October 15, 2020
Morgan Taschuk reflects on a decade of supporting critical cancer research and on her new role as OICR’s Director of Genome Sequence Informatics
Cancer genomics research depends on infrastructure and analysis tools that collect, process, analyze and annotate vast quantities of valuable sequencing data. Behind these systems at OICR is a team of individuals dedicated to enabling cancer research discoveries. OICR is proud to announce that Morgan Taschuk will now lead this essential team as Director of Genome Sequence Informatics (GSI).
Here, she reflects on her new role and her outlook on the next few years.
Your behind-the-scenes work is essential to the cancer research we do at OICR. How would you describe your work?
Our team makes sequencing data analysis and management easier for researchers and clinicians in several different ways. We create and maintain the infrastructure and computational tools that researchers need to process, analyze and annotate sequencing data, so they can spend their time working on other challenging research questions.
GSI also offers expert bioinformatics support services directly to researchers to collaborate on challenging research projects. In addition, OICR Genomics is pursuing clinical accreditation this year and so we have a team of clinical genome interpreters who can issue reports on a patient’s unique genome. There’s a lot going on!
How has your work evolved since you’ve been at OICR?
I began at OICR nearly a decade ago, when most of our bioinformatics work was custom for every project, and our sequencing instruments produced a fraction of the data of instruments today. Any kind of automation was quite limited and the amount of analysis we could scale up was limited by the number of people we could hire. Back then, the biggest projects were analyzing human whole genomes for research and participating in international consortia.
In the last nine years, I’ve seen us scale up our sequencing and analysis capabilities, expand a fantastic team of highly educated experts from computer science through data analysts to clinical genome interpreters, and reinforce our reputation of excellence in bioinformatics and computational biology. We’re doing everything we were doing a decade ago plus much more. We sequence single cells, cell free and circulating tumour DNA, analyze immune profiles, participate in international consortia like ICGC-ARGO, contribute to SARS-CoV-2 projects, and will soon produce clinically accredited genome reports, all while still sequencing whole genomes for research.
Today, our team oversees around two petabytes of data, and runs about 3,000 workflows and about 1.8 terabytes of analysis, per day. Genome Sequence Informatics is a team of about 20 people, including bioinformaticians, software developers and engineers, currently supporting 155 research projects – and their resulting research discoveries – each year.
As the Director of Genome Sequence Informatics, what are you most looking forward to?
This new role allows me to focus on the bigger picture rather than on technical challenges. I see this as an opportunity to unify efforts across teams, departments, and across the institution. For example, if one team that we support is doing a task differently than another, I can help bring them together to work towards a common solution for everyone so we can learn from each other, maintain more consistent quality control, and make the best use of the resources and funds we have. I’m looking forward to more productive interactions with the phenomenal teams at OICR and with other organizations around the country and world.
What are your top priorities over the next couple of years?
My goal over the next few years is to share what we’ve created with the community while growing our network. We’ll continue to create solutions to fulfill the evolving needs of researchers and clinicians. We’ll continue to publish our code so other bioinformaticians can confirm what we’ve done and start their own analysis pipelines. We’ll publish protocols and guidelines that we’ve created for our clinically accredited analysis as well as our core assays. And we’ll share our challenges and solutions with the community so we can build on our collective expertise. In addition, we’ll reach out to other teams and organizations to collaborate and learn from them. The bioinformatics, software development, and clinical genomics communities have vast knowledge that we want to take advantage of, improve and share.
The next couple of years for GSI are going to be about collaborative, open science so the scientific and clinical communities can all benefit from the progress made by Genome Sequence Informatics and OICR as a whole.
August 3, 2018
OICR researchers have contributed to major open source projects available to the global research community in order to accelerate cancer research. Click the link below to read about more of OICR’s open source software projects.
August 1, 2018
In the effort to bring better disease prevention and treatment to patients faster, cancer researchers are thinking more creatively about ways to conduct high-quality scientific research. Concerns about the quality, efficiency and reproducibility of research have motivated the open science movement – the growing trend of making data, methods, software and research more accessible to the greater scientific community.
Open source software (OSS), a major component of open science, enables research groups to reduce redundant efforts in software engineering by sharing software code and methods. In addition to improving efficiency, OSS promotes high-quality research by enabling collaboration, and helps make research easier to reproduce by making it more transparent.
March 17, 2017
On International Women’s Day, OICR scientists attended the first-ever Metamorphosis Girls STEM Conference at John Polanyi Collegiate Institute in Toronto. There, the researchers helped expose female grade seven and eight students to the various fields and career opportunities within science, technology, engineering and math (STEM) – with an emphasis on encouraging the next generation of female scientists to pursue a career in STEM fields.
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).