July 17, 2019
Ten years, 330,000+ Canadians: CPTP connects participants from coast to coast with shared goal of a healthier future
After losing her aunt to breast cancer, Krista felt powerless and wanted to help make a difference.
Marc felt empowered when he started taking a more active role in his health following his sleep apnea diagnosis.
Her Indigenous family roots motivated Sandra to get involved since she thought her genetic information might be particularly useful to researchers.
Their stories are unique, but Krista, Marc and Sandra actually have a lot in common. They’re three of the more than 330,000 participants in the Canadian Partnership for Tomorrow Project (CPTP) who share a vision of a healthier Canada.
By connecting six regional cohorts across nine provinces, the CPTP is the largest data collection of its kind in Canadian history. Hosted by the University of Toronto, the CPTP allows researchers to explore how genetics, environment, lifestyle and behavior interact and contribute to the development of cancer and other chronic diseases.
When Krista Osborne of St. Albert, Alberta found out about her aunt’s breast cancer, she donated her long hair to make wigs, but she wanted to do more.
“I heard about Alberta’s Tomorrow Project in the news and knew that I wanted to take part and help researchers in a personal way. I wanted my life to have some value to later generations,” said Osborne, who joined Alberta’s Tomorrow Project in 2011.
Osborne, like most CPTP participants, has lived experience with cancer or another chronic illness. In fact, cancer is the leading cause of death in Canada with one in two Canadians affected during their lifetime.
“Canadians can have a direct impact on health research through the project and we’re tremendously grateful for participants’ time and investment,” said Dr. Philip Awadalla, National Scientific Director of the Canadian Partnership for Tomorrow Project.
“The CPTP has united Canadians from coast to coast over the last decade, creating a living population laboratory that will improve our understanding of disease risk factors and unlock the mysteries of cancer and other chronic diseases,” said Awadalla, who is also Executive Scientific Director of the Ontario Health Study (OHS) and principal investigator of Genome Canada’s Canadian Data Integration Centre.
Unlocking a mystery is exactly how Marc André Sirois felt when he was diagnosed with sleep apnea in September 2016.
“I had concerns about my sleep quality and was asked to participate in a sleep study. I wore the monitor and after one month, I received some negative results. Bad sleeping habits can negatively impact your health in so many ways,” said Sirois, an OHS participant who lives in Ottawa.
Sandra Slobodian agrees that mega-data studies like CPTP can uncover hidden solutions to health issues, which she believes is important for all Canadians, including Indigenous peoples.
“I think First Nations people are a great source of generational information, but may be wary of participating in research projects because many have been over studied, abused by government policies and may not trust the process,” said Slobodian, who lives in Esquimalt, British Columbia and joined the BC Generations Project in 2008.
There are close to 8,000 self-reported Indigenous participants in the CPTP and Awadalla is encouraging Indigenous researchers to utilize the platform for a variety of Indigenous-led projects.
Trust is critical, not only for Indigenous participants, but for everyone. And with more than one billion pieces of health information, the size and scope of CPTP’s dataset is enormous. Privacy and protection of participant data is absolutely critical, underlining the importance of CPTP’s partnership with the Ontario Institute for Cancer Research, a globally recognized institute in genomic and clinical data storage expertise.
As a lawyer, Sirois understands how difficult trust can be in today’s world, but his message to Canadians about the CPTP is simple:
“I’d say trust the scientific process. CPTP scientists are doing good work that’s making a difference on health and it’s empowering to be a part of that process,” said Sirois.
“We need to stick with CPTP for the long term to make an impact, and in the meantime, let’s enjoy the baby steps and small wins.”
Learn more about seven CPTP participants, including their personal stories with cancer or chronic disease, why they joined the study, and how they’d improve health care in their communities.
Manitoba is the only province currently recruiting new participants via the Manitoba Tomorrow Project.
July 17, 2019
Collaborative research group maps the three-dimensional genomic structure of glioblastoma and discovers a new therapeutic strategy to eliminate cells at the roots of these brain tumours
Current treatment for glioblastoma – the most common type of malignant brain cancer in adults – is often palliative, but new research approaches have pointed to new promising therapeutic strategies.
A collaborative study, recently published in Genome Research, has mapped the three-dimensional configuration of the genome in glioblastoma and discovered a new way to target glioblastoma stem cells – the self-renewing cells that are thought to be the root cause of tumour recurrence.
The research group integrated three-dimensional genome maps of glioblastoma with other chromatin and transcriptional datasets to describe the mechanisms regulating gene expression and detail the mechanisms that are specific to glioblastoma stem cells. They are one of the first groups in the world to perform three-dimensional genomic analyses in patient-derived tumour samples.
“The 3D configuration of the genome has garnered much attention over the last decade as a complex, dynamic and crucial feature of gene regulation,” says Dr. Mathieu Lupien, Senior Scientist at the Princess Margaret Cancer Centre, OICR Investigator and co-author of the study. “Looking at how the genome is folded and sets contacts between regions tens to thousands of kilobases apart allowed us to find a new way to potentially tackle glioblastoma.”
Through their study, the group discovered that CD276 – a gene which is normally involved with repressing immune responses – has a very important role in maintaining stem-cell-like properties in glioblastoma stem cells. Further, they showed that targeting CD276 may be an effective new strategy to kill cancer stem cells in these tumours.
Lupien adds that advancements in three-dimensional genomics can only be made through collaborative efforts, like this initiative, which was enabled by OICR through Stand Up 2 Cancer Canada Cancer Stem Cell Dream Team, OICR’s Brain Cancer Translational Research Initiative and other funding initiatives.
“This research was fueled by an impressive community of scientists in the area who are committed to finding new solutions for patients with brain cancer,” Lupien says. “Our findings have emphasized the significance of three-dimensional architectures in genomic studies and the need to further develop related methodologies to make sense of this intricacies.”
Senior author of the study, Dr. Marco Gallo will continue to investigate CD276 as a potential therapeutic target for glioblastoma. He plans to further delineate the architecture of these cancer stem cells to identify more new strategies to tackle brain tumours.
“A key problem with current glioblastoma treatments is that they mostly kill proliferating cells, whereas we know that glioblastoma stem cells are slow-cycling, or dormant. Markers like CD276 can potentially be targeted with immunotherapy approaches, which could be an effective way of killing cancer stem cells, irrespective of how slowly they proliferate,” says Gallo, who is an Assistant Professor at the University of Calgary. “Being able to kill cancer stem cells in glioblastoma could have strong implications for our ability to prevent relapses.”
July 3, 2019
The Lebovic Fellowship program connects scientists in Israel and Ontario, leading to the validation of a new drug candidate for leukemia and the optimization of a new potential cancer vaccine
Three years ago, the Institute for Medical Research Israel-Canada (IMRIC) received a donation from Joseph and Wolf Lebovic – two brothers who are Holocaust survivors, Canadian immigrants, avid philanthropists and recently-appointed Members of the Order of Canada. Their vision was to strengthen collaboration between the outstanding researchers in Israel and those in Ontario to accelerate cancer research.
They created the Joseph and Wolf Lebovic Fellowship Program, which paired together laboratories specializing in complementary subjects. The Program’s first round of projects officially came to a successful close today and here we recognize the progress made thanks to the generous donation of the Lebovic brothers.
Developing a drug for leukemia
Israel lead researcher: Dr. Yinon Ben-Neriah, IMRIC
Israel fellows: Waleed Minzel and Eric Hung, PhD Candidates, Hebrew University of Jerusalem
Ontario lead researcher: Dr. John Dick, Princess Margaret Cancer Centre (PMCC)
Ontario fellow: Dr. Laura Garcia-Prat, Postdoctoral Fellow, PMCC
Ben-Neriah’s lab in Israel had developed a new compound and showed it may be a valuable anti-leukemia drug, but they couldn’t explain why the drug was only effective in animal models that had strong immune systems. Understanding the relationship between the drug and the immune system would allow them to validate which leukemia subtypes would respond to their therapeutic approach.
John Dick’s lab had developed the gold standard for evaluating the efficacy of leukemia drugs in animal models using sophisticated patient-derived xenograft mouse models. Through this fellowship, the Ben-Neriah Lab teamed up with the Dick lab to learn from their expertise and gain insights into their experimental models.Continue reading – Five fellows, four labs, three years, two countries, and a generous donation
July 3, 2019
Bridges built between Israel and Canada thanks to philanthropic donation from Joseph and Wolf Lebovic
TORONTO (July 3, 2019) – The Ontario Institute for Cancer Research (OICR), the Institute for Medical Research Israel-Canada (IMRIC) at the Hebrew University of Jerusalem and the Canadian Friends of Hebrew University (CFHU) today honour the successful conclusion of the first round of the Joseph and Wolf Lebovic Cancer Genomics and Immunity Fellowship Program, a cross-continent multidisciplinary collaboration between experts in cancer research. The Program forged two new partnerships between labs in Canada and Israel and provided a unique training opportunity for early career researchers in both countries. These collaborations led to the development of a new potential cancer-killing virus and a new drug candidate for leukemia.
Fellowships were awarded to Adrian Pelin from the lab of Dr. John Bell at The Ottawa Hospital Research Institute, in Ottawa, Ontario and Yoav Charpak Amikam from the lab of Dr. Ofer Mandelboim at IMRIC in Jerusalem, Israel. The collaboration improved the specificity and immune-triggering abilities of the potential oncolytic Vaccinia virus.
Another pair of fellowships were awarded to Dr. Laura Garcia-Prat from the lab of Dr. John Dick at the Princess Margaret Cancer Centre, in Toronto, Ontario and Waleed Minzel and Eric Hung from the lab of Dr. Yinon Ben-Neriah at IMRIC. This partnership enabled the development of leukemia xenograft models to help validate the efficacy of a new drug candidate, as recently published in the scientific journal Cell.
The Lebovic Fellowship Program was established by a philanthropic donation provided to IMRIC by Joseph and Wolf Lebovic – two brothers who survived the Holocaust, immigrated to Canada and have recently been appointed as Members of the Order of Canada for their contributions to the Toronto community.
“We’d like to congratulate the fellows today on their progress which was made possible by the generous support of Joseph and Wolf Lebovic. The funding provided by the Lebovic brothers allowed us to create a platform for Ontario scientists to establish collaborations with researchers in Israel and we look forward to strengthening this platform for future collaborative work,” says Dr. Laszlo Radvanyi, President and Scientific Director of OICR.
“We congratulate the fellows today on their achievements during this first round of the program. IMRIC is proud to continue our collaboration with an institute as distinguished as OICR, supported by the inspiring philanthropy of Joseph and Wolf Lebovic,” says Prof. Haya Lorberboum-Galski, Chairman of IMRIC. “We feel that this collaboration between top Canadian and Israeli researchers will surely lead to significant and game-changing advances in the world arena.”
“Thanks to the vision and generosity of Joseph and Wolf Lebovic, they have been instrumental in creating an international collaboration that will continue to strengthen Israel-Canada connections while benefitting humankind,” says Rami Kleinmann, CEO and President of Canadian Friends of Hebrew University. “CFHU is grateful for their continuing and dedicated support.”Continue reading – Bridges built between Israel and Canada thanks to philanthropic donation from Joseph and Wolf Lebovic
June 26, 2019
University Health Network pathologist teams up with OICR researchers to develop an improved pancreatic cancer classification test that can better predict the severity of the disease
Under a microscope, pancreatic cancer often looks like a haphazard collection of cells with various shapes and sizes, but Dr. Sangeetha N Kalimuthu saw something different.
She had been analyzing hundreds of pancreas resections, which are classified using the current three-tiered staging system – well, moderate and poor – but found that the vast majority of cases fell into the moderate category, offering little information to physicians about how best to treat these patients.
N Kalimuthu, a gastrointestinal pathologist at the University Health Network (UHN), noticed that certain patterns in cell shape matched the molecular profile of tumours with poorer survival for patients. She teamed up with Drs. Runjan Chetty and Steven Gallinger at UHN to see if what she noticed was true. Gallinger is Director of OICR’s PanCuRx Translational Research Initiative.
In a study recently published in Gut BMJ, the study group assessed more than 800 pancreatic ductal adenocarcinoma (PDAC) slides and developed an improved classification method that could help differentiate patients with the most aggressive tumours.
“Our aim was to revise and reappraise the current grading system to find features that correlated with these molecular subtypes,” says N Kalimuthu.
By linking molecular profiles of tumours with their appearance, N Kalimuthu was able to develop a classification method that can be easily integrated into current pathology laboratories.
“Any pathologist in any part of the world can do this,” says N Kalimuthu. “It’s the bread and butter of what pathologists do. It’s fast, cheap and accessible.”
N Kalimuthu also says that this method can be augmented using deep learning methods to reduce turn-around times and variability from one pathology laboratory to another.
“Pathologists have had a long, rich history in their vital roles to diagnose and stage pancreas cancer,” says Gallinger, who is co-author of the publication. “This study is an elegant demonstration of the potential of personalized medicine, with the promise of improved outcomes for our patients.”
June 18, 2019
Toronto-based entrepreneur Zaid Atto receives FACIT’s Ernsting Entrepreneurship Award to further develop his new device for safer and less invasive surgeries
Ten years to the day after he and his family landed in Canada from Iraq, Zaid Atto stood in front of a panel of judges and pitched his idea. He had developed a new surgical device – a port that could allow for safer and more efficient minimally invasive surgeries – but he needed commercialization support and resources to move it into the next stage of development.
Surgeons use ports, also known as trocars, to make a tunnel into the body for laparoscopic surgeries. Complications with ports include accidental organ perforation, hernias and potentially death from incorrect insertions. Adding to the risk of complications, sometimes surgeons have to switch an inserted port for one with a larger diameter during the procedure to accommodate larger surgical instruments, or reinsert a port that slipped out of the abdomen accidentally. Through interviewing surgeons and shadowing dozens of surgeries, Atto recognized these concerns and saw an opportunity to address an unmet need and help both patients and surgeons.
After graduating with a biomedical engineering degree from the University of Toronto, Atto and his team at Xpan Inc. developed an expandable port that reduces the risk of complications associated with port insertion and alleviates the need to remove and reinsert ports. The team has consulted stakeholders and device manufacturers throughout the development of their device and have received support and validation from surgeons with multiple minimally-invasive surgical specialties.
“We saw that our device could assist surgeons across many subspecialties, especially those who have to exchange ports often, like in surgeries for colorectal cancer, pediatric surgeries or emergency procedures” says Atto. “Our port, however, is not limited to cancer surgeries. It’s a device that can make a difference for all laparoscopic surgeons and the five million patients who undergo minimally invasive surgery every year in North America.”
Earlier this year Atto pitched his technology at the FACIT Falcons’ Fortunes pitch competition. In addition to creating exposure for novel oncology innovations and providing training support for entrepreneurs, FACIT’s annual pitch competition celebrates a culture of commercialization in Ontario. Atto was one of six finalists who were pre-selected by the FACIT team to deliver pitches. Impressing the judges with an innovation developed based on a clearly-identified market need, Atto was ultimately awarded the $50,000 Ernsting Entrepreneurship Award. Xpan Inc. plans to use this funding to complete proof-of-concept animal studies and prepare for regulatory submission.
“By partnering with FACIT, we hope to bring our device one step closer to patients,” says Atto. “This means one step closer to safer and more efficient surgeries for all of us who may need these surgeries in the future.”
Read more about this story in FACIT’s most recent announcement of investments.
June 10, 2019
OICR-supported researcher Dr. Nicole Mittmann leads collaborative initiative to determine the value of new cancer solutions and the burden of cancer care on Canada’s healthcare system
Canada is well known for its publicly funded healthcare system, its universal health coverage, and in most recent news – for the Toronto Raptors.
What is less recognized, however, is that with its distinctive healthcare system, Canada has unique healthcare reimbursement processes and resource needs, especially for the delivery of cancer care. While Canada collects some of the most robust and comprehensive healthcare data, Canadian datasets are underutilized in research and policy decision making.
Dr. Nicole Mittmann has set out to close this gap and, in turn, transform our administrative health information into tangible healthcare improvements.
“As cancer-drug costs continue to rise, there is – now more than ever before – a need to understand the Canadian context with respect to costs and health system resource use,” she writes in Current Oncology.
Turning data into action
Mittmann, who was recently appointed as the Chief Scientist and Vice-President of Evidence Standards at the Canadian Agency for Drugs and Technologies in Health (CADTH), sees Canada’s rich data as a goldmine for improving the management of diseases and the delivery of care.
“This information can be used to help us make decisions, help us plan and help us understand the value of new technologies,” she says. “It could also show us areas where we need to improve, or problems that weren’t apparent through practice alone, but we needed to reduce the barriers to using these data for research.”Continue reading – It’s our health information: a goldmine for improving the quality of cancer care
June 4, 2019
New research projects to drive clinical adoption of novel cancer technologies and find ways to better deliver cancer services
10 projects to receive funding through OICR-CCO Health Services Research Network
Toronto (June 4, 2019) – The Ontario Institute for Cancer Research (OICR) today announced funding for 10 projects as part of the OICR-Cancer Care Ontario (CCO) Health Services Research Network (HSRN). As part of the HSRN, these projects are focused on optimizing the delivery of existing cancer services and guiding the dissemination of new practices and technologies in cancer prevention, screening and care in Ontario.
The funded projects, which involve 103 researchers and clinicians based at 29 institutions across Ontario, as well as five institutions outside of the province, focus on at least one of six priority areas: using real-world evidence to advance innovations; data infrastructure, integration and mobilization studies; use of artificial intelligence and digital health tools; the adoption of accepted best practices related to precision medicine; knowledge translation and dissemination; and population health studies.
“Improving the delivery of cancer-related healthcare and ensuring that new innovations are properly introduced into clinical use is an essential part of improving outcomes for cancer patients,” says Dr. Christine Williams, Deputy Director and Interim Head, Clinical Translation, OICR. “The projects funded today will help integrate more leading-edge technologies and practices – such as artificial intelligence, immunotherapies and precision medicine – into Ontario’s healthcare system. OICR is proud to help enable improvements in frontline care for the people of Ontario through these projects.”
In total, the projects announced today will receive more than $2.7 million in funding over the next two years. These projects were awarded funding after a competitive process, including review by an expert panel. Together, these projects are a key arm of OICR’s Clinical Translation initiative, which is driving the translation of research findings into patient impact by partnering with the healthcare system.
“I congratulate the researchers who have received funding today and laud their efforts to optimize how we prevent, diagnose and treat cancer in Ontario,” says Hon. Merrilee Fullerton, Ontario’s Minister of Training, Colleges and Universities. “As new technologies and best practices emerge, it is important that Ontario use its research expertise to deliver these advancements to the people as quickly and efficiently as possible.”
For details about the funded projects please visit: https://oicr.on.ca/research-portfolio/health-services-research/Continue reading – New research projects to drive clinical adoption of novel cancer technologies and find ways to better deliver cancer services
May 31, 2019
In May, OICR welcomed Dr. Trevor Pugh as Director of Genomics and Senior Principal Investigator. Trevor is a cancer genomics researcher and board-certified molecular geneticist who has led the Princess Margaret Cancer Centre-OICR Translational Genomics Laboratory (PM-OICR TGL) since 2016.
In his new role, he will lead the OICR Genomics program, which brings together the Princess Margaret Genomics Centre, OICR’s Genome Technologies, Translational Genomics Laboratory and Genome Sequence Informatics teams under an integrated initiative to support basic, translational and clinical research. Here, Pugh describes some of his strategies and how he plans to take on this ambitious mandate.
You’re involved with a number of projects across many disease sites and you collaborate with researchers from vastly different areas of cancer research. Can you summarize what you focus on?
Simply put – I want to use genome technologies to guide the best patient care. The overall philosophy is to extract as much genomic information as we can from small amounts of tumour tissue, and turn that information into knowledge so that clinicians and patients can make targeted treatment decisions. I also want to open up these comprehensive data for researchers to mine and find new cures for these cancers.
Whether they are a graduate student working on myeloma or a postdoc working on liver cancer, we all learn from one another’s disease specialties.
And yes – I am involved with many areas of cancer research. Every member in my lab speaks the same genomics language. Whether they are a graduate student working on myeloma or a postdoc working on liver cancer, we all learn from one another’s disease specialties. We do genomics in a similar way as there are many genomic commonalities across cancer types and computational algorithms or infrastructure we build for one project invariably get reused for another project.
You are a board-certified molecular geneticist and a genomics researcher, but you also have a background in bioinformatics and software development. How do you balance making tools and making discoveries?
The tools we create and the research we perform go hand in hand. You can’t make discoveries without the infrastructure, and it is hard to develop technologies successfully without a guiding scientific question. With that said, the software that we make is designed to help not only our own research and clinical projects, but those of others. If we can make software work for us really well, we want to share it and make it easier for groups and labs across Ontario and around the world. This also holds for the data we generate, as there is great value to integrating our data with similar data sets from other hospitals.
How will this new role help you do that?
I have a few main goals in this role that I’m excited about. The first and the largest is to integrate the Princess Margaret Genomics Centre, PM-OICR TGL, Genome Technologies and Genome Sequence Informatics into one fully-coordinated machine. The people, tools and methods that we have at OICR and Princess Margaret are incredible and the infrastructure already in place can serve as a powerful vehicle for both research and clinical applications. In the first two weeks, I’ve been really impressed with how the leads of these programs have come together to form concrete plans for making this a reality.
The part that excites me about my new role is the O in OICR. Within this position, I can have a provincial outlook on translational research which is important as genomics research becomes increasingly dependent on multi-centre studies and inter-institutional collaborations. I think OICR can help facilitate a future where sharing ideas, data, and knowledge between institutions is much easier than it is today. I’m excited to help take things that work locally and make them available and easy-to-use across the entire province, so that we can benefit from the advances made by our neighbours. We are stronger when we work together in a collaborative way.
OICR is well-known as a developer of similar high-quality data sharing systems and I am looking forward to integrating these efforts to support our internal genomics enterprise
It sounds like a lot of your work addresses local needs, but how do you have so many international collaborations?
In computational biology, a lot of our concerns and challenges are shared with other groups as well. For example, the cBioPortal data sharing platform was originally built at Memorial-Sloan Kettering to allow researchers to easily query data from The Cancer Genome Atlas project. This initiative soon grew to include a team at Dana-Faber and now the software is fully open-source with five core, NIH-funded teams contributing to its development, including my own lab. In addition, there are groups working on improving and enhancing cBioPortal instances around the world as it expands to new applications beyond genomics. cBioPortal has emerged as a very powerful resource rooted in an international crowdsourcing model. Naturally, OICR is well-known as a developer of similar high-quality data sharing systems and I am looking forward to integrating these efforts to support our internal genomics enterprise, as well as national and international data sharing networks.
You’ve been involved with the evolution of genomics over the last two decades. What technologies excite you these days?
Hands down, it’s single cell sequencing. This is an amazing technology that allows us to see parts of the tumours that we could never see before. In one of my projects, we’re looking at each cancer population within a tumour sample and mapping each population to a drug treatment. With Drs. Benjamin Haibe-Kains, we’re applying this concept across hundreds of thousands of cells from brain tumours we have sequenced in collaboration with Peter Dirks and from myeloma cells with Suzanne Trudel. If we can find distinct clones – or types of cells – with tailored treatment options, we could potentially eradicate the cancer entirely using combination therapies. I think the future of precision medicine is dependent on single cell technology and I look forward to integrating this technology into clinical studies with collaborators at cancer centres across the province.
May 30, 2019
Meta-analysis of 1,200 patients with pancreatic cancer reveals a new way to identify those with very aggressive tumours who may benefit from alternate treatment approaches
Only half of pancreatic cancer patients who undergo standard chemotherapy and surgery live a year after their initial diagnosis. In the face of these dismal statistics, patients are faced with the challenge of deciding whether they want to proceed with treatment that may have unpleasant side effects. If clinicians could identify patients who would not benefit from standard therapies, they could help these patients make more informed treatment decisions or recommend alternative palliative treatment approaches.
As part of OICR’s Pancreatic Cancer Translational Research Initiative (PanCuRx) team led by Dr. Steven Gallinger, Dr. Benjamin Haibe-Kains recognized that computational modeling can be used to help inform these decisions, but to design a robust predictive model he would need much more data than any individual study had ever collected.
Building the data foundations
Haibe-Kains, who is a Senior Scientist at the Princess Margaret Cancer Centre and OICR Associate, began his investigation with a dataset from PanCuRx – the largest collection of genomic and transcriptomic data on primary and metastatic pancreatic tumours to date. He and his lab then incorporated an additional 1,000 cases of pancreatic tumours from studies around the world that had collected both patient samples and information about how each patient responded to treatment.
“The datasets that we aggregated were a mixed bag of different types of data collected through different profiling platforms by different institutions,” says Haibe-Kains. “We took on the challenge of harmonizing the heterogeneity of these resources which nobody else had done.”
Previously, the Haibe-Kains Lab developed a computational method that could make incompatible transcriptomic data compatible. They had used this method to find four new breast cancer biomarkers to predict treatment response and they recognized that they could apply similar methods to harmonize pancreatic cancer data as well.
The dataset resulting from the harmonization is now the largest pancreatic cancer dataset, and Haibe-Kains has made it freely available for other researchers to use and study through the MetaGxPancreas package.
Making a predictive model
Haibe-Kains and his team set out to develop a computational model that could predict if a patient would survive for a year after their biopsy. They used machine learning techniques to exploit their rich dataset, find common patterns in the genomic data of aggressive tumours, and developed PCOSP – the Pancreatic Cancer Overall Survival Predictor.
“Our approach was to look at how one gene was expressed relative to another and relate that to how long a patient lived after biopsy,” says Haibe-Kains. “That may sound simple, but that means dealing with nearly 200 million pairs of genes, which is a significant amount of data to compute.”
As recently described in JCO Clinical Cancer Informatics, the group refined PCOSP using ensemble learning – the combination of several machine learning techniques to improve a model’s accuracy of predictions.
“PCOSP is actually a combination of hundreds of models and not just one,” says Haibe-Kains. “We tested about a thousand models, selected the models that could predict early death very well and combined them to make a stronger classifier.”
Using prediction to power patient decisions
Haibe-Kains says that as the infrastructure for routine sequencing progresses, PCOSP can be translated into clinical practice to help clinicians determine which patients would not benefit from standard treatment and which may benefit from alternative treatment approaches.
“Pancreatic cancer is a challenging disease but if we can predict the course of the disease, we can give clinicians and patients more information. With that information, they can make more personalized decisions to improve their treatment and ideally, their lives.”
May 27, 2019
Dr. Monika Krzyzanowska and collaborators develop app for cancer patients to manage and understand their treatment symptoms from the comfort of their own home
Patients undergoing cancer treatment face a lot of uncertainty. They often experience symptoms and treatment side effects at home, which often leads them to the emergency room. But in many cases, their side effects could have been better managed remotely and prevented from getting worse. Dr. Monika Krzyzanowska, Medical Oncologist at the Princess Margaret Cancer Centre, wanted a better option for her patients to understand and manage their symptoms comfortably at home.
“Almost half of women undergoing treatment for breast cancer visit the emergency room between treatment sessions and many of these visits can be avoided,” says Krzyzanowska. “We give our patients a lot of information up front, but we can do a better job at remote monitoring and providing them with the information they need when they need it. There’s a clear need for decision aids, self-management support, improved communication and options in care delivery.”
Krzyzanowska teamed up with the University Health Network’s Healthcare Human Factors team to explore how to improve symptom management for patients with a more personalized approach. In response to this need, they created bridges, a web-based app to facilitate remote management of chemotherapy-related side effects.
As recently described in the Journal of Medical Internet Research, the team refined their design over two rounds of usability testing with patients. They incorporated toxicity tracking, self-management advice and health care provider communication functionalities so that both physicians and patients can track and manage the patient’s symptoms.
With their pilot complete, Krzyzanowska is looking to partner with health care providers and decision makers to expand the project and explore how to integrate bridges into current systems and processes.
“Bringing bridges into the hands of patients is going to require a coordinated effort between decision makers, patients, care providers and hospitals,” says Krzyzanowska. “Helping patients who need it when they need it is our top priority and I look forward to developing bridges to help in that goal.”
Krzyzanowska’s project is one of the many research projects funded through OICR and Cancer Care Ontario’s Health Services Research Network.
May 21, 2019
Dr. Brigitte Thériault, a Senior Research Scientist at OICR, discusses the work of the Drug Discovery team to develop new drugs that awaken the body’s immune system to recognize and attack cancer cells.