September 18, 2019

When the tools you need don’t exist, create them

Dr. Ina Anreiter.

Dr. Ina Anreiter joins OICR as a Schmidt Fellow, bringing her background in behavioural genetics to bioinformatics

While writing her doctoral thesis, Dr. Ina Anreiter realized that there was a missing piece to her research. What she didn’t realize was that this missing piece would lead her into a prestigious postdoctoral fellowship in an entirely new scientific discipline. For decades, scientists have known that RNA – often referred to as DNA’s cousin – undergoes chemical modifications before running its course. These modifications, like RNA methylation, have an important effect in cancer cells, but without the tools to study RNA modifications, progress in this field had stalled for many years.

Recently, the study of these modifications – also known as the field of “epitranscriptomics” – has garnered new attention as the research community develops new methods to study RNA. These methods, Anreiter says, still rely on common chemistry lab techniques and cumbersome procedures that make studying RNA methylation difficult, especially in application to diseases like cancer.

“I found myself in need of a tool,” says Anreiter. “I needed a way to easily analyze RNA methylation across large datasets and found that nothing existed – well, nothing existed yet.”

From fruit flies to machine learning

Anreiter’s doctoral research focused on the behaviour of fruit flies, specifically how inherited characteristics and environmental factors influence their feeding patterns. While searching for a way to study RNA methylation, her background led her to a unique idea.

Anreiter knew of nanopore sequencing – a relatively new type of sequencing technology that could decode DNA and RNA as it passes through a tiny channel. By directly reading a strand of RNA, Anreiter says, nanopore sequencing has the potential to revolutionize how we study RNA modifications. To this day, however, there are no algorithms or tools that can accurately find RNA methylation patterns in the output data of a nanopore sequencer.

Anreiter had also heard of Dr. Jared Simpson’s breakthrough methods for detecting DNA methylation using nanopore sequencing. His computational methods allowed the nanopore community to sequence the entire – highly-methylated – human genome in 2017, and since, he has been working in part to study RNA modifications, like RNA methylation, using nanopore sequencing.

Anreiter pitched her idea to Simpson.

“RNA methylation occurs in normal fruit flies, but not in a certain type of mutant fly,” says Anreiter. “I had a crazy idea that we could sequence both of these types, and use the datasets to develop a machine learning algorithm that could find RNA methylation on its own.”

The potential of her idea would win her the prestigious Schmidt Science Fellowship and a $100,000 USD stipend to work with Simpson for a year.

From machine learning to cancer patients

Anreiter recently began her year-long postdoctoral fellowship in the Simpson Lab at OICR where she is working alongside a team of computational biologists to turn her idea into an algorithm. She is cross-appointed with the University of Toronto’s Department of Computer Science.

“At this point, we’re working on a preliminary dataset, but I’ve already learned so much. The team has been very welcoming and supportive and we’re working together to make better tools to understand diseases.”

The Schmidt Fellowship, which was co-founded by the former CEO of Google, is awarded to exceptional, early-career researchers making a “pivot” in their work.  Anreiter saw the fellowship as an opportunity to immerse herself in a completely new field.

“If we can develop this tool, it would allow us to study human diseases in a new way,” Anreiter says. “When we look at a problem in a new way, we don’t know what solutions we’ll find, but this angle could lead us to new cures.”

Read the UofT News release on Anreiter’s award.

April 23, 2019

Advancement in nanopore sequencing opens new areas of cancer biology to exploration

Dr. Jared Simpson, OICR Investigator.

OICR’s Dr. Jared Simpson and collaborators at the University of Oxford create a new method that allows researchers to explore the fundamental, but hard-to-study biological process of DNA replication

How DNA replicates in a cancer cell is difficult to understand, in large part due to the limitations of current technologies. Nanopore sequencing – a fast, portable way to read very long molecules of DNA – could allow researchers to detect DNA replication patterns. Experts in DNA replication from Oxford University, led by Drs. Carolin Müller, Michael Boemo and Conrad Nieduszynski, teamed up with OICR’s expert in nanopore sequencing, Dr. Jared Simpson, to tackle this challenge.

Together, they developed D-NAscent, a sophisticated laboratory protocol and computational tool that together allow researchers to detect and study how DNA is replicated. Recently, the group’s techniques were published in Nature Methods.

“Traditional methods of studying DNA replication have limited resolution – how finely we can see these patterns,” says Simpson, an Investigator at OICR, who helped develop the computational methods used in the study. “With our methods, we can now look at DNA replication on individual, long molecules of DNA at high throughput. This gives us the ability to look for biological patterns that we were once unable to see, for example, in repetitive areas of the genome.”

The collaborators built on the methods that were previously developed by Simpson et al. which have allowed the researchers to study epigenetic changes in cancers and track other diseases like Ebola.

In the study published today, the group used their methods to study yeast cells, which have a simpler and smaller genome than human cells. Now, the group will apply D-NAscent to study the DNA replication dynamics of human cancer biology. They’ve released their software freely to allow other researchers to do so as well.

“We’re very excited to apply D-NAscent in human cancer cells,” says Simpson. “The potential of this technology is what excites me. We’ve opened up an entirely new way to look at genomic diseases – one that can potentially turn an unexplored aspect of biology into new cancer research discoveries.”

August 3, 2018

Open source in open science: Accelerating cancer research (Part 2)

Part 2 of Open source software

Find part 1 here: Open source in open science: Accelerating cancer research


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.

Continue reading – Open source in open science: Accelerating cancer research (Part 2)

August 1, 2018

Open source in open science: Accelerating cancer research (Part 1)

Open source

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.

Continue reading – Open source in open science: Accelerating cancer research (Part 1)

January 29, 2018

Breakthrough leads to sequencing of a human genome using a pocket-sized device  

Jared Simpson with MinION sequencer

A new nanopore technology for direct sequencing of long strands of DNA has resulted in the most complete human genome ever assembled with a single technology, scientists have revealed.

The research, published today in Nature Biotechnology, involved scientists from the University of Nottingham, University of Birmingham and the University of East Anglia in the UK; UC Santa Cruz at the University of California, Genome Informatics Section of the NIH and the University of Salt Lake City in the USA; and the University of British Columbia and the Ontario Institute for Cancer Research in Canada.

Using an emerging technology – a pocket sized, portable DNA sequencer – the scientists sequenced a complete human genome, in fragments hundreds of times larger than usual, enabling new biological insights.

Continue reading – Breakthrough leads to sequencing of a human genome using a pocket-sized device  

January 25, 2018

The Canadian Data Integration Centre receives new funding to help cancer researchers translate findings to patients

CDI - LogoToronto (January 25, 2018) – The Canadian Data Integration Centre (CDIC) has received $6.4 million in funding from Genome Canada to help the research community translate the biological insights gained from genomics research into tangible improvements for cancer patients.

CDIC is a “one-stop shop” service delivery platform for cancer researchers, helping streamline research by providing coordinated expertise on a broad range of services, including data integration, genomics, pathology, biospecimen handling and advanced sequencing technologies. It is an international leader in genomics, bioinformatics and translational research, supporting some of the world’s largest programs in genomic data analysis, genomic and clinical data hosting, cancer data analyses and access, and the development of algorithms for advanced sequencing technology.

Continue reading – The Canadian Data Integration Centre receives new funding to help cancer researchers translate findings to patients

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

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

September 15, 2016

Canadian government makes big investment in big data research

OICR's server room

On September 13 the Government of Canada, through Genome Canada, made a $4 million investment in Canadian big data research to help improve real world challenges such as infectious disease outbreaks, managing food crops and combating cancer.

Of the 16 projects funded across Canada, three are based at OICR. Led by OICR Principal Investigators Drs. Paul Boutros, Vincent Ferretti, Jared Simpson and Lincoln Stein (Stein is also OICR’s Interim Scientific Director and leader of the Institute’s Informatics and Biocomputing Program), the projects are developing ways to make genomics and health data more manageable, securely accessible and easily understood. Together these projects will help to facilitate cancer research and assist in the adoption of more precision medicine. As well, they have applications in other fields of genomics research beyond cancer, such as agriculture and energy.

Continue reading – Canadian government makes big investment in big data research

June 16, 2016

OICR-developed software helping track Zika in Brazil

Field Laboratory tracking Zika
Photo: University of Birmingham

Scientists from the University of Birmingham in the U.K. have established a mobile DNA sequencing lab in Brazil to help that country track the spread of the Zika virus. The lab, based inside a minibus, is travelling through the areas of Brazil that have been most affected. A central part of the technology they are using is the small, USB-powered MinION genome sequencer. OICR’s Dr. Jared Simpson, an Investigator in the Informatics and Bio-computing Program, developed the software used to sequence samples on the device.

Read the news release: Mobile laboratories help track Zika spread across Brazil

Related: Tracking Ebola with portable sequencers: Could this technology be the key monitoring the spread of Zika?

May 3, 2016

Tracking Ebola with portable sequencers

Could this technology be the key to monitoring the spread of Zika?

Jared Simpson with MinION sequencer

As West Africa was dealing with a massive outbreak of the Ebola virus, a group of researchers answered the call for assistance with a palm-sized device. Dr. Nick Loman and Mr. Josh Quick from the Institute of Microbiology and Infection at the University of Birmingham in the U.K., together with the help of OICR Investigator Dr. Jared Simpson, developed a ‘genome sequencing lab in a suitcase’ based around the tiny MinION sequencer. It was deployed to Conakry, Guinea in April of 2015 to test Ebola samples in the field.

Continue reading – Tracking Ebola with portable sequencers

February 3, 2016

Real time outbreak surveillance using genomics now possible in resource-limited conditions

New research published in Nature has shown how genome sequencing can be rapidly established to monitor outbreaks.

Dr. Simpson.TORONTO, Feb. 3, 2016 /CNW/ – Researchers designed a “genome sequencing laboratory in a suitcase”, employing a novel DNA sequencer, transporting the equipment in less than 50kg of airline luggage. This was initially deployed in Conakry, Guinea in April 2015 where Ebola samples from patients could be sequenced as soon as new cases were diagnosed. This reduced delays shipping to traditional genome laboratories often located on a different continent. The team found that they could generate sequencing information in as little as 24 hours after receiving a sample, with the sequencing process taking less than an hour.

Continue reading – Real time outbreak surveillance using genomics now possible in resource-limited conditions

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