Genome BC News | Summer 2013
NO.43 Contents Feature Story | Message from the President & CEO | Profile | Social Sciences | News & Announcements
BIOINFORMATICS: BIG DATA! Yet a lack of efficient tools and methodologies available to effectively access, mine and analyze these vast quantities of genomic datasets and integrate it with other knowledge bases is a major challenge for the research community. Dr. Sohrab Shah, who recently received funding from
Genome Canada and Genome BC to develop innovative software to identify and analyze mutations in cancer genomes, says: “Genome sequencing is becoming almost commoditized—there are cost-effective ways to sequence genomes and the bottleneck to progress has shifted from data generation to data analysis and interpretation.” This can only be adequately addressed with innovation in computational methods and software. An Assistant Professor in the Department of Pathology and Laboratory Medicine at The University of BC (UBC) and a Scientist at the BC Cancer Agency (BCCA), Dr. Shah is focused on developing novel statistical methods and algorithms to understand the genetic underpinnings of cancer. Bioinformatics is defined as the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied to molecular genetics and genomics. Simply put, bioinformatics is the backbone of genomics research, providing critical mathematical and computational tools to accelerate and enable discovery and application. Massive amounts of data, otherwise known as “big data,” are being generated by genomics technologies across life science sectors including human health, agri-food, forestry, energy and mining, and fisheries and aquaculture.
There are cost-effective ways to sequence genomes and the bottleneck to progress has shifted from data generation to data analysis and interpretation.
BIOINFORMATICS: BIG DATA! Cont’d from cover
Dr. Shah notes that “cancer genomes are unlike genomes from healthy cells” and thus the emphasis of his work is on modeling the tumour-specific properties of cancer-focused genome sequencing projects. His hope is that this work will ultimately produce clinical grade software for use at the BC Cancer Agency and beyond. Dr. Shah’s work on the characterization of cancer genomes is being recognized - his recent research describing new cancer genes in ovarian cancer has been published in the New England Journal of Medicine and his work describing mutational evolution in breast cancer has been featured in Nature. Dr. Shah is also the recipient of a Terry Fox New Investigator Award and is a Michael Smith Foundation for Health Research Career Investigator. Including Dr. Shah’s two projects, seven out of the 17 projects funded in the recent Genome Canada/ CIHR national funding competition will be led by BC researchers and $2.7 million of the total $6.2 million awarded is coming to our province. The projects include technologies to research microbial public health genomics, computational interpretation for cancer genomics, improved examination and processing times for cancer samples and applied tools for exploratory genomics. The researchers funded hail from the BCCA, UBC, Simon Fraser University and the UBC Centre for Molecular Medicine & Therapeutics.
The research projects will be conducted over a threeyear period starting this summer and fall. Expected outcomes of the work include improved analytical approaches to the detection of variations and mutations in DNA and RNA related to cancer diagnosis and care, and easy-to-use bioinformatics and genomic analytical tools to allow health care workers to better manage communicable diseases and provide quicker responses to infectious disease outbreaks.
[The bottleneck] can only be adequately addressed with innovation in computational methods and software.
For more info on Genome BC’s research projects, visit our website at www.genomebc.ca.
MESSAGE FROM THE PRESIDENT & CEO
BIG DATA, BIGGER SOLUTIONS In the same way the introduction of the first products based on genetic engineering in the 1980’s transformed the pharmaceutical and plant breeding industries, genome sciences are fueling a second wave of biotechnological innovation that will have far-reaching impacts on society, the economy and our world. This second biotechnology wave is driven by the convergence of knowledge from the life sciences, nanotechnology, information technology and bioinformatics.
In this era of ‘big data’ genomics, traditional data processing systems are unable to handle the analytical requirements being generated in the genome sciences. Thanks to the simultaneous reduction in computing, storage and sequencing costs, the current explosion of genomic and proteomic data is bringing bioinformatics to the forefront. The Science & Technology Innovation Centres (STICs), or technology platforms, are keepers of much of this big data. From these complex terabytes and petabytes of information, the puzzle is in how to distill and make sense of it. Recent re-funding for the STICs include: • Canada’s Michael Smith Genome Sciences Centre at the BC Cancer Agency $8.7 million • The UVic – Genome BC Proteomics Centre $4.3 million • The Metabolomics Innovation Centre $1.7 million
This convergence will push the translation of new discoveries into the knowledge-based bio-economy, generating innovative products and services in many sectors of interest to BC, as well as potentially leading to the development of new sectors. Furthermore, the extraordinary speed at which new discoveries are being made in some of these fields will foster the inclusion and application of genome sciences tools in many disciplines. Thanks to further funding in bioinformatics as outlined in our cover story, Genome BC researchers are positioned to lead in this shift and ably respond to opportunities for the application of research.
In this issue of Signals, you will read about two researchers tackling big data. Dr. Sohrab Shah at the BC Cancer Agency (see cover story) is building software tools to help researchers distill and use complex data in clinical decision-making. Dr. Peter Chow-White at SFU (see profile) is working with cancer researchers on ways to best integrate new technologies. I look forward to more good news about BC’s successes in putting “big data” to work.
Alan E. Winter President & CEO, Genome British Columbia
PROFILE: PETER CHOW-WHITE
Today, one of Peter’s roles at that juncture is exploring big data and the potential risks and opportunities of genomics and personalized medicine. He’s collaborating on a genomics research project with the Genome Sciences Centre at the BC Cancer Agency to develop a genomic test – the first of its kind in Canada – to help with clinical decision-making in cancer treatment. His job, he says, “is to help figure out how to best integrate the new technology. Good science and good practice, while crucial, aren’t enough – you need to carefully consider the role of communication in how to implement the test.”
Social scientist Dr. Peter Chow-White likes to take things that seem completely unrelated and bring them into the same conversation. It’s no wonder, then, that he’s built a research career talking about genomics, Facebook, and NBA basketball. A communication professor at Simon Fraser University (SFU), Peter studies the applications and social impacts of using information technologies to organize massive amounts of data in health care, social media and professional sports. Following his BC-based education (a BA from UBC and an MA in sociology from SFU), Peter headed south to Los Angeles to pursue his studies at University of Southern California’s Annenberg School for Communication and Journalism. It was there, during his doctoral work several years ago, that his path started to take shape. Internet research was all the rage at the time, but Peter wanted to explore it within a novel area. A mentor led him to the intersection between genomic and Internet technologies.
So how does basketball fit in? Like genomics and social media, professional sports have a whole new type and scale of data on their hands. Data they can use to organize human behaviour and look for hidden patterns. And that gets Peter, who played basketball himself at university, excited. “Sports are probably the epitome of human agency,” he says. “Computers don’t move you, you move yourself. Some of the patterns being found, they challenge preconceived notions of what’s real. Seeing the sport in a different way that impacts organizational practice is fascinating to me.” Off the courts, Peter is the Associate Director for the Centre for Policy and Research in Science and Technology at SFU and also manages his Genomics and Networks Analysis (GeNA) lab, which looks at the social and economic life of big data. He’s also in the midst of writing a book about big data in his three research areas. Looking across his areas of work, Peter sees an underlying theme: a move to instrument the world. “Quantifying isn’t new. Trying to understand human behaviour isn’t new. But at this scale? We haven’t seen this before… And communication is at the core. For social scientists to be in the middle, as it develops, is very exciting for me.”
SOCIAL SCIENCE: TO DISCLOSE, OR NOT TO DISCLOSE?
With the increasing cost-effectiveness of genomic sequencing technology, researchers have the ability to access and analyze unprecedented amounts of genetic information. This paradigm shift has exciting potential, suggesting genomic tests could soon become part of routine medical care. However, the deluge of data brings up several issues: the limitations of our ability to interpret the data, concerns about storage and privacy protection, and what to do with “incidental findings” – findings that may have health implications for research participants, but are unrelated to the purpose of the study. The issue of how to deal with incidental findings in research isn’t a new one. Researchers performing imaging studies, for example, sometimes encounter an incidental finding in the form of a tumor during CT colonography, or a heart problem during a screening echocardiogram. Blood samples collected for research purposes are routinely screened for certain infectious diseases (such as HIV) which, if detected, are required by law to be reported back to participants. The consensus, however, about genomic findings is that they just aren’t as clear cut. Genomic research may incidentally reveal that a healthy individual is at a higher risk for breast cancer, but not whether or not they have breast cancer, nor whether they will develop it.
This paradigm shift has exciting potential, suggesting genomic tests could soon become part of routine medical care.
Weighing the risks and benefits of disclosing genomic research incidental findings involves consideration of the potential severity of the finding, the likelihood of developing the associated condition, the availability of clinical intervention or treatment, and the potential personal or psychological impact of the information.
Genomic research may incidentally reveal that a healthy individual is at a higher risk for breast cancer, but not whether or not they have breast cancer, nor whether they will develop it. There is increasing discussion in the research ethics community about the participant’s right to know their own genetic information, and just as importantly, their right not to know information as well. People seek out genetic information for a number of reasons – to make decisions about managing their health, for family planning, to be able to provide relatives with important information, or even just out of curiosity. But sometimes certain information may do more harm than good – causing anxiety, leading to excessive medical follow-up, or making it difficult to obtain insurance coverage. And maybe, there are some things that we’d just rather not know.
ERIC TOPOL “How Digitizing Humans Changes the Future of Medicine” is the title of this year’s Don Rix Distinguished Keynote Address featuring Dr. Eric Topol on September 30. Register now at www.genomebc.ca
TO DISCLOSE, OR NOT TO DISCLOSE? Cont’d from previous
It’s not only participants who may be affected by the disclosure of information. Incidental findings may also have a significant impact on researchers, who now need to address issues surrounding informed consent, costs and resources, privacy protection, and ensuring adequate follow-up. Some experts have raised concerns that asking researchers to bear these new responsibilities may blur the boundary between research and clinical care, and place unreasonable demands on our scientists’ time or ability, or both. Others, however, maintain that researchers do, in fact, have a duty to give back to their participants - to ethically and respectfully reciprocate when individuals volunteer their time and body tissues. Many participants may even expect such communication, and think that silence on the researcher’s part is equivalent to a clean bill of health. In dealing with incidental findings in genomic research, neither extreme will do: complete non-disclosure is no longer ethically defensible, while complete full disclosure is just not feasible. Determining, however, what and where the middle ground should be is no easy task.
Complete non-disclosure is no longer ethically defensible, while complete full disclosure is just not feasible. At this stage, one of the biggest questions that still remains is how often researchers will actually come across incidental findings. Being a newly-accessible domain, the human genome is, for the most part, not yet well understood. As we delve into this promising new era of genomics, researchers, clinicians and participants remain key players in the careful consideration and management of many of these social, ethical and practical questions. To delve further into current issues facing researchers and research ethics boards in dealing with incidental findings, Genome BC is organizing a workshop this fall to facilitate the discussion of relevant research ethics considerations, as well as an overview of existing guidelines on managing incidental findings in the research context. Participants of this workshop include research ethics board chairs, co-chairs, committee members and administrative staff from BC.
NEWS & ANNOUNCEMENTS
At the Annual General Meeting on June 7, Genome BC thanked Don Enns and Michael Stevenson for their invaluable contributions over many years as board members. Two new members have joined the board: Neena Chappell, Canada Research Chair in Social Gerontology, and Professor of Sociology and Centre on Aging at the University of Victoria and John Thompson Consultant, PetraScience Consultants, Professor, Cornell University and past Vice President, Technology & Development, Teck Resources.
Genome BC was a proud partner of the Canadian delegation at BIO2013 in Chicago earlier this spring. Minister Christian Paradis officially opened the Canadian CafĂŠ.
Representatives from Genome BC and Genome Canada were at the Smithsonian Institution in Washington , DC with Eric Green and Francis Collins to attend the opening of the high-tech, highintensity exhibition Genome: Unlocking Lifeâ€™s Code to celebrate the 10th anniversary of researchers producing the first complete human genome sequence.
A BC Cancer Agency research team, led by Dr. Joe Connors, received a $10M investment to further their work in finding a cost-effective, genomic approach to treat lymphoid cancer patients. The substantial support from Genome BC, the BC Cancer Foundation, Genome Canada and the Canadian Institutes of Health Research will dramatically advance therapies for patients diagnosed with the fourth most common cancer disease in BC.
“Who Killed Dr. Little?” was one of the activities at Geneskool Summer Camp in Nanaimo from August 5-9. Through fun, hands-on activities in state-of-the-art labs facilities, students learned about genetics, DNA profiling, bacterial transformation and much more. This popular one-week summer camp illustrates the use of genomics in everyday life and provides opportunities for high-school students to learn new methods and techniques that they can apply to upcoming science courses.
Ventures West Capital Ltd.
Blake, Cassels & Graydon LLP
lan de la Roche
University of British Columbia
Ocean Fisheries Ltd.
J.E. Halliwell Associates Inc.
University of British Columbia
Neena L. Chappell
John F.H. Thompson
University of Victoria
Terry Fox Research Institute
PetraScience Consultants Inc.
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Published on Aug 29, 2013