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

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

February 5, 2020

Unraveling the story behind the cancers we can’t explain

Dr. Philip Awadalla
Dr. Philip Awadalla

The Pan-Cancer Analysis of Whole Genomes Project has shown that despite cancer’s complexities, researchers are close to cataloguing all of the biological mechanisms that lead to the disease.

Today, Nature released a special collection of 23 publications related to the analysis, one of which presents the most comprehensive catalogue of RNA alterations in cancer to date.

We sat down with Dr. Philip Awadalla, OICR investigator and National Scientific Director of the Canadian Partnership for Tomorrow Project, and Dr. Fabien Lamaze, Postdoctoral Fellow in the Awadalla Lab, to discuss.

What can RNA show us about cancer?

PA: Cancer is thought to be a disease of the genome, where changes – or mutations – in an individual’s DNA accumulate and eventually lead to the development of the disease. Often, we can identify the mutations that drive this development, figure out the related mechanisms and design new therapies with that information, but sometimes no such ‘driver mutation’ exists.

We believe that RNA can help us unravel the story behind these cancers that we can’t yet explain.

What did the study find?

Dr. Fabien Lamaze
Dr. Fabien Lamaze

FL: In this study, we took a deep dive into the transcriptome – the RNA – of nearly two thousand tumour samples donated by patients from around the world, representing 27 different types of tumours. The group found more than 1.5 million different RNA alterations and related mechanisms in these samples, exposing the true complexity of the disease.

Interestingly, the study found key RNA alterations in patient samples with no DNA driver mutation. This suggests that some of the cellular changes that lead to cancer may manifest in RNA rather than DNA mutations.

What does this mean for the future of cancer research?

PA: We see that cancer is complex and we need even more data to fully understand it, but we’ve also shown that we can make this happen by working together.

FL: The Pan-Cancer Analysis of Whole Genomes Project was the product of an enormous international study that was only made possible by the dedication and true collaboration between thousands of researchers from around the world. For this study, in particular, I’d like to recognize the scientific leadership of Dr. Angela Brooks and collaborators from the University of California, Santa Cruz.

PA: As more patient samples are collected and sequenced, we look forward to using the software tools and infrastructure from the Pan-Cancer Project to gain further insights into cancer biology.

How can this help cancer patients?

FL: Understanding the changes that lead to cancer can help us design better tests and new treatments for future cancer patients. This study, for example, discovered six interesting gene fusions involved with cancer, where two genes come together, join in an abnormal way and wreak havoc. In the future, we could potentially develop new drugs that target the downstream products of these fusions and stop them from causing further damage in the cell.

PA: With the knowledge we’ve gained in this study, we look forward to furthering diagnostic and therapeutic research and development so we can ultimately treat patients more successfully. Work is already underway to make this happen.


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July 23, 2019

Blood samples, biostatistics and a fresh perspective: The makings of a cancer prediction machine

Jordyn Walton and David Soave
Jordyn Walton and Dr. David Soave

Biostatistics Training Initiative (BTI) alumnus brings on new BTI trainee to study Canada’s largest population health dataset using today’s top technologies

Recently, circulating tumour DNA (ctDNA) – DNA released from cancer cells that freely circulates in the blood – has garnered much attention not only as an alternative to traditional tissue biopsies, but as a potential blood-based biomarker for early cancer diagnosis.

The ability to detect the earliest blood-borne traces of cancer largely rests in our ability to determine which molecular markers indicate that a cancer is developing – or which patterns in ctDNA can predict whether a cancer will grow. Dr. David Soave sees this as a mathematical challenge that, if solved, could have huge impact for better predicting and diagnosing a wide variety of cancers.

“To find cancer earlier or predict who will develop the disease, we need to carefully compare human samples from those who will develop cancer and samples from those who won’t,” Soave, an Assistant Professor at Wilfrid Laurier University and OICR Associate, says. “This type of challenge requires new statistical models, methods and computational techniques that can decipher large, complex and high-dimensional data.”

Last year, the Canadian Partnership for Tomorrow Project (CPTP) unified the data from several provincial longitudinal health studies into a national cohort consisting of more than 325,000 participants who are voluntarily donating their health and biologic samples to research. As some CPTP participants will develop disease and others will not, this dataset provides an unprecedented resource for researchers like Soave to discover the earliest traces of cancer that appear several months to years prior to an initial diagnosis.

Continue reading – Blood samples, biostatistics and a fresh perspective: The makings of a cancer prediction machine

August 7, 2018

Data integration for the future of precision oncology

CDIC Banner images

Big data are ushering in a new era of individualized cancer care and prevention, but not without conceptual and practical challenges. Canadian advances in genomics will be made by or limited by bioinformatics analytical capacity as well as the ability to store and analyze data in new and more sophisticated ways.

To help realize the potential of genomics research in cancer, the Canadian Data Integration Centre (CDIC) platform, led by OICR, offers third generation bioinformatics and genomics tools to support both functional and clinical genomics research. CDIC is the largest academic cancer informatics program in the country – offering customizable, client-oriented access services for data challenges across diverse research areas.

Continue reading – Data integration for the future of precision oncology

July 10, 2018

Researchers find early indicators of leukemia in genomes up to 10 years before symptoms surfaced

Immature blood cells in leukemia

Acute myeloid leukemia (AML) progresses quickly and requires treatment soon after diagnosis, but the disease begins long before becoming symptomatic. Early indicators of AML were thought to be indistinguishable from healthy aging. But now, an international group of researchers led in part by Dr. Sagi Abelson, a postdoctoral fellow in the lab of Dr. John Dick at the Princess Margaret Cancer Centre, has discovered distinctive traces of AML in patients up to 10 years before they were diagnosed with the disease.

Continue reading – Researchers find early indicators of leukemia in genomes up to 10 years before symptoms surfaced

June 19, 2018

More than 300,000 Canadians enrol in multi-decade research initiative to monitor disease trends

CPTP Leaders in OICR Data Centre

From left, Dr. John McLaughlin, executive director of CPTP, Cindy Morton, chief executive officer of the Canadian Partnership Against Cancer, and Dr. Philip Awadalla, national scientific director of CPTP

Over the past 10 years, more than 300,000 Canadians have volunteered to be part of the Canadian Partnership for Tomorrow Project (CPTP), a research platform that tracks the development of cancers and chronic diseases in the population over several decades to better understand risk factors.

Researchers from across Canada and the University of Toronto published a manuscript in the Canadian Medical Association Journal last week, marking a culmination of effort from hundreds of Canadian researchers to build the project with support from multiple national and provincial funders.

Continue reading – More than 300,000 Canadians enrol in multi-decade research initiative to monitor disease trends

March 29, 2018

Q and A with Dr. Philip Awadalla, Scientific Director of the Canadian Partnership for Tomorrow Project

Dr. Philip Awadalla poses for a photo in a hallway

Since 2008, the Canadian Partnership for Tomorrow Project (CPTP) has collected health data and biological samples from more than 300,000 volunteer participants across Canada. Now that its primary data collection phase has concluded, the Project is sharing this data with qualified researchers to help uncover the factors behind cancer and other diseases. It was recently announced that OICR’s Dr. Philip Awadalla will serve as the Project’s National Scientific Director and that OICR will host the Project’s national database and other scientific activities. We sat down with Awadalla to learn more about his vision for CPTP’s future. Continue reading – Q and A with Dr. Philip Awadalla, Scientific Director of the Canadian Partnership for Tomorrow Project

March 29, 2018

Canada’s largest health research platform teams up with University of Toronto to accelerate cancer and chronic disease research

The leaders of the CPTP stand in front of servers storing the Project's data.

Pictured (left to right): Dr. John Mc Laughlin, Executive Director of CPTP; Cindy Morton, Chief Executive Officer of the Canadian Partnership Against Cancer.; and Dr. Philip Awadalla, National Scientific Director of CPTP.

Canadian Partnership for Tomorrow Project (CPTP) enters a new era of scientific activity under the leadership of newly appointed National Scientific Director, Dr. Philip Awadalla

March 29, 2018 (Toronto) – The Canadian Partnership Against Cancer (“the Partnership”) today announced The University of Toronto’s Dalla Lana School of Public Health will be the new national scientific partner of the Canadian Partnership for Tomorrow Project (CPTP) – Canada’s national population cohort for precision health. This new scientific partner will enable a strong national scientific vision for CPTP and support leading-edge research on the possible causes of cancer and chronic diseases, leading to more made-in-Canada discoveries and breakthroughs. In addition, the University has announced that Ontario Institute for Cancer Research (OICR) will be its strategic partner to deliver the expertise and services needed to lead this key research platform.

Continue reading – Canada’s largest health research platform teams up with University of Toronto to accelerate cancer and chronic disease research

March 6, 2018

Study shows that environmental exposures such as air pollution are more determinant of respiratory health than inherited genetics

Toronto (March 6, 2018) – Researchers have found strong evidence that environmental exposures, including air pollution, affect gene expressions associated with respiratory diseases much more than genetic ancestry. The study, published today in Nature Communications, analyzed more than 1.6 million data points from biological specimens, health questionnaires and environmental datasets, making this study one of the largest ever to examine the relationship between gene expression and environmental stimuli. These findings represent a groundbreaking use of big data to uncover the environmental factors that are behind diseases and inform strategies for prevention, an approach that would apply to a number of diseases, including cancer.

Continue reading – Study shows that environmental exposures such as air pollution are more determinant of respiratory health than inherited genetics

January 25, 2018

The Canadian Data Integration Centre receives new funding to help cancer researchers translate findings to patients

CDI - LogoToronto (January 25, 2018) – The Canadian Data Integration Centre (CDIC) has received $6.4 million in funding from Genome Canada to help the research community translate the biological insights gained from genomics research into tangible improvements for cancer patients.

CDIC is a “one-stop shop” service delivery platform for cancer researchers, helping streamline research by providing coordinated expertise on a broad range of services, including data integration, genomics, pathology, biospecimen handling and advanced sequencing technologies. It is an international leader in genomics, bioinformatics and translational research, supporting some of the world’s largest programs in genomic data analysis, genomic and clinical data hosting, cancer data analyses and access, and the development of algorithms for advanced sequencing technology.

Continue reading – The Canadian Data Integration Centre receives new funding to help cancer researchers translate findings to patients

May 3, 2017

Study bringing more precision medicine to Ontario’s cancer patients

A technician holds a blood sample and writes down information.

The advent of genomic sequencing and targeted therapies has opened the door to new ways of diagnosing and treating cancer. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) program is a new, province-wide initiative supported by OICR that will allow more patients to benefit from these innovations while also helping to advance cancer research in Ontario.

Continue reading – Study bringing more precision medicine to Ontario’s cancer patients

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