March 16, 2017

Researchers discover new test that could change the diagnosis and treatment of prostate cancer

Dr. Paul Boutros

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.

Continue reading – Researchers discover new test that could change the diagnosis and treatment of prostate cancer

March 9, 2017

Innovative technique greatly increases sensitivity of DNA sequencing

Dr. Paul Krzyzanowski

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.

Continue reading – Innovative technique greatly increases sensitivity of DNA sequencing

February 23, 2017

New Gene Sequencing Software Could Aid in Early Detection, Treatment of Cancer

A closeup of the nanopore sequencing device

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.

Continue reading – New Gene Sequencing Software Could Aid in Early Detection, Treatment of Cancer

February 13, 2017

International collaboration cooks up powerful new software: MISO

LIMS system

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).

Continue reading – International collaboration cooks up powerful new software: MISO

January 18, 2017

Interested in bioinformatics? Come to TorBUG on January 25

Torbug - Lecture illustration

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.

Event details

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 src=q298n32s05bs5l3160afh302hk@group.calendar.google.com

Missed a session? Videos of the latest TorBUG talks are below.

January 13, 2017

Decoding the beaver genome

Jared Simpson

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.

Continue reading – Decoding the beaver genome

December 1, 2016

Expanding the DNA alphabet to understand cancer

Dr. Michael Hoffman poses for a photo at his desk.

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.

Continue reading – Expanding the DNA alphabet to understand cancer

November 25, 2016

TorBUG welcomes Arfon Smith from GitHub on Wednesday, November 30

Torbug - Lecture illustration

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.

Continue reading – TorBUG welcomes Arfon Smith from GitHub on Wednesday, November 30

October 12, 2016

OICR’s Natalie Fox awarded Philip Feldberg Studentship by Prostate Cancer Canada

Natalie Fox and supporters

Prostate cancer is a complex disease. In a clinical setting it can be hard for doctors to accurately predict outcomes for prostate cancer patients, especially for those deemed to be at an intermediate risk of recurrence. With intermediate risk cancers, unlike those that are high or low risk, it is unclear how the cancer will develop. This makes it difficult to choose exactly the right therapy and avoid unnecessary treatments and their associated side effects.

Continue reading – OICR’s Natalie Fox awarded Philip Feldberg Studentship by Prostate Cancer Canada

July 14, 2016

International team launches community competition to unravel how cancer changes a cell’s RNA

Logos of the Challenge partners

An open challenge that merges the efforts of the International Cancer Genome Consortium, The Cancer Genome Atlas, and the NCI Cloud Pilots with Sage Bionetworks and the open science DREAM Challenge community

Continue reading – International team launches community competition to unravel how cancer changes a cell’s RNA

July 14, 2016

OICR informatics researchers play key role in newly launched Genomic Data Commons

Screenshot of GDC website

Researchers have been given a powerful new tool to search for the mutations behind the development of cancer, leading to a better understanding of the disease, and ultimately, better care for patients. On June 6, U.S. Vice President Joseph Biden announced the launch of the Genomic Data Commons (GDC), an ambitious new project that is making a staggering amount of data available to scientists for analysis while also allowing researchers to share their own data with the wider research community.

Continue reading – OICR informatics researchers play key role in newly launched Genomic Data Commons

July 8, 2016

Bioinformatics.ca is keeping Canadian bioinformaticians at the top of their game

A bioinformatics.ca class.

Since 1999, the Canadian Bioinformatics Workshop series has been training the next generation of Canadian bioinformaticians and helping current bioinformaticians keep their skills up to date. This year’s series is well underway with a summer session of classes in Toronto and Vancouver recently wrapped and another session set to launch in the fall. The bioinformatics.ca workshop series is funded by registration fees paid by participants, led by OICR’s Francis Ouellette and facilitated by staff at OICR, including Ann Meyer, Manager, Knowledge and Research Exchange. We spoke to Ann about the series, why it is necessary and what the next steps for bioinformatics.ca will be.

Continue reading – Bioinformatics.ca is keeping Canadian bioinformaticians at the top of their game