June 23, 2020

FACIT backs made-in-Ontario data science and medtech innovations through Prospects Oncology Fund

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Replica Analytics & Sunnybrook’s Czarnota Lab receive key seed funding to de-risk Ontario intellectual property

TORONTO, ON (June 23, 2020) – FACIT, a commercialization venture firm, announced the newest recipients of Ontario First seed capital through the latest round of its Prospects Oncology Fund: Ottawa-based data science start-up Replica Analytics Ltd., and medtech innovator Dr. Greg Czarnota of Toronto’s Sunnybrook Research Institute.

Replica Analytics Ltd. is a new venture created by Dr. Khaled El Emam, a serial entrepreneur whose previous venture, FACIT-backed Privacy Analytics, was acquired by IMS Health. Replica Analytics is developing modeling software to create synthetic data based on real clinical datasets. High quality synthetic data is increasingly sought after by researchers, the pharmaceutical industry, and other entrepreneurs who require the datasets to build new models and enable AI innovation in healthcare.

Continue reading – FACIT backs made-in-Ontario data science and medtech innovations through Prospects Oncology Fund

April 8, 2020

Accelerating the development of new cancer drugs in Ontario

Drs. Lisa Porter and John Trant from the University of Windsor are working to develop a drug to block a protein that is elevated in some types of aggressive cancer. Disrupting the activity of this unique protein complex could slow or stop the disease. By providing researchers such as Porter and Trant with funding support and access to expertise, OICR’s Cancer Therapeutics Innovation Pipeline initiative is enabling the development of the next wave of made-in-Ontario cancer therapies.

February 26, 2020

How HER CODE CAMP aims to fix the diversity gap in computer science

OICR staff members Joanna Pineda, a Master’s Student, and Heather Gibling, a PhD Student, talk about how important it is to introduce young women, non-binary and transgender students to computer science.

February 5, 2020

Unprecedented exploration generates most comprehensive map of cancer genomes charted to date

Pan-Cancer Project discovers causes of previously unexplained cancers, pinpoints cancer-causing events and zeroes in on mechanisms of development 

Toronto – (February 5, 2020) An international team has completed the most comprehensive study of whole cancer genomes to date, significantly improving our fundamental understanding of cancer and signposting new directions for its diagnosis and treatment.

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Project (PCAWG), known as the Pan-Cancer Project, a collaboration involving more than 1,300 scientists and clinicians from 37 countries, analyzed more than 2,600 genomes of 38 different tumour types, creating a huge resource of primary cancer genomes. This was then the launch-point for 16 working groups studying multiple aspects of cancer’s development, causation, progression and classification. 

Previous studies focused on the 1 per cent of the genome that codes for proteins, analogous to mapping the coasts of the continents. The Pan-Cancer Project explored in considerably greater detail the remaining 99 per cent of the genome, including key regions that control switching genes on and off — analogous to mapping the interiors of continents versus just their coastlines.

The Pan-Cancer Project has made available a comprehensive resource for cancer genomics research, including the raw genome sequencing data, software for cancer genome analysis, and multiple interactive websites exploring various aspects of the Pan-Cancer Project data.

The Pan-Cancer Project extended and advanced methods for analyzing cancer genomes which included cloud computing, and by applying these methods to its large dataset, discovered new knowledge about cancer biology and confirmed important findings of previous studies. In 23 papers published today in Nature and its affiliated journals, the Pan-Cancer Project reports that:

  • The cancer genome is finite and knowable, but enormously complicated. By combining sequencing of the whole cancer genome with a suite of analysis tools, we can characterize every genetic change found in a cancer, all the processes that have generated those mutations, and even the order of key events during a cancer’s life history.
  • Researchers are close to cataloguing all of the biological pathways involved in cancer and having a fuller picture of their actions in the genome. At least one causal mutation was found in virtually all of the cancers analyzed and the processes that generate mutations were found to be hugely diverse — from changes in single DNA letters to the reorganization of whole chromosomes. Multiple novel regions of the genome controlling how genes switch on and off were identified as targets of cancer-causing mutations.
  • Through a new method of “carbon dating, Pan-Cancer researchers discovered that it is possible to identify mutations which occurred years, sometimes even decades, before the tumour appears. This opens, theoretically, a window of opportunity for early cancer detection. 
  • Tumour types can be identified accurately according to the patterns of genetic changes seen throughout the genome, potentially aiding the diagnosis of a patient’s cancer where conventional clinical tests could not identify its type. Knowledge of the exact tumour type could also help tailor treatments.

“The incredible work of the Pan-Cancer Project team that was unveiled today is the culmination of a remarkable international collaboration that has enriched our understanding and provided new ways to approach the prevention, diagnosis and treatment of cancer,” said The Honourable Ross Romano, Ontario’s Minister of Colleges and Universities. “I congratulate the entire research group on this ground-breaking achievement in cancer research. Ontarians can be proud of the leading role OICR played in this initiative.”

“The findings we have shared with the world today are the culmination of an unparalleled, decade-long collaboration that explored the entire cancer genome,” says Dr. Lincoln Stein, member of the Project steering committee and Head of Adaptive Oncology at the Ontario Institute for Cancer Research (OICR). “With the knowledge we have gained about the origins and evolution of tumours, we can develop new tools to detect cancer earlier, develop more targeted therapies and treat patients more successfully.”

“The Pan-Cancer Project has generated a much-needed deeper understanding of the biology of cancer and how the elusive and untapped “dark matter” in the human genome drives cancer,” says Dr. Laszlo Radvanyi, OICR’s President and Scientific Director. “These discoveries can lead to totally new area of targets for cancer therapy. It is gratifying to know that OICR helped to lead the international effort, while also integrating a collaborative network of Ontario researchers to play a leading role in this global project. It is a further indication of the value of our strategic investments into data infrastructure, research and informatics expertise, as well as the value the Ontario government continues to create in supporting OICR. I congratulate Dr. Stein, his team and all Pan-Cancer researchers on this landmark achievement.”

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Backgrounder

More information

Nature landing page – https://www.nature.com/collections/pcawg/
ICGC – International Cancer Genome Consortium (https://icgc.org/)
TCGA – The Cancer Genome Atlas (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga)
PCAWG – PanCancer Analysis of Whole Genomes (dcc.icgc.org/pcawg)
UCSC – University of California Santa Cruz (pcawg.xenahubs.net)
Expression Atlas (www.ebi.ac.uk/gxa/home)
PCAWG-Scout (pcawgscout.bsc.es)
Chromothripsis Explorer (compbio.med.harvard.edu/chromothripsis)
COSMIC – Catalogue of Somatic Mutations in Cancer (https://cancer.sanger.ac.uk/cosmic)

About the Ontario Institute for Cancer Research

OICR is a collaborative, not-for-profit research institute funded by the Government of Ontario. We conduct and enable high-impact translational cancer research to accelerate the development of discoveries for patients around the world while maximizing the economic benefit of this research for the people of Ontario. For more information visit www.oicr.on.ca.

Media contact

Hal Costie
Ontario Institute for Cancer Research
647-260-7921
hal.costie@oicr.on.ca


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February 5, 2020

Dr. Lincoln Stein talks about the Pan-Cancer Project

An overview of the Pan-Cancer Project with Dr. Lincoln Stein.


Watch more Pan-Cancer Project videos


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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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February 5, 2020

Discovering cancer’s vulnerabilities: The whole may be greater than the sum of its parts

OICR and Pan-Cancer Project researchers map key cancer pathways, signposting new directions for its diagnosis and treatment

What works in a lab experiment doesn’t always work in the complex human body. But as technology advances, researchers are gaining the ability to study different features of a cancer cell and the interactions, mechanisms and pathways between them. As more data become available, however, it is becoming increasingly difficult to find the most important molecular pathways that, when blocked, can stop the progression of the disease.

Dr. Jüri Reimand’s lab specializes in this area.

“Researchers often collect molecular data on one aspect of a cancer cell at a time, like its DNA, RNA or proteins,” says Reimand, who is an OICR Investigator. “If we can weave these complex molecular datasets together into a bigger picture, we can gain a more thorough understanding of cancer and potentially find new ways to tackle the driving mechanisms behind the disease.”


Decoding the donors’ data

Thanks to more than 2,500 patient donors from around the world, the Pan-Cancer Project presented one of the largest cancer datasets to date. The Project made hundreds of terabytes of data available to the global cancer research community in a coordinated effort to advance our understanding of the disease.

To help interpret these data, the Reimand Lab developed ActivePathways – a statistical method that can discover significant pathways across multiple molecular omics datasets. These methods, published today in Nature Communications, allow researchers to characterize the cell at a systems-level, decipher how the components interact and tease out the most important pathways.

“We designed a simplified approach to tackle one of the largest cancer genomics datasets to date,” says Reimand. “With these methods we can now chart important interactions that we wouldn’t have recognized by looking at one component or dataset alone.”


The power of the ensemble

The Reimand Lab teamed up with researchers in Belgium, Norway, Spain, Switzerland and across the U.S. who were also interested in analyzing the important pathways within the Pan-Cancer Project dataset. They combined their methods and expertise and identified nearly 200 important driver pathways across 38 different cancer types.

Their findings showed that cancer cells often have related or coordinated mutations in the coding regions and the non-coding regions of the genome.

Now, we have better methods and stronger evidence to move forward as we investigate how to block these pathways, and further, block the progression of the disease.
– Dr. Jüri Reimand

“Together, we came to a consensus list of frequently mutated molecular pathways, processes and target genes,” says Reimand. “Now, we have better methods and stronger evidence to move forward as we investigate how to block these pathways, and further, block the progression of the disease.”

All tools, methods and data related to the collaboration are freely available for the research community to use for future research.

“We’re proud of this progress,” says Reimand. “We look forward to the future research that will build on these findings towards better cancer diagnostic tests and treatment options.”


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January 10, 2020

New open-source software judges accuracy of algorithms that predict tumour evolution

Adriana Salcedo
Adriana Salcedo

OICR-led international research group develops new open-source software to determine the accuracy of computational methods that can map the genetic history of tumour cells.

A cancer patient’s tumour is often made up of many cells with different genetic traits that can evolve over time. Interest in tumour evolution has grown over the last decade, giving rise to several new computational tools and algorithms that can characterize genetic diversity within a tumour, and infer patterns in how tumours evolve. However, to date there has been no standard way to compare these tools and determine which are most accurate at deciphering these data.

The genetic differences between tumour cells can tell us a lot about a patient’s disease and how it evolves over time – Adriana Salcedo

In a study recently published in Nature Biotechnology, an OICR-led international research group released new open-source software that can be used to judge the accuracy of these novel algorithms.

Continue reading – New open-source software judges accuracy of algorithms that predict tumour evolution

December 5, 2019

Bridging the GAPP: Bringing new diagnostic tests to patients

Dr. Jane Bayani discusses how OICR is partnering with Thermo Fisher Scientific to bring new diagnostic tests from the lab into the clinic and how Genome Canada’s Genomic Applications Partnership Program (GAPP) is making that possible.

November 11, 2019

Solving Big Data problems

Dusan Andric talks about Overture and how its interchangeable tools can help scientists to “worry less, science more”
https://www.overture.bio/

November 6, 2019

FACIT launches assessment of venture philanthropy models to scale Canadian commercialization of cancer research

Ms. Donna Parr and Dr. Niclas Stiernholm recruited to broaden public/private equity expertise

Ms. Donna Parr and Dr. Niclas Stiernholm

TORONTO, ON (November 6, 2019) – FACIT, a commercialization venture venture firm, reported on the expansion of its Executive-in-Residence program and new strategic initiatives. Ontario is home to world-leading cancer research connected through the collaboration model established by the Ontario Institute for Cancer Research (OICR), FACIT’s strategic partner. Growing market signals suggest Canadian philanthropy, oncologists and patients want more discoveries translated into therapies and technologies that directly impact cancer care, while also supporting Canadian entrepreneurialism. Commercialization of innovations is aligned with OICR’s translational mission and a strategic imperative for the province’s university and research hospital partners. 

Continue reading – FACIT launches assessment of venture philanthropy models to scale Canadian commercialization of cancer research

November 1, 2019

Dr. Rima Al-awar promoted to Head of Therapeutic Innovation and Drug Discovery at OICR


Al-awar joins OICR’s executive team with plans to expand drug discovery and development initiatives across Ontario

Dr. Rima Al-awar has joined OICR’s executive team as Head, Therapeutic Innovation and Drug Discovery. In this role, she will lead one of OICR’s three key priority areas, Therapeutic Innovation, which focuses on validating novel cancer drug targets and advancing therapeutic candidates through pre-clinical development. She will continue leading OICR’s Drug Discovery Program and will build upon that team’s exceptional work in her new position. 

Here she discusses her new role and her plans to grow OICR’s Therapeutic Innovation platform.

What does this promotion mean for you and your team?

Since joining OICR, I have spent several years building an experienced and talented team that I’m very proud of. We have developed great assets and established fruitful partnerships with collaborators and industry partners. We have a very rich and promising portfolio of potential new cancer therapeutics.

I believe we are in a great position to expand and capitalize on our successes. My new position will allow me to take a strategic role in therapeutic innovation at OICR so that we can enable future successes both here, in Toronto, and across the province. I need to think of creative and strategic funding models, how best to strengthen the platform’s structure and establish additional synergistic partnerships in the community. In the long run, this means advancing more projects into development.

How will this new role allow you to do that?

I’ll have a seat at the table in strategic conversations with our executive team. I’ll bring a unique perspective with my expertise in drug discovery and development, and I look forward to representing Therapeutic Innovation, an important part of OICR.

In this role I will also help ensure that resources are allocated to the most promising projects. I’m a big proponent of focusing on select projects and doing them well and in a timely and competitive fashion as opposed to stretching our resources across too many projects, which often ends up slowing progress. In this position, I believe I can do that more effectively.

Dr. Rima Al-awar

My goal is to continue to strengthen our current collaborations and forge new ones. 

How does this new appointment differ from your previous position as Director of Drug Discovery?

I will still be leading the Drug Discovery team, but I’ll be relying on leaders within the team to take on some of my previous day-to-day responsibilities, and in turn, they will delegate some of their current responsibilities. I see this role as an opportunity to strengthen the Drug Discovery team and encourage the pace of career development within the team.

Within the scope of my new role, we are going to have to think creatively about progressing additional projects forward faster, which will mean harnessing new technologies and recruiting new expertise in different scientific disciplines.

When it comes to collaborations, I expect that my role will be just as collaborative as it was before. My goal is to continue to strengthen our current collaborations and forge new ones.  We can’t bring new therapeutics to patients on our own.

What can we expect to see over the next year?

I want to explore the idea of expanding our breadth of collaborations to include biologics, immunotherapies, and novel drug delivery methods, technologies and models that impact drug discovery. I will be travelling to different research institutes across the province and outside of Ontario to look for more opportunities. The goal of this effort would be to identify and build on strengths in the community. We’re looking to enable and facilitate new, promising projects in areas of unmet needs. Expanding our network across Ontario is very important. We have built a strong foundation, we have deep expertise, a rich portfolio and now we are going to take it to the next level. I look forward to encouraging more synergy across our organization and Ontario.

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