Bioinformatics, genomics and imaging key themes at OICR's 2009 Annual Scientific Meeting
Scientists and others involved in making the Ontario Institute for Cancer Research’s (OICR) ambitious Strategic Plan a reality came together in February for three days of learning, strategizing and networking.
OICR held its second Annual Scientific Meeting February 22-24. The meeting included delegates from Thunder Bay to Ottawa, representing most of the province's major academic laboratories involved in cancer research as well as key stakeholders including the Ontario Government’s Ministry of Research and Innovation. It was convened by Tom Hudson, OICR's President and Scientific Director.
“Since I came to Ontario in 2006, I've been consistently impressed by the calibre of research and talent we have across this province. Throughout the year they do great work on their own and in collaboration with each other. Our Annual Scientific Meeting provides a rare opportunity for all of these very busy people to come together,” Hudson explains. “This meeting gives researchers an opportunity to learn more about OICR and to meet potential collaborators. Meanwhile, it gives OICR an opportunity to receive feedback on whether we’re meeting our mandate and to find ways to do things better.”
The focus of this year’s meeting was on research platforms, an area in which OICR has made great progress since its Strategic Plan was approved by the Government of Ontario in 2007. In that year, OICR announced it would establish three platforms: imaging, cancer genomics, and informatics and biocomputing.
An OICR platform is a research cluster focused on the development of innovative technologies that can be applied to multiple problems. Unlike a research project, which is usually centred around a hypothesis, a platform is centred around a technology-based discipline. Researchers who work on platforms enable other researchers to carry out their projects, usually through collaborations, and are also involved in their own projects related to improving the research process. If the platform’s technologies are well-developed and validated, the platform could become a “core,” which is essentially a tried-and-tested, permanent version of a research platform.
After an overview of OICR’s Strategic Plan by Tom Hudson, Todd Golub, a researcher at the Broad Institute, a Boston-based collaboration of Harvard and MIT, gave a keynote address that outlined some challenges on the horizons of cancer research related to making the promises of individual, genome-based diagnostic tools and therapies a reality.
“We’re on the wrong path toward cancer genome diagnostics. In our current model, scientists find a mutation or other piece of IP and they build a company around it,” Golub said. “However, this process is getting cumbersome. With many molecular tests on the market, in some cases we’ll need to cut up a sample of tissue and send it to 15 different companies. This model evolved because we didn’t imagine a few years ago that we could sequence the whole genome.”
To contend with these challenges and make the promise of personalized medicine a reality, researchers need new strategies that use new technologies in areas such as genomics more effectively. On this note, the meeting was turned over to platform leaders, who chaired sessions related to each of OICR’s three existing platforms.
Dr. Aaron Fenster, a scientist at the Robarts Research Institute in London, invited a number of Ontario imaging researchers to discuss how their work fits into OICR’s strategy. Fenster is co-director with Dr. Martin Yaffe, a Senior Scientist at Sunnybrook Research Institute in Toronto, of OICR’s Imaging Pipeline Platform, which is based in London but collaborates closely with researchers in other cities.
Dr. Glenn Baumann, a radiation oncologist based in London, described how he and other researchers are working to integrate imaging technologies into clinical trials.
“There has been an explosion in the number of emerging imaging modalities, but they are not being introduced to clinical trials,” Baumann said. Often, these imaging technologies could provide investigators with better information about how patients are responding to new treatments. Baumann’s group is developing strategies to offer the benefits of new imaging technologies to researchers in Ontario who are involved in conducting clinical trials.
Dr. Yaffe, a senior scientist at Sunnybrook Research Institute in Toronto and co-director of the Imaging Pipeline Platform, is developing new technologies that help physicians detect cancer at earlier stages. Yaffe is leading an ambitious research program called the One Millimetre Cancer Challenge, aimed at detecting tumours when they are just one millimetre in size; in current practice, physicians usually detect tumours when they can be measured in centimetres.
Dr. John Valliant, Scientific Director of the Centre for Probe Development and Commercialization (CPDC) and Fenster also gave updates on their research. Based in Hamilton, the CPDC is one of few centres in the world devoted to developing and testing medical imaging probes. (Probes are isotopes that are ingested by or injected into patients; medical images are produced when imaging equipment detects the probe within the body.) Fenster is working with graduate students and postdoctoral fellows to develop new ultrasound-guided techniques for developing and treating prostate cancer.
For the cancer genomics panel, members of the OICR Cancer Genomics Platform presented on the Institute’s progress in making Ontario a world-leader in cancer genomics research.
Greg Hines, President of ArcticDX Inc., gave the group a business perspective on genomics, speaking about his work to commercialize intellectual property, some of which was discovered in Ontario. ArcticDx is developing a test for colon cancer based on intellectual property licensed from Cancer Care Ontario, which was discovered by a group led by Hudson and Dr. Brent Zanke, Vice-President and Director, Ontario Tumour Bank at OICR. The company is also developing a test for age-related macular degeneration.
Four scientists working on genomics projects based at other institutions were also invited to present. John Bell, Director of OICR’s Ottawa-based Immuno- and Bio-therapies Program, spoke on integrating genomics into his work on using viruses and the body’s own immune system to kill cancer. David Stojdl, a scientist at the Apoptosis Research Centre at the Children’s Hospital of Eastern Ontario in Ottawa, spoke about the application of functional genomics of host/virus interactions to oncolytic virus therapy. Sachdev Sidhu, an OICR investigator affiliated with the University of Toronto’s Donnelly Centre for Cellular and Bio-molecular Research (the CCBR), spoke about using synthetic antibodies in cancer research. Jason Moffatt, also an OICR investigator at the CCBR, discussed his progress with relocating an RNA interference library developed in Boston to Toronto, where he will collaborate with Ontario-based researchers to offer them a powerful new tool that can potentially knock out any gene.
The bioinformatics panel followed a similar format, with bioinformaticians from OICR’s Informatics and Bio-computing Platform updating the group, and representatives from other laboratories and the private sector offering their perspectives.
The Informatics and Bio-computing Platform develops and implements cutting-edge technologies that allow genome scientists and other researchers to manage the staggering amounts of data generated by bioinformatics research. Dr. Lincoln Stein, Director of Informatics and Bio-computing at OICR, gave an overview of OICR’s Informatics and Bio-computing Platform and demonstrated GBrowse, a web-based genome browser. Francis Ouellette, Associate Director of OICR’s Platform, described OICR’s in-house tools in detail, and Dr. Vincent Ferretti spoke about his work to support cancer-related populated health studies in Canada.
Guanming Wu, a scientific programmer at the Cold Spring Harbor Laboratory on Long Island, New York, described his work on the Reactome project. Reactome is a versatile computer program that allows researchers to view datasets, including data on cancer, in a variety of graphical formats.
Mary Mangan, an education specialist at OpenHelix Inc., spoke about her company’s strategy to build a business around supporting researchers who use open-source software tools. In general, bioinformaticians prefer to work with open-source software because it allows them to customize it to meet the specific needs of their projects. However, there is very little support and documentation for this type of software, and there are thousands of open source applications, meaning that choosing the right tool involves making tough choices with limited information. OpenHelix specializes in compiling and disseminating information about open source software, allowing researchers to reap the benefits of open code without getting bogged down studying the abilities and limitations of every new offering.
The focus of the meeting was on science and on OICR’s plans for the future. However, Dr. Calvin Stiller, newly appointed Chair of OICR’s Board of Directors, also encouraged participants at the meeting to reflect on the progress they’ve already made.
OICR was founded just three years ago, when Dr. Bob Phillips, OICR’s current Deputy Director, and other members of the research community encouraged the province to fund a large-scale cancer research institute. Hudson was recruited in 2006 and developed the Strategic Plan that is guiding the development of OICR’s programs and platforms. Early in 2007, none of the platforms discussed at this year’s ASM existed.
“Dr. Bob Philips and Dr. Tom Hudson have shown us that it’s possible to do the impossible – if only you try,” Stiller said.
Links referenced in this article
Centre for Probe Commercialization and Development
GBrowse
