November 21, 2019
International research group unlocks the promise of nanopore native RNA sequencing
Studying RNA may offer new answers to cancer – and the tools to read RNA directly are now in our hands.
An international research consortium, led in part by Dr. Jared Simpson at OICR, has developed new laboratory protocols and a suite of software tools that will allow the research community to exploit the promise of direct RNA sequencing.
These techniques, published recently in Nature Methods, represent the first large-scale exploration of human RNA using nanopore sequencers – the advanced handheld sequencing devices that can read long strands of RNA.
“Unlike traditional sequencing devices that read copies of RNA strands that are cut into little pieces, nanopore sequencing allows us to study long strands of RNA directly without losing important information in the copying and cutting process,” says Paul Tang, Computational Biologist at OICR and co-first author of the publication. “Our methods combine the power of reading RNA directly with the power of long-read sequencing, enabling an entirely novel way to study cancer biology.”
In collaboration with researchers at Johns Hopkins University and the University of California Santa Cruz, Tang and Simpson developed the software methods that could decode the output data from a nanopore sequencer. Their methods used a machine learning technique, called a Hidden Markov Model, to determine the letters of code within an RNA strand.
“With these methods, we’ve shown that you can leverage nanopore RNA sequencing to gain a lot of valuable information that we couldn’t have otherwise,” Tang says. “We’re very happy to see this work published because we are enabling others to study a new aspect of cancer biology and we look forward to the research discoveries to come.”
These new methods have been integrated into Simpson’s already-popular nanopolish software suite which is routinely used by the nanopore community around the world.
November 14, 2018
Researchers find a new way to detect small traces of tumour DNA in blood and determine the tumour’s tissue of origin
A blood sample can be used to detect and monitor certain cancers in select patients, but there are significant technical barriers that prevent the widespread adoption of this “liquid biopsy”. This type of blood test analyzes the rare traces of tumour DNA that are circulating in the blood, but distinguishing tumour DNA from healthy DNA is both difficult and expensive. New methods are needed to improve the accuracy, sensitivity and cost-effectiveness of liquid biopsies so that more patients can benefit from this less-invasive test.
April 4, 2017
For three science-obsessed high school students March Break wasn’t a time to kick back and relax. Instead the students, Cameron, Chris and Zev, spent the week at OICR gaining knowledge and hands on experience in genomics and bioinformatics as part of the Gene Researcher for a Week program.
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.