November 2, 2017
Biomarkers that can help predict a patient’s response to a given drug are central to testing new therapies in clinical trials as well as selecting which drugs to use in the clinic. Some of the biomarkers in use today rely on the overall expression of a given gene to predict if a drug will be of benefit. While these types of biomarkers have aided cancer research and treatment, a group led by Dr. Benjamin Haibe-Kains recently published research that is ushering in a new class of biomarkers – those based on gene isoforms (the different expression of the same gene within an individual). This work opens the door to more precise biomarkers.
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.
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.
March 29, 2017
Polymerase chain reactions (PCR) are one of the most common tools used in molecular biology labs worldwide. This technique allows researchers to amplify, or increase, the amount of DNA in a sample so that they have more to work with. To keep track of the original molecules from a sample, chemical ‘barcodes’ are added. While barcodes serve an important purpose they can lead to errors and interfere with results. To prevent these cross-reactions a small team of international researchers have devised an ingenious method to ‘hide’ the barcodes when needed, leading to increased sensitivity and more reliable results.
Continue reading – New approach improves sensitivity of DNA sequencing, producing more reliable results
March 16, 2017
Genetic tests are being used more commonly in the diagnosis of many types of cancer. However, there currently isn’t a highly accurate test that can identify men with aggressive forms of prostate cancer, making it more difficult to choose the most appropriate course of treatment.
March 9, 2017
New molecular barcode technology reduces error rate in genomic sequencing to 1 in 10,000
Toronto (March 9, 2017) – Researchers at the Ontario Institute for Cancer Research (OICR), together with international collaborators, have invented a technique to avoid a major problem with common laboratory techniques and improve the sensitivity of important cancer tests.
February 23, 2017
Digital Detection Tool Will Be Shared Freely Over the Web
Toronto, ON and Baltimore, MD (February 23, 2017) A research team from the United States and Canada has developed and successfully tested new computational software that determines whether a human DNA sample includes an epigenetic add-on linked to cancer and other adverse health conditions.
February 13, 2017
Keeping track of samples and organizing their associated data is a crucial part of the research process. Like many labs around the world, those at OICR were using a commercially available Laboratory Information Management System (LIMS) to perform this task. However, the researchers using it found that this tool placed far too many constraints on their work. So what did they do? They built their own in partnership with the Earlham Institute (EI) in the U.K. This collaboration has resulted in powerful, flexible and open source software called MISO (Managing Information for Sequencing Operations).
January 18, 2017
The Toronto Bioinformatics User Group (TorBUG) will hold its first session of the New Year on January 25. Anyone with an interest in bioinformatics is encouraged to attend and hear from Katie Pollard, Director and Senior Investigator at Gladstone Institutes and Davide Chicco from the University of Toronto.
January 25, 2017
4-4:15 p.m. Trainee Speaker: Davide Chicco, University of Toronto: “Siamese neural network for prediction of long-range interactions in chromatin”
4:15-5 p.m. Guest Speaker: Katie Pollard, Gladstone Institutes: “Most transcription factors recognize DNA shape”
5-7 p.m. Reception
Location: 160 College St., Toronto, Red Room, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto
A calendar of upcoming TorBUG events can be found at: https://www.google.com/calendar/embed firstname.lastname@example.org
Missed a session? Videos of the latest TorBUG talks are below.
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.
December 1, 2016
The base components of DNA – adenine, thymine, cytosine and guanine (commonly referred to as ATCG) are so fundamental to the study of genetics that they are probably familiar to anyone who has taken a high school biology class. Now, one team of researchers has expanded the ‘DNA alphabet’ to help aid in efforts to learn how cancers develop.
November 25, 2016
The Toronto Bioinformatics User Group (TorBUG) continues on Wednesday, November 30 with another session of leading-edge bioinformatics topics and speakers. TorBUG sessions encourage learning, sharing and networking with colleagues in bioinformatics. All those who are interested are welcome to attend.