March 29, 2018
Q and A with Dr. Philip Awadalla, Scientific Director of the Canadian Partnership for Tomorrow Project
Since 2008, the Canadian Partnership for Tomorrow Project (CPTP) has collected health data and biological samples from more than 300,000 volunteer participants across Canada. Now that its primary data collection phase has concluded, the Project is sharing this data with qualified researchers to help uncover the factors behind cancer and other diseases. It was recently announced that OICR’s Dr. Philip Awadalla will serve as the Project’s National Scientific Director and that OICR will host the Project’s national database and other scientific activities. We sat down with Awadalla to learn more about his vision for CPTP’s future. Continue reading – Q and A with Dr. Philip Awadalla, Scientific Director of the Canadian Partnership for Tomorrow Project
March 8, 2018
OICR’s Brain Cancer Translational Research Initiative (TRI) and the Terry Fox Precision Oncology for Young People Program (PROFYLE) are partnering to share data and deliver improved treatment options to young brain cancer patients.
February 9, 2018
The Global Alliance for Genomics and Health (GA4GH) has laid out its plans for the next five years as it continues to align its activities with meeting the key needs of the genomics data community. The Strategic Roadmap encompasses the standards and frameworks that will be developed by GA4GH and will be updated with new deliverables annually. OICR is a GA4GH Host Institution.
December 7, 2017
The link between some viruses and cancer has long been established. Now, researchers like OICR’s Dr. Ivan Borozan are using genomic sequencing to analyze common viruses like Epstein-Barr (also called human herpes virus 4). This knowledge could ultimately be used to develop new therapeutic vaccines to keep these viruses from taking hold in the body and prevent associated cancers from ever developing in the first place.
October 18, 2017
Orlando, Florida (October 17, 2017) – The Global Alliance for Genomics and Health (GA4GH) has struck formal collaborations with 15 international genomic data initiatives as 2017 Driver Projects, including Genomics England, Australian Genomics and the U.S. All of Us Research Program. The announcement, made at the GA4GH 5th Plenary Meeting, comes as part of the launch of GA4GH Connect: A 5-year Strategic Plan. GA4GH Connect aims to drive uptake of standards and frameworks for genomic data sharing within the research and healthcare communities in order to enable responsible sharing of clinical-grade genomic data by 2022.
October 17, 2017
The Global Alliance for Genomics and Health (GA4GH) has launched a new five-year strategic plan to develop international standards that will enable the responsible and secure sharing of genomic data for both scientific and clinical purposes. The plan, known as GA4GH Connect, was launched at the organization’s 5th Plenary Meeting in Orlando, Florida.
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.
September 6, 2017
Toronto (September 6, 2017) – Understanding a cancer’s genetics is key to selecting targeted therapies that are likely to be of the most benefit to a patient. The Ontario Institute for Cancer Research (OICR) today announced a new study, called Ontario-wide Cancer TArgeted Nucleic Acid Evaluation (OCTANE). OCTANE will use next-generation genome sequencing technology to bring a unified molecular profiling approach to five Ontario cancer centres.
August 9, 2017
Prostate cancer researchers have mapped the impact of an acquired mutation that alters epigenetic identity, the make-up of DNA, in about 50 per cent of patient tumour samples. The discovery also identifies a new opportunity for targeted therapy.
August 9, 2017
A newly published paper in Genetics in Medicine has reinforced the fundamental importance of collecting information about genetic variances in a single large database. With so much important genetic information being used globally to understand the underlying genetic influences of diseases, researchers and clinicians need an accessible repository to share this information.
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.
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