Reading DNA in real time: Garvan’s new long-read sequencing capability
04 December 2017
Update: As of 18 October 2018, Garvan is also certified to offer research sequencing on the Oxford Nanopore PromethION. This had increased Garvan’s nanopore sequencing capability more than 50 fold at a reduced cost.
Nanopore sequencing is a valuable complement to Garvan’s existing genomic sequencing technologies as it can read very long DNA and RNA molecules then make this data available almost instantly.
Garvan is one of only two worldwide to have achieved certification to provide nanopore sequencing as a service, following its acquisition of Oxford Nanopore Technologies’ GridION sequencer.
“Nanopore sequencing provides alternative yet complementary capabilities to our existing short-read technologies, allowing us to rapidly identify genetic features that can be difficult to assess with other approaches, such as large genome rearrangements or epigenetic marks,” said Dr Martin Smith, Genomic Technologies Program leader at Garvan’s Kinghorn Centre for Clinical Genomics (KCCG).
Click to watch the 60 second explainer video here:
Nanopore sequencing works by driving DNA or RNA molecules through thousands of tiny tubes, called nanopores, that sit in a membrane. As the molecules move through a nanopore, each base creates a disruption in the electric current. These disruptions are analysed to determine the sequence.
This technology allows researchers to watch DNA and RNA being sequenced in real-time, and even interact with their experiments while they are running.
“Analysing genomic data in real-time can drastically improve the turn around time for genomic research, from several weeks to a few days and potentially even hours to sequence and analyse a sample,” said Dr Smith, “so this can have a real impact for translational research.”
“The real-time interactivity of this technology also allows us to make decisions about the sequencing on the fly, such as switching to another sample or scaling up an experiment.”
As nanopore sequencing looks at largely unprocessed DNA, it can pick up important epigenetic changes, such as whether a gene is turned on or off. Similarly, since DNA is not broken into small sections for sequencing, it also detects large structural changes.
“Sequencing native DNA molecules allows us to investigate multiple biological features in a single experiment. We can observe how chromosome structure is altered in cancer, or whether long-range genetic variations contribute to disease,” said Dr Smith.
“Much of the function of the human genome remains a mystery. Nanopore sequencing represents an exciting new capability in our technology arsenal to better understand the genetic origins of disease and ultimately unlock further clinical value from the genome,” said A/Prof Marcel Dinger, Head of KCCG.
KCCG claimed the world record for longest genome sequencing read with a 1.015 megabase read in December, using the GridION.
Garvan’s Kinghorn Centre for Clinical Genomics acquired and configured the GridION. Research sequencing services will be made available in 2018 through the Garvan-Weizmann Centre for Cellular Genomics. For more information, please contact nanopore@garvan.org.au or + 61 02 9355 5842.