December 17, 2020
Dr. Jared Simpson and collaborators develop new nanopore-based methods to investigate two understudied aspects of disease biology
Studying DNA modifications may offer new insights into cancer – and the tools to read these changes are now in our hands.
In a recent publication in Nature Methods, OICR Investigator Dr. Jared Simpson and collaborators at Johns Hopkins University describe a new method to investigate two key aspects of disease biology, methylation and chromatin accessibility, simultaneously. These aspects can help describe how genes are organized and switched on and off in a cell, which may enable future progress in cancer research and discovery.
The group’s new method, coined nanoNOMe-seq, is built for nanopore sequencing – a fast, portable way to read long molecules of DNA. nanoNOMe serves as an additional tool that extends the utility of nanopore sequencing technologies.
“Our collaborators developed the lab protocols and we developed the analysis software to determine where DNA modifications occurred,” says Simpson. “Now, with this method, other researchers can investigate how DNA is modified within a cell to give an extra layer of information that the community can decode into new insights and discoveries.”
Dr. Michael Molnar, Scientific Associate in the Simpson Lab at OICR, led the development of the analysis software behind nanoNOMe.
“At times, it seemed like it might not be possible to develop a statistical model that could make sense of all the data,” says Molnar. “But we were able to persist and develop the nanoNOMe software, which showed a high degree of accuracy. We hope this method will enable others to discover long-range patterns and make new connections in sequencing data.”
nanoNOMe was first released as a preprint, which has already been cited in other scholarly articles including a tool for methylation pattern visualization, an analysis of human chromosome 8, and a published review on long-read sequencing among other publications. Simpson and Molnar’s collaborators plan to further investigate methylation and chromatin accessibility in human cancer cells with nanoNOMe.
“If you’re interested in understanding how methylation relates to open chromatin, then you can use this protocol,” says Simpson. “This is opening a new space for the community to explore interactions between chromatin and DNA methylation.”
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.
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.”
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.
June 15, 2015
Researchers sequence and assemble first full genome of a living organism using technology the size of smartphone
TORONTO, ON (June 15, 2015) Researchers in Canada and the U.K. have for the first time sequenced and assembled de novo the full genome of a living organism, the bacteria Escherichia Coli, using Oxford Nanopore’s MinIONTM device, a genome sequencer that can fit in the palm of your hand.
The findings, which were published today in the journal Nature Methods, provide proof of concept for the technology and the methods lay the groundwork for using it to sequence genomes in increasingly more complex organisms, eventually including humans, said Dr. Jared Simpson, Principal Investigator at the Ontario Institute for Cancer Research and a lead author on the study.
“The amazing thing about this device is that it is many times smaller than a normal sequencer – you just attach it to a laptop using a USB cable,” said Simpson. “And while our work is a demonstration of the capabilities of the technology, the most significant advance is in the methods. We were able to mathematically model nanopore sequencing and develop ways to reconstruct complete genomes off this tiny sequencer.”
While standard sequencing platforms can either generate vast amounts of data, or read long enough stretches of the genome to allow complete reconstruction, the Nanopore device has the potential to achieve both goals according to Simpson. “Long reads are necessary to assemble the most repetitive parts of genomes but we need a lot of reads if we want to sequence human genomes. The small size of the MinION suggests there is room to scale up and sequence larger and more complex samples,” Simpson said.
A drawback of the technology is that the single reads it produces are currently much less accurate than the reads produced by larger devices. Strong bioinformatics tools are needed to correct errors. The methods Simpson and colleagues developed are able to overcome the error rate and compute a more accurate final sequence.
“This was a fantastic example of a successful long distance research collaboration between Canada and the U.K.,” said Dr. Nicholas Loman, a co-lead author on the paper and an Independent Research Fellow from the Institute of Microbiology and Infection at University of Birmingham. “We explored new ways of working, including hosting a hackathon to explore new algorithm development and using shared computing resources on the Medical Research Council funded Cloud Infrastructure for Microbial Bioinformatics (CLIMB) based in the U.K. Midlands and Wales.”
The method of assembly the authors devised had three stages. First, overlaps between sequence reads are detected and corrected using a multiple alignment process. Then the corrected reads are assembled using the Celera assembler and finally the assembly is refined using a probabilistic model of the electric signals caused by DNA moving through the nanopore.
“This work has incredible potential,” said Dr. Tom Hudson, President and Scientific Director of the Ontario Institute for Cancer Research. “Scaled up, this technology could one day be used to sequence tumour genomes. The device’s portable nature would allow for sequencing to become far more accessible, bringing the option of more personalized diagnosis and treatment to more patients.”