Next generation sequencing

Compute, connectivity and collaboration.
Breakthrough technologies are helping researchers to sequence huge amounts of genetic data quickly.


  • There are many infrastructure challenges in the field of bioinformatics due to the scale of the data that is produced.
  • The Institute of Environmental Science and Research (ESR) Human Genomics Group have come up with a solution for portable, in-the-field genomics sequencing.

  • REANNZ are working closely with the team to take their research to the next level through connectivity and service solutions.

Breakthrough technologies are helping researchers to create new ways to sequence huge amounts of genetic data quickly. ESR researchers are innovating these technologies to be able to remotely sequence genomes far from the lab, improving treatment times and helping communities keep their people and environments safe.

The Human Genomics Group are collaborating with international partners to make portable sequencing technologies readily available to the research community. Senior bioinformatician, Dr Miles Benton leads the research into portable sequencing. It uses technology from Oxford Nanopore that sequences genomes using less compute power. It lets researchers perform genome sequencing in any environment by making it easy and portable.

Long read genomics sequencing produces large amounts of data. Nanopore devices can generate gigabytes of data every few hours, the larger GridION sequencers that ESR have onsite generate up to four terabytes a day.

Data-driven genome research

ESR bioinformatician Leah Kemp, specialises in analysis of these large datasets. As part of the Clinical Genomics Project, Leah went from analysing single genes when diagnosing patients with genetic disorders, to whole genomes.

“We're taking a big leap in data scale, so that brings in a whole different set of tools that researchers need to utilise to work with that data. The scale of data computation has dramatically increased in recent years, so genomic technologies have also advanced.”

The Human Genomics Group are using portable sequencing to make real-time point-of-care diagnosis for hospital emergency patients. The technology makes diagnosis cheaper and faster.

“We have a couple of use cases where we are working with a hospital’s emergency department, looking at screening blood or spinal fluid of suspected sepsis patients. That usually requires culturing the bacteria and takes about three to four days for the results,” says Miles.

Through portable sequencing diagnoses is available in as little as an hour, transforming emergency patient care.

“We’ve also been working with the neonatal unit which is great because my story has come full circle. My son was born 8 weeks premature, and he had to have a lumbar puncture a couple of days in. That’s where this idea of portable, bedside sequencing came from.”

Computing on the fringe

This new wave of remote compute processing is being termed fringe computing. It allows researchers to move beyond the lab bench and conduct data processing in the field. The equipment itself is cheap, portable and self-sufficient, typically using 15 watts of energy, running on batteries or solar panels.

“Much of my research is trying to make the smaller devices portable; the devices are literally the size of a Mars Bar and they can be powered by very small computers. At $600 a unit you can deploy it anywhere, stow it beneath your work table when you’re done, and plug it into a touch-screen monitor to see your results. That's one of the really exciting things about this new wave of sequencing technology - the fact that it has many use cases and is not limited to the lab bench anymore.”

Molecular microbiologist, Matt Storey is another Human Genomics Group researcher. You can find him in the field as often as you will find him in the lab undertaking the DNA extraction and processing that to be sequenced and analysed.

“Fringe computing is where we take reasonably high-performance computing hardware out to point-of-care place or places where we don't have access to the computing resources that we need. It allows us to process the data on-site, rather than transporting it to a central place,” says Matt.

There are technical challenges that make accessing and processing the data onsite difficult. Genome sequencing produces huge data sets. Moving this raw data to the lab is almost impossible using standard methods. To solve this, the group designed its fringe computers to process data on-site, reducing the size needed for transport.

With successful use cases and the portable nature of the devices already having an impact for the wider community, Miles, Matt and the team are looking to take their fringe computers even further.

“We have partnered with local Iwi in Christchurch to monitor bacteria present in the harbour. We're hoping that we can stream the data from the device to the Cloud while we are on site. You take a sample of the water, load it onto the device, get the read, then you're able to identify the types of bacteria in the water and stream the raw data to the Cloud. If we stream the raw data, a solid connection would mean that we can use cheaper compute or offload some of the heavy lifting to Cloud GPU compute. To do that we'd need a really solid and fast network connection.”

Collaboration is key

REANNZ works closely with member’s technology teams and researchers, like Miles and the team at the Human Genomics Group, to support their use of the network and develop solutions that resolve technical issues.

Currently the teams are working together to come up with a solution for taking these devices further afield. “I think the big thing for me with partnering with REANNZ would be the remote connectivity, so we can really push the boundaries of where we can take these devices. We can sequence anywhere but having that network connectivity would really take it to the next level.”

REANNZ was able to support ESR’s ability to transfer whole human genomes from testing points to their lab at University of Otago, which would fail due to the datasets size.

We had a back-and-forth with REANNZ trying to fix these issues and within a few days the connection was faster than ever. I think that close relationship and being able to troubleshoot these issues had a huge impact for transferring data at fast rates. The latest 10 Gbps connection upgrades to all ESR sites made a huge difference as well.

Dr Miles Benton, ESR

Collaboration is paramount ESR and the Human Genomics Group. They work closely with Crown Research Institutes and Universities both in New Zealand and internationally and are dedicated to making their research accessible. A large community of researchers worldwide are using this portable sequencing technology for multiple use cases. Making this technology readily available is having a huge impact.

“A PhD student from Germany has been monitoring the health of insect colonies using the device. There was also the first use case reported where DNA was extracted during a surgical procedure, put through the sequencer, classification happened within an hour, and they had the results back to the surgeon while they were still operating. The surgeon was then able to tailor the surgery based on that report,” says Miles. “It's just really humbling seeing all of these ideas, the international community is amazing. Collaboration has been key to the successes this technology has had.”

ESR’s Miles, Leah and Matt are paving the way for the next generation of genomic sequencing technologies. It’s improving the treatment of patients, helping communities, and making access to sequencing cheaper and easier than ever before. REANNZ supports ESR and its members by providing fast, stable connectivity across New Zealand and expertise on data intensive transfer capability. Collaborations like these are leading to impactful innovations across multiple fields of research including bioinformatics and healthcare.

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