision and effective treatment for patients with this devastating disease.”
In December 2015, PanCuRx launched a clinical trial called Comprehensive Molecular Characterization of Advanced Ductal Pancreas Adenocarcinoma for Better Treatment Selection: A Prospective Study (COMPASS). The trial is designed to show that the sequencing of pancreatic tumours can be performed in a clinical setting and results delivered within a clinically-relevant timeframe to help guide treatment for individual patients. Read more on the latest COMPASS findings.
September 21, 2020
Q&A with new OICR Investigator Dr. Anastasia Tikhonova on tackling cancer cell cross-talk and adapting in a rapidly evolving field
OICR welcomes Dr. Anastasia Tikhonova to Toronto as an OICR Investigator and Scientist at the Princess Margaret Cancer Centre
The pandemic has compelled many people to adapt, and researchers are no exception. For Dr. Anastasia Tikhonova, adapting has always been an essential part of her career.
Tikhonova recently joined the OICR community as an OICR Investigator working at the Princess Margaret Cancer Centre. Her research focuses on hematological malignancies – or blood cancers – and how the environment around these cells can regulate their growth or help them resist standard treatments. Her research in this area will support the development of new cancer therapies that can ultimately help patients live longer and healthier lives.
Here, she describes her research program and why this community is a great place for her.
What is your research all about?
AT: Cancer cells do not exist in isolation. They are surrounded – and influenced – by their healthy neighbouring cells. For a long time, we didn’t fully understand the interactions between a cancer cell and its surrounding environment and how this dialogue impacts tumour growth. The last five years have significantly advanced imaging and genomic technologies that allow us to precisely decode the cross-talk between diseased cells and their environment – or their niche.
This is what my research is all about. My team uses single-cell transcriptomics, high-resolution imaging, and functional genomics to understand the connection between the complex elements in the bone marrow and cancer. Our goal is to untangle these connections and devise new strategies to target the interaction between leukemic cells and their environment, with the goal of eliminating blood cancers.
What got you interested in this space?
AT: I was fascinated by biology as a child. I remember learning about evolution in my first biology class in the fifth grade – I have been hooked ever since! I love being in the lab. I am exhilarated by seeing results for the first time and being able to connect the dots between different experiments. When I recognize a gap in my understanding, I feel compelled to learn more. This is how I became interested in the stem cell niche and leukemic microenvironment. As a Postdoctoral Fellow, I was fortunate to have had the opportunity to work in a top hematopoietic lab where I started to scratch the surface of understanding the niche’s molecular architecture, but many questions remain. Continuing this line of inquiry, I look forward to translating my findings into innovative therapies here in Ontario.
Why did you choose to come to Ontario?
AT: Princess Margaret is one of the top cancer research centres in the world. During my recruitment I had an amazing experience interacting with the faculty and trainees here. They were highly engaged and asked great questions, indicating a rich intellectual environment. Since most of my ideas come to me when I am working with others, this is the ideal place for my young lab to grow intellectually. Plus, the people here are genuinely supportive. My move was delayed due to COVID, but everyone here has been exceptionally helpful.
How has COVID impacted your work?
AT: An important trait to have as a scientific researcher is agility or the ability to quickly adapt to changing environments. Furthermore, COVID made me realize that nothing can shake my enthusiasm for starting a research group.
As a result of pandemic, I think people have become more open to collaboration. In some ways, online communication has leveled the playing field, bringing geographically distant researchers into the same space as colleagues accustomed to side-by-side interactions.
I also think COVID has brought science into public view. For the first time in my life, I hear immunology terms on the morning news. I’m excited by the prospect of biomedical research being a common discussion topic.
Does your work apply to other diseases?
AT: Yes, it does. I have a specific focus in a rare form of leukemia, called T-ALL. My research applies to other cancers as well. Insights from one disease can often guide our understanding of other malignancies.
Notably, my research in the regenerative medicine space of the bone marrow niche has the potential to impact thousands of patients treated every year with bone marrow transplantation. Additionally, if we can better understand how to regenerate the bone marrow microenvironment, we could bring a whole new treatment paradigm to patients with a wide spectrum of benign and malignant diseases. At the end of the day, this is what it’s all about.
September 16, 2020
Scientists discover mechanism of bone loss caused by acute lymphocytic leukemia, identify targeted therapy for children
OICR-supported research team discovers new pathway through which leukemia cells damage bone and a treatment that may protect children with leukemia from these effects
Due to remarkable progress in the treatment of pediatric leukemias with multi-drug chemotherapy, upwards of 85 per cent of children with the disease survive. One consequence of this success, is that more than a third of these patients suffer from in-bone fractures and pain during leukemia and for years following their treatment. In a recent study, Ontario researchers at the Hospital for Sick Children (SickKids) have discovered a process by which leukemia cells damage bone and discover that a targeted therapy may be able to prevent this damage.
In their study, published in Science Translational Medicine, the research group discovered that the bone degradation in leukemia patients is triggered by a protein called RANKL on the surface of the leukemic cells interacting with receptors called RANK on the surface of bone-degrading cells. The group showed that a drug, which is similar to one that is currently in clinical trials for other cancers, could specifically block this RANKL-RANK interaction and prevent further bone damage.
“A pan-Canadian study demonstrated that 15 per cent of children display bone fractures at the time they are diagnosed with acute lymphocytic leukemia, or ALL,” says lead author Dr. Jayne Danska, Senior Scientist in the Genetics & Genome Biology program at SickKids and Associate Chief, Faculty Development and Diversity at the SickKids Research Institute. “In addition, standard ALL chemotherapy protocols include corticosteroids which further damage the bone. Survivors of childhood ALL experience fractures and pain, and some cases are so severe that they require a hip replacement in their teenage years. We have discovered one mechanism that contributes to ALL-associated bone damage and a potential way to prevent it.”
To make these discoveries, first author of the study, Dr. Sujeetha Rajakumar, a postdoctoral fellow at SickKids, transplanted ALL cells from patient donors into experimental mouse models to examine the effect of leukemia cells on bone and how to disrupt the RANKL-RANK interaction. This so-called xenotransplantation method was pioneered by Dr. John Dick at the University Health Network’s Princess Margaret Cancer Centre.
Using these animal models, Danska’s group showed that treatment of the ALL-transplanted mice with a protein therapeutic that blocks the RANKL-RANK interaction prevented bone damage despite high number of leukemia cells in the bone compartments.
“There are clinical trials underway to test whether RANKL-RANK antagonists can prevent bone degradation in adults with metastatic prostate and breast cancers,” says Danska, who is also a Professor in the University of Toronto’s Faculty of Medicine. “The data we report in the human ALL transplant model is encouraging because the availability of clinical data with this class of drug can accelerate application of our discoveries to clinical trials in youth with ALL.”
“Children with leukemia sustain unbelievably rigorous and lengthy chemotherapy treatments,” says Danska. “We’re eager to bring our discoveries into clinical trials that may help minimize these painful and life-altering late effects of this disease.”
Danska and study collaborators Drs. Cynthia Guidos and Johann Hitzler of SickKids, and Drs. Mark Minden and John Dick of the Princess Margaret Cancer Centre are members of OICR’s Acute Leukemia Translational Research Initiative (TRI), which partially funded the study.
September 16, 2020
This post was edited and republished with the permission of CanPath.
CanPath is pleased to announce that, with funding support from the Canadian Partnership Against Cancer, a Saskatchewan cohort will be developed and join the CanPath study. The Saskatchewan Partnership for Tomorrow’s Health (Saskatchewan PATH) will add approximately 9,000 participants to the existing cohort of over 330,000 Canadian participants. The addition of Saskatchewan means that all 10 Canadian provinces have now joined CanPath.
Saskatchewan PATH will create a platform and resource for fostering research in cancer and chronic disease prevention within the province. The Saskatchewan PATH study will be led by Scientific Director, Riaz Alvi and hosted by the Saskatchewan Cancer Agency.
“We are excited to officially welcome Mr. Alvi and the Saskatchewan PATH team to the CanPath partnership. We look forward to working together to develop a truly pan-Canadian study and sharing learnings from our other regional cohorts to support Saskatchewan PATH as they move forward,” says John McLaughlin, Executive Director of CanPath.
“We are proud to be a part of this truly national program. Saskatchewan holds a prominent place in the history of healthcare in Canada, and houses one of the world’s oldest cancer registries. We are confident that the people of Saskatchewan will welcome this opportunity to participate in Saskatchewan PATH to help further a better understanding of cancer and other chronic diseases, and to assist with the future development of prevention, early detection, diagnosis and treatment programs. There is exciting and highly rewarding work ahead of us.” says Riaz Alvi, Scientific Director of Saskatchewan PATH.
Saskatchewan has a unique and diverse population, with roughly half living in the province’s largest city, Saskatoon, or the provincial capital of Regina. The province’s economy is primarily associated with agriculture and more recently mining. The burden of cancer in Saskatchewan is significant with about 5,600 new cancers diagnosed in 2018 and just over 2,000 cancer deaths in the same year. In 2018, the number of people living with cancer that had been diagnosed within the last 5 years (5-year prevalence), was approximately 17,000 people.
“Since CanPath began almost 11 years ago, we have sought to ensure representation of all provinces. Now being able to include participants from the province of Saskatchewan fills an important gap, and builds upon the hard work of many of us who started and have maintained the CanPath cohort and vision since the beginning,” says Philip Awadalla, National Scientific Director for CanPath.
With CanPath’s guidance and support of the development of Saskatchewan PATH, the new cohort will benefit from the experience and lessons learned by CanPath’s other regional cohorts. Saskatchewan PATH joins the six regional cohorts that currently makeup CanPath: BC Generations Project, Alberta’s Tomorrow Project, Manitoba Tomorrow Project, Ontario Health Study, CARTaGENE (Quebec), and Atlantic PATH.
The development of Saskatchewan PATH will consist of three phases:
- Phase I – Planning & Implementation (Present to March 2022)
- Phase II – Participant Recruitment and Collection of Data and Biological Samples
- Phase III – Maintenance and Use of Participant Data and Biological Samples
The Canadian Partnership for Tomorrow’s Health (CanPath) is Canada’s largest population health cohort and a national platform for health research. Comprised of more than 330,000 volunteer participants, CanPath is a unique platform that allows scientists to explore how genetics, environment, lifestyle and behaviour interact and contribute to the development of cancer and other chronic diseases. CanPath is hosted by the University of Toronto’s Dalla Lana School of Public Health with national funding from the Canadian Partnership Against Cancer. The Ontario Institute for Cancer Research (OICR) hosts CanPath data in a safe and secure environment. To learn more, visit www.canpath.ca.
The original post can be viewed here: https://canpath.ca/2020/09/canpath-completes-provincial-map-with-addition-of-a-saskatchewan-cohort/
September 10, 2020
OICR-supported researcher Dr. Harriet Feilotter leads liquid biopsy research program
As the COVID-19 pandemic has impacted many areas of life, including the diagnosis and treatment of other health conditions, people have chosen to forgo cancer screening and care in attempt to minimize their potential exposure to the virus. Relative to the general population, people living with cancer are more susceptible to the virus, but delaying cancer treatment may allow the disease to grow or spread.
Dr. Harriet Feilotter has teamed up with members of the pan-Canadian Digital Technology Supercluster to bring greater access to cancer testing and treatment during the pandemic and beyond. Through the $2.59 million Project ACTT (Access to Cancer Testing & Treatment in Response to COVID-19), they aim to provide liquid biopsy solutions, which require only a simple blood draw, as alternatives to surgical tissue biopsies for cancer diagnosis and care.
“The goal is to allow patients alternatives to invasive procedures that may be difficult to access during a pandemic,” says Feilotter, Molecular Geneticist and Scientist at Kingston Health Sciences Centre, faculty member of Queen’s Cancer Research Institute and OICR Associate. “Not only would this benefit those patients who live far from large cancer centres, but it could limit patient exposure to COVID-19 and increase health system capacity.”
The collaborative team is led in part by Canexia Health, which develops specialized cancer genomic assays, and Patriot One Technologies Inc.’s subsidiary Xtract AI, which specializes in machine learning solutions across a variety of applications, among other private and public partners. Together, they will work to enhance their current tests that detect mutations in circulating tumour DNA (ctDNA) from blood and deploy these tests for multiple cancer types across Canada.
Now through ACTT, some patients have access to these tests in British Columbia, Ontario, Quebec and Saskatchewan. The long-term objective is to increase access across the country.
“The development of liquid biopsies and ctDNA testing has been accelerated by this pandemic,” says Feilotter. “We’re proud to team up in this cross-disciplinary, cross-sector collaboration to bring these promising solutions to more patients.”
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.”
August 31, 2020
Learn about the research that the Ontario Health Study has been doing during COVID-19 and how scientists have managed to do this work from home.