August 28, 2020

Tumour traces in blood could predict which cancer patients will benefit from immunotherapy

OICR-supported researchers and collaborators discover indicators in the blood that may predict which patients will respond to the immunotherapy drug, pembrolizumab

Dr. Scott Bratman, Cindy Yang, Dr. Lillian Siu, Dr. Trevor Pugh

Adapted from UHN’s Media Release.

Immunotherapy can shrink tumours and prolong survival for certain cancer patients, but clinicians don’t yet know which patients will benefit from these treatments. OICR-supported researchers and collaborators at the Princess Margaret Cancer Centre have made a discovery that could help identify those patients who may benefit and match them with potentially life-saving therapies.

In their study, recently published in Nature Cancer, the research group found that the changing levels of tumour fragments, or circulating tumour DNA (ctDNA), in a patient’s blood can be used to predict whether they will respond to the immunotherapy drug pembrolizumab.

The study lays the foundation for researchers to develop an easy, non-invasive and quick blood test to determine who will benefit from the drug and how well their disease is responding to treatment.

“While we have known for some time that cancer disease burden can be monitored by measuring tumour DNA in the blood, we are excited to report that the same concept can be applied to track the progress of patients being treated with pembrolizumab,” says co-first author Cindy Yang, PhD Candidate in Dr. Trevor Pugh’s lab at the Princess Margaret Cancer Centre and OICR. “This will hopefully provide a new tool to more accurately detect response and progression in patients undergoing immune checkpoint inhibitor therapy. By detecting progression early, patients may have the opportunity to undergo subsequent lines of treatment in a timely fashion.”

The benefits of blood tests

Conventionally, imaging scans – such as computerized tomography (CT) scans – and other methods are used to monitor a patient’s cancer. This study suggests a simple and quicker blood test as an alternative to these scans.

“Although important, computerized tomography (CT) and other scans alone will not tell us what we need to know quickly or accurately enough,” says senior author Dr. Lillian Siu, Senior Scientist and medical oncologist at the Princess Margaret Cancer Centre.

Dr. Scott Bratman, radiation oncologist and Senior Scientist at the Princess Margaret Cancer Centre and co-first author of the study, points out that it may take many months to detect whether a tumour is shrinking with various imaging scans. 

“New next-generation sequencing technologies can detect and measure these tiny bits of cellular debris floating in the blood stream accurately and sensitively, allowing us to pinpoint quite quickly whether the cancer is active.”

This study represents one of the many emerging applications of using ctDNA to guide treatment decisions. It is one of the first to show that measuring ctDNA could be useful as a predictor of who responds well to immunotherapy across a broad spectrum of cancer types. 

The prospective study analyzed the change in ctDNA from 74 patients, with different types of advanced cancers, being treated with pembrolizumab. Of the 74 patients, 33 had a decrease in ctDNA levels from their original baseline levels to week six to seven after treatment with the drug. These patients had better treatment responses and longer survival. Even more striking was that all 12 patients who had clearance of the ctDNA to undetectable levels during treatment were still alive at a median follow-up of 25 months.   

Conversely, a rise in ctDNA levels was linked to a rapid disease progression in most patients, and poorer survival.   

“Few studies have used a clinical biomarker across different types of cancers,” says Siu, who also co-leads OICR’s OCTANE trial. “The observation that ctDNA clearance during treatment and its link to long-term survival is novel and provocative, suggesting that this biological marker can have broad clinical impact.” 

Innovation and translation

This study is part of a larger flagship clinical trial, INSPIRE, which has enrolled more than 100 patients with head and neck, breast, ovarian, melanoma and other advanced solid tumours. INSPIRE brings together researchers from many disciplines to investigate the specific genomic and immune biomarkers in patients that may predict how patients will respond to pembrolizumab.

INSPIRE is made possible by collaborations across institutes and industries with expertise from those applying genomics to research and those applying genomics in the clinic.

“INSPIRE is an incredibly collaborative initiative that is a blend of big genomics – looking at large trends across many individuals – and highly-personalized genomics – looking at mutations within each patient sample,” says Pugh, co-senior author, Senior Scientist at Princess Margaret and Senior Investigator and Director of Genomics at OICR. “This is a modern approach to the translation of clinical genomics.”

“As a PhD student, this project gave me the unique opportunity to work in a highly collaborative intersection with industry, clinical, and academic partners,” says Yang. “It is very exciting to see translational research in action.”

Read the UHN Media Release.

December 3, 2019

OICR’s Dr. Trevor Pugh receives $1 million grant from The TD Ready Challenge

Funding will support Pugh’s innovative work in blood-based cancer detection and screening

OICR’s Dr. Trevor Pugh poses for a photo with his co-applicant Dr. Raymond Kim. (TD Bank Group)

Dr. Trevor Pugh, OICR’s Director of Genomics and Senior Investigator, has been named one of ten winners of the 2019 TD Ready Challenge.

The award, which is valued at $1 million, will support Pugh’s research over the next three years as he and collaborators, including Dr. Raymond Kim at the Princess Margaret Cancer Centre, develop an effective blood test for early cancer detection. The test will aim to help those with hereditary cancer syndrome, including individuals with Lynch Syndrome and people that carry BRCA1/2 mutations.

“People who carry genetic changes that place them at a high risk of cancer often face significant health, travel and financial burdens,” says Pugh. “Not all surveillance tests are readily accessible in remote or lower-income regions, so many of these people do not undergo necessary proactive preventative screening. We want to help fix that.”

With TD’s funding, Pugh, Kim, and collaborators across Canada will work to create an accessible blood-based screening test that can detect cancers earlier than current methods, and guide more personalized management of individuals at high risk of developing the disease.

“This project hinges on close collaboration and coordination with patients and clinical teams caring for them,” says Pugh. “TD’s support will further amplify the impact of our work, especially that of our team’s clinical lead, Dr. Kim, as he mobilizes hereditary genetics clinics for the benefit of patients across Canada.”

“TD’s support will allow our Ontario scientists to build on their leadership in early cancer detection and screening,” says Dr. Laszlo Radvanyi, President and Scientific Director of OICR. “We would like to thank TD for having the vision to support such an important project that will positively impact the health of Canadians. We would also like to congratulate Dr. Pugh and his team, and look forward to their continued progress in making cancer screening more accessible.”

As part of TD’s $1 billion commitment to community giving, the 2019 TD Ready Challenge encouraged organizations across North America to create innovative solutions that help increase equitable health outcomes and focus on preventative efforts. In total, TD awarded $10 million for the 2019 Challenge to deliver innovative healthcare solutions to those that need it most.

“OICR has brought forward a creative and scalable solution to help increase equitable health outcomes for underserved and remote communities,” says Andrea Barrack, Global Head, Sustainability and Corporate Citizenship, TD Bank Group. “Being a winner of the TD Ready Challenge is a testament to the skill, ingenuity, and vision of its creators, as well as their dedication to improving the health of their communities and opening doors to a more inclusive tomorrow.”

A full list of The 2019 Ready Challenge winners as well as more information about the challenge can be found at www.td.com/thereadychallenge.

May 31, 2019

Q&A with Dr. Trevor Pugh, OICR’s new Director of Genomics

Trevor Pugh
Dr. Trevor Pugh

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

Trevor Pugh

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.

December 13, 2018

What can we gain from looking at the outliers?: An investigation into long and short-term ovarian cancer survivors

Kayla Marsh, a Research Technician, wiorks at a bench in the OICR-PM Translational Genomics Laboratory.

Researchers investigate the clinical, molecular and microenvironment factors that contribute to extreme therapy response and resistance in ovarian cancer patients

Some patients with high-grade serous ovarian cancer (HGSOC) respond exceptionally well to therapy, while others experience rapid disease relapse. The mechanisms behind these disparate outcomes are poorly understood, but a group of researchers based at the Princess Margaret Cancer Centre (PM) supported by OICR’s Ovarian Cancer Translational Research Initiative (TRI) are working to change that.

Continue reading – What can we gain from looking at the outliers?: An investigation into long and short-term ovarian cancer survivors