April 23, 2019
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.”
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
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.
January 29, 2018
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.
January 25, 2018
The Canadian Data Integration Centre receives new funding to help cancer researchers translate findings to patients
Toronto (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.
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.
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.
September 15, 2016
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.
June 16, 2016
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
May 3, 2016
Could this technology be the key to monitoring the spread of Zika?
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.
February 3, 2016
New research published in Nature has shown how genome sequencing can be rapidly established to monitor outbreaks.
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.
December 15, 2015
Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone
Genome sequencers today are extremely powerful devices found in labs around the world (including labs here at OICR). They are reshaping how we see cancer and providing the roadmap for future, more personalized treatments. Most are also extremely large – about the size of a small oven – expensive and stationary.
But new technology is emerging that will change this. A device called the MinIONTM, which has been developed by Oxford Nanopore Technologies over the last decade, is a sequencer that fits in the palm of your hand and can be plugged into a laptop using a conventional USB cable, like you would plug in a camera or a phone. The technology is still in early stages, but has enormous potential for genomic sequencing and, eventually, for human health.