July 23, 2019

Blood samples, biostatistics and a fresh perspective: The makings of a cancer prediction machine

Jordyn Walton and David Soave
Jordyn Walton and Dr. David Soave

Biostatistics Training Initiative (BTI) alumnus brings on new BTI trainee to study Canada’s largest population health dataset using today’s top technologies

Recently, circulating tumour DNA (ctDNA) – DNA released from cancer cells that freely circulates in the blood – has garnered much attention not only as an alternative to traditional tissue biopsies, but as a potential blood-based biomarker for early cancer diagnosis.

The ability to detect the earliest blood-borne traces of cancer largely rests in our ability to determine which molecular markers indicate that a cancer is developing – or which patterns in ctDNA can predict whether a cancer will grow. Dr. David Soave sees this as a mathematical challenge that, if solved, could have huge impact for better predicting and diagnosing a wide variety of cancers.

“To find cancer earlier or predict who will develop the disease, we need to carefully compare human samples from those who will develop cancer and samples from those who won’t,” Soave, an Assistant Professor at Wilfrid Laurier University and OICR Associate, says. “This type of challenge requires new statistical models, methods and computational techniques that can decipher large, complex and high-dimensional data.”

Last year, the Canadian Partnership for Tomorrow Project (CPTP) unified the data from several provincial longitudinal health studies into a national cohort consisting of more than 325,000 participants who are voluntarily donating their health and biologic samples to research. As some CPTP participants will develop disease and others will not, this dataset provides an unprecedented resource for researchers like Soave to discover the earliest traces of cancer that appear several months to years prior to an initial diagnosis.

Continue reading – Blood samples, biostatistics and a fresh perspective: The makings of a cancer prediction machine

April 18, 2019

OICR welcomes new Principal Investigator, Dr. Sagi Abelson

Dr. Sagi Abelson, OICR Principal Investigator.

OICR is proud to welcome Dr. Sagi Abelson to its Computational Biology Program as a Principal Investigator. Here, Abelson discusses some of his past successes, including his recent leukemia research and his wide range of research interests.

How have you been involved with OICR in the past?

I came to Toronto and joined Dr. John Dick’s lab at the Princess Margaret Cancer Centre as a Postdoctoral Fellow, where I had the opportunity to work with OICR’s Genomics and Genome Sequence Informatics teams. I was investigating the differences between normal aging cells and the cells that lead to leukemia. To do that, we had to look into blood-derived DNA samples from many individuals that develop leukemia following blood collection and search for common genetic markers that indicated a high risk of developing leukemia. I worked closely with OICR teams to prepare and sequence these patient samples. We also collaborated to deploy specialized methodology that enabled us to accurately interpret the genomic data and to identify those harmful mutations.

What motivated you to become involved with that subject?

Far too many patients are diagnosed with leukemia when it is too late. This applies to many other cancers as well. If we can detect a disease earlier, we may benefit from a larger window of opportunity to prevent, manage, or treat the disease. There are many biological and computational challenges that need to be addressed in this area, including finding extremely small traces of a disease amidst a lot of noise in genomic data. I’m interested in the development and the optimization of methods and computational tools to find these first traces of a developing disease.

What will your future research focus on?

In the future I would like to expand my research program to other types of cancers. I truly believe that as a researcher I can achieve more by having a multidisciplinary team that address questions in other biological systems as well. In this era of big data, we are not the only ones realizing that multiple research skills are necessary to tackle the toughest problems. Research institutes and universities understand it as well and therefore introduced computational courses in their biology curricula. That said, conducting research is a team effort and collaboration is the key to approaching scientific problems in areas where you don’t have the expertise.

When approaching the end of your postdoctoral studies and deciding the next step in your career, what opportunities were you considering?

Well, I was looking for a combination of things. I was looking for a place that shares the same vision as I do, the same values of collaboration and translation and a place that has a high caliber of scientists. I believe in the things that OICR works on and how research is done here, so I think it’s a great fit.

What advice would you give to aspiring academics?

To do research well, you first need to love it. You need to be curious, know to identify the needs and ask the right question at the right time. Furthermore, you have to have persistence. You cannot give up in the pursuit of new knowledge.

February 26, 2019

Meet the researchers – Rosita Bajari

Find out what a Technical Business Analyst does and why this job is so important in helping researchers and software engineers work together.

February 21, 2019

New step-by-step protocol for common omics analyses fills 10-year gap in training resources

Juri Reimand

Expert group develops comprehensive guide for the interpretation and visualization of gene lists, replacing outdated, decade-old protocols

The importance of understanding biological pathways – or how our genes work together – is becoming increasingly evident, but pathway analysis remains a major challenge for many basic and biomedical researchers. Current computational tools can help simplify this analysis, but there is no established guide or standard for using these tools in practice.

To fill this gap, a team of experts from OICR and the Bader Lab at the University of Toronto recently published a comprehensive, step-by-step guide to pathway enrichment analysis that brings together their highly-recommended tools into one protocol. The complete protocol, which is now published in Nature Protocols, can be performed in less than five hours and can be used by researchers with no prior training in bioinformatics or computational biology.

“These days, almost every omics study needs to include pathway enrichment analysis, but it has been over a decade since a comprehensive protocol for these analyses has been published,” says Dr. Jüri Reimand, Principal Investigator at OICR and co-lead author of the protocol. “Our new methods are designed to guide researchers through their analyses and serve as a practical resource for their studies.”

Each step of the protocol is supported with detailed instructions and valuable troubleshooting information, which were designed in large part by Ruth Isserlin, co-lead author and Senior Bioinformatics Analyst in the Bader Lab.

Recently, the methods were used to identify a therapeutic target for ependymoma, a prevalent type of childhood brain cancer that is notoriously difficult to treat. The pathway analysis, as described in Nature, led to a better understanding of why most ependymoma treatments are not effective and revealed a new treatment option that could stop the progression of the disease.

“Future cancer research discoveries rely on our understanding of biological pathways,” says Reimand. “This protocol provides a resource from which we can build our understanding and explore previously uncharted relationships between our genes.”

January 22, 2019

OICR’s Dr. Ann Meyer receives Community Engagement Fellowship from AAAS to advance Canada’s bioinformatics community

Dr. Ann Meyer

On January 3, 23 community engagement professionals – including OICR’s Dr. Ann Meyer – were named AAAS Community Engagement fellows for 2019.

The Community Engagement Fellowship Program (CEFP) brings together professionals from a diverse range of scientific communities to share insights and develop strategies to strengthen their respective communities. CEFP aims to improve collaboration and community building in science – and that’s exactly what Meyer will continue to do in Canada’s bioinformatics space.

“Over the last few years, we’ve been working on filling the educational needs of Canada’s bioinformatics community,” says Meyer, Knowledge and Research Exchange Manager at OICR and Manager of Bioinformatics Education at bioinformatics.ca. “This fellowship will help us expand our efforts to foster and strengthen ongoing collaboration amongst research groups in Canada with similar interests.”

Meyer is the only individual from a Canadian institute who has been selected to participate in the CEFP since its inception. The 2019 cohort includes community leaders from the Chan Zuckerberg Science Initiative, the National Geographic Society and the Data Commons Pilot Phase Consortium.

“Alongside these talented community managers, I hope to bring back new techniques to better engage the bioinformatics community,” says Meyer. “Further developing our community will facilitate ongoing learning collaborations and strengthen this research network across our geographically disperse nation.”

January 14, 2019

Researchers discover common markers of tumour hypoxia across 19 cancer types

Landmark pan-cancer study analyzes mutation signatures of low oxygen in more than 8,000 tumours

TORONTO (January 14, 2019) – Unlike healthy tissues, tumours thrive in low-oxygen environments, often acquiring the ability to resist treatment and spread to other sites in the body. Despite being a well-known cause of therapy resistance and metastasis, the impact of low oxygen, known as hypoxia, on tumour cells is poorly understood. As reported today in Nature Genetics, researchers have discovered molecular hallmarks of hypoxia in the first-ever pan-cancer analysis of low oxygen in human tumours, with a special focus on prostate cancer.

The study investigated more than 8,000 human tumours across 19 different cancer types, including prostate tumours from the Canadian Prostate Cancer Genome Network (CPC-GENE).  The authors discovered common markers of hypoxia that could help predict cancer aggressiveness and inform treatment decisions.

Continue reading – Researchers discover common markers of tumour hypoxia across 19 cancer types

November 8, 2018

Meet the researchers: Lawrence Heisler

Lawrence Heisler, Project Manager in the Genome Sequence Informatics team at OICR, talks about how new technologies are making genetic sequencing faster and cheaper. But turning data into discoveries requires the right behind-the-scenes support. That’s where Heisler’s team comes in.

October 2, 2018

Understanding how cancer differs between sexes

Connie Li

OICR researchers uncover sex-linked genetic differences that may be able to predict cancer severity and response to therapy

Cancer differs in males and females but the origins and mechanisms of these sex differences remain unresolved. A better understanding of sex-linked differences in cancer could lead to more accurate tests and treatments that are personalized for patients based on their sex.

Continue reading – Understanding how cancer differs between sexes

September 11, 2018

Portal to access world’s largest database of pediatric genomic data goes live

OICR’s Genome Informatics team plays key role in development of the Gabriella Miller Kids First Data Resource Portal

Toronto (September 11, 2018) – Today, the Gabriella Miller Kids First Data Resource Center (DRC) at the Children’s Hospital of Philadelphia launched the Kids First Data Resource Portal, which will advance personalized medicine for the detection, therapy, and management of childhood cancer and structural birth defects. As the Kids First DRC’s chief outward-facing tool, the Kids First Data Resource Portal serves the needs of a diverse group of patients, researchers, and clinicians partnering to create the world’s largest database of pediatric genomic data, and provides the necessary tools and computational resources for their analysis and interpretation.

Continue reading – Portal to access world’s largest database of pediatric genomic data goes live

September 6, 2018

Q&A with Dr. Christina Yung, OICR’s new Director of Genome Informatics

OICR welcomes Dr. Christina Yung as Director of Genome Informatics. Yung is returning to OICR from the University of Chicago where she led and managed the National Cancer Institute’s Genomic Data Commons (GDC) – a unified data system that promotes the sharing of genomic and clinical data between researchers.

Continue reading – Q&A with Dr. Christina Yung, OICR’s new Director of Genome Informatics

September 4, 2018

Meet our students – 2018

Meet Dike Aduluso-Nwaobasi, Sarah Donald and Benson Wan. Find out how summer co-op positions affected their career and educational journeys.

August 21, 2018

Leader in data access and CEO of DNAstack, Dr. Marc Fiume, joins OICR as its newest Associate

Dr. Marc Fume poses for a photo in an atrium

Formalizing his longstanding relationship with OICR, Dr. Marc Fiume joins the Institute as an Associate to turn big data into a cure

“We know there are valuable – potentially life-saving – genomics and clinical data that are locked away in the sever rooms in hospital basements,” says Dr. Marc Fiume, CEO of DNAstack, Adjunct Professor at the University of Toronto, and OICR’s newest Associate. “We’re working to make these data more findable, accessible and useful to help researchers find cures for diseases faster than ever before.”

Continue reading – Leader in data access and CEO of DNAstack, Dr. Marc Fiume, joins OICR as its newest Associate

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