October 4, 2017
New software uses machine learning to identify mutations in tumours without reference tissue samples
One of the main steps in analyzing cancer genomic data is to find somatic mutations, which are non-hereditary changes in DNA that may give rise to cancer. To identify these mutations, researchers will often sequence the genome of a patient’s tumour as well as the genome of their normal tissue and compare the results. But what if normal tissue samples aren’t available?
September 25, 2017
Since mitochondria are inherited maternally, it may strike some as an odd place to go looking for connections to prostate cancer. But recently an international research team explored that relationship by looking at how the small amount of DNA contained in mitochondria, a cellular structure, is involved in prostate cancer.
August 15, 2017
New data resource centre will help better understand links between birth defects and childhood cancer
Researchers from the Ontario Institute for Cancer Research playing major role in the design and development of the new initiative.
Toronto (August 15, 2017) – Children with structural birth defects are at a much higher risk of developing certain types of childhood cancers but scientists currently lack vital information about why this occurs.
June 7, 2017
Researchers from OICR and other institutions have created a new software program called EAGLE that mines data to understand the interactions between a person’s environment and their genetics. The tool has far-reaching uses, including oncology, and can provide researchers and clinicians with important information that can help personalize treatments for patients.
To learn more we spoke to Dr. Hillary Edgington, a Postdoctoral Fellow in OICR’s Informatics technology platform, which is led by Dr. Lincoln Stein. Edgington and her collaborators recently shared their research in the journal Nature Methods.
What was reported in your recent article?
One of the most important goals in biological research is to understand the ways that our genes can be impacted by the environment around us. The activity of genes can change due to a number of external factors from medication use to air pollution. This study introduces a new software tool called EAGLE to investigate how interactions between a person’s genotype and environmental exposures affect the way his or her genes are expressed.
What is unique about EAGLE?
EAGLE takes advantage of the fact that sometimes the two copies of a gene are unequally expressed, which allows us to compare small differences in those two copies within an individual where they operate in the same environmental conditions. This tool was shown to improve, in both power and accuracy, on detecting associations over standard interaction testing methods. Using EAGLE to test for interactions in two large cohorts (the Depression Genes and Networks study cohort and CARTaGENE) revealed significant associations between gene expression and environmental variables, including depression, exercise, blood pressure medication use and body mass index. This information is critical in advancing personalized healthcare initiatives, as it gives researchers and clinicians information with which to predict an individual’s health risks based on their unique genomic profile and lifestyle factors.
How can these findings be used in the area of cancer?
EAGLE is a tool that can be applied to data from any source. The information gleaned from the application of EAGLE to data provided by cancer patients – including testing for interactions between patients’ specific mutational profiles and exposures such as therapeutic treatments, the microenvironment of the tumour, or properties of the immune system – could help clinicians make more accurate predictions about individual patients’ prognoses and therapeutic options in the future.
What challenges did you and your collaborators face while creating EAGLE?
One of the main challenges with developing any new method is making sure that the results will be consistent across different groups of individuals. It is critical to perform tests in different groups in order to make sure that there is replication of any findings. For this reason, collaboration between different research groups is critical, and this is what brought the groups from OICR and Stanford University together on this project. At OICR we were able to use the resources that we have through the CARTaGENE cohort to perform a replication study. It showed that the associations EAGLE detected in the Depression Genes and Networks cohort are consistent across populations.
What are the next steps planned with this research project?
We will be able to use EAGLE in many future projects as a way to discover previously unknown interactions between any environmental variable of interest and the regulation of genes. As a follow-up to this study we may look more specifically at the gene-environment associations we observed in order to determine what the mechanism is that causes differences in gene expression.
May 3, 2017
The advent of genomic sequencing and targeted therapies has opened the door to new ways of diagnosing and treating cancer. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) program is a new, province-wide initiative supported by OICR that will allow more patients to benefit from these innovations while also helping to advance cancer research in Ontario.
April 4, 2017
For three science-obsessed high school students March Break wasn’t a time to kick back and relax. Instead the students, Cameron, Chris and Zev, spent the week at OICR gaining knowledge and hands on experience in genomics and bioinformatics as part of the Gene Researcher for a Week program.
February 9, 2017
The ability to sequence and study the human genome and the genomes of different cancer types has allowed scientists to increase our understanding of the biology of these diseases. In turn this has helped to create new preventative strategies, diagnostic and prognostic tools as well as better treatments. But what if there was a way to make this information even more useful? An international group is working to establish a project that will do just that.
January 13, 2017
What does a beaver’s genome look like? And how can understanding the beaver genome help us to improve human health? A group of Canadian researchers led by Drs. Stephen Scherer and Si Lok at The Centre for Applied Genomics and The Hospital for Sick Children today published the sequenced genome of the Canadian beaver in order to answer these questions and others (and just in time for Canada’s 150th anniversary, no less).
Dr. Jared Simpson led a team at OICR who provided their bioinformatics expertise on the project. We spoke to Simpson about his team’s role in the study and how their findings could contribute to a better understanding of cancer.
January 10, 2017
The Global Alliance for Genomics and Health’s (GA4GH) Beacon Project has partnered with ELIXIR, the body that organizes Europe’s infrastructure for life science data, to make genomic data in that continent more easily discoverable by researchers. The Beacon Project is a demonstration project that enables genomic data centres to make their data more easily discoverable to users by allowing them to use simple queries to explore a dataset’s contents.
November 18, 2016
OICR was part of a group of organizations to achieve history when they helped reach an important milestone in Canadian computing. As part of the ORION network, OICR participated in an exercise to perform the fastest, long-distance big data transfer between academic institutions in Canada.
October 21, 2016
OICR-led study finds four unique genomic signatures in pancreas cancer, uncovers potential of immunotherapies
Pancreas cancer is one of the most aggressive and deadly forms of the disease. According to the Canadian Cancer Society, only 8 percent of pancreas cancer patients survive more than five years after diagnosis. OICR’s PanCuRx Translational Research Initiative has recently published the results of an international collaboration that increases understanding of this complex disease and how to treat it based on a patient’s unique profile.
October 18, 2016
Reactome releases 10,000th annotated human protein, a major milestone that will benefit research community
Open source tools like Wikipedia and Google Maps help us get things done faster in our daily lives. In the same way, researchers rely on a variety of open source tools to help them make discoveries faster. Reactome (www.reactome.org) is one such tool. Researchers use it because it relates human genes, proteins and other biomolecules to the biological pathways and processes in which they participate, helping to facilitate new cancer research breakthroughs. Earlier this month Reactome reached a major milestone when it released its 10,000th annotated human protein to the research community. We spoke to OICR’s Dr. Robin Haw, who is Project Manager and Outreach Coordinator at Reactome, about the history of the project, the importance of this particular milestone and where the project is headed next.
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