Scientists describe new approach in NEJM, using Oxford Nanopore DNA sequencing technology to improve prognosis in critically ill patients, in less than 8 hours

Oxford Nanopore worked with a team led by Stanford University School of Medicine in a research study to develop a rapid, whole genome sequencing approach, that:

  • Improves prognosis in critically ill patients and guides clinical management at least as well as current short read technologies.
  • Reduces the time to identify disease-causing genetic variants — to as little as 7 hours and 18 minutes, a world record.
  • Provides the potential to identify large and complex disease-causing variants, missed by previous approaches, while enabling phasing and detection of epigenetic markers, which are known to have clinical impact.

Traditionally, rapid characterisation of variants that cause genetic disease, from whole human genome sequencing, has been challenging. Whole genome sequencing enables better detection of such variants but has typically taken days or weeks to return a result. This timescale can be particularly problematic in time-critical contexts, such as identification of suspected pathogenic variants in a critically ill patient.

Scientists from Oxford Nanopore Technologies, NVIDIA, Google and others worked with a research team led by Euan Ashley, MB ChB, DPhil, professor of medicine, of genetics and of biomedical data science at the Stanford University School of Medicine, to develop a whole genome nanopore sequencing approach that can characterise pathogenic variants in as little as 7 hours and 18 minutes — faster than any previously published approach in clinical samples.

Euan Ashley and John Gorzynski, Stanford University School of Medicine. Photo credit: Steve Fisch

Prioritising time to result

The team used PromethION 48 — Oxford Nanopore’s highest-throughput sequencing device, capable of running up to 48 flow cells at once — to sequence 12 unique research samples from patients aged 3 months to 57 years. Each PromethION Flow Cell has the capacity to sequence at least one whole human genome on its own, but when multiple flow cells are used concurrently to sequence one genome, the time taken to complete the whole genome sequence is significantly reduced.

The team were able to take advantage of this and prioritise time to result, to generate a whole human genome and list of variants in as little as 5 hours and 2 minutes — a new Guinness World Record. Manual review of this list of variants that followed enabled disease-causing variants to be identified in 7 hours and 18 minutes.

A pathogenic or likely pathogenic variant was identified in five of the 12 samples analysed as part of the research. According to the study authors, this “informed clinical management (including sympathectomy, heart transplantation, screening, and changes in medication) for each of the five patients or their family members.”

Each genome was sequenced to a minimum of 173Gb, with a mean read N50 of 25kb. Variant calling resulted in a median of 4,490,490 small variants, and 22 prioritised structural variants per sample. The base calling was accelerated using NVIDIA V100 and P100 GPUs.

Gordon Sanghera, CEO, Oxford Nanopore Technologies commented:

“Genomic information can provide rich insights and enable a clearer picture to be built. A workflow which could deliver this information in near real time has the potential to provide meaningful benefits in a variety of settings in which rapid access to information is critical.

“We designed PromethION to be able to prioritise time-to-result by using multiple flow cells together, just like cluster computing. We’re delighted to see the research team demonstrate the real life potential of Nanopore technology through their research. I look forward to seeing the impact of real-time sequencing technology in the clinic in the near future.”

Speed is of the essence

This new approach for rapid whole genome analysis using nanopore sequencing enabled insights from whole genome sequencing data to be gained within hours and not days or weeks, which could provide real benefits if applied in the clinic in the future. Further to this, nanopore sequencing enables a more comprehensive genetic picture to be built because of the technology's ability to generate very long reads, which can span large and complex disease-causing regions.

The Oxford Nanopore team worked with researchers at the Stanford School of Medicine to modify library preparation for optimum time efficiency and maximum yield. They also helped establish the framework for the cloud-based analysis and introduced a washing step that removed the need for barcoding, significantly reducing the cost per sample whilst retaining the rapid turnaround time.

These research findings point to the potential utility of validating a rapid whole genome sequencing platform for management of critically ill patients. This rapid whole genome sequencing approach was developed by a large group of contributors, including scientists from UCSC, Google and NVIDIA — who optimised and accelerated the small variant pipeline and cloud analysis — and Baylor College of Medicine, who contributed the structural variant pipeline.

Kimberly Powell, Vice President of Healthcare, NVIDIA commented:

“NVIDIA and Oxford Nanopore Technologies have a longstanding partnership in accelerating real-time genomic sequencing, and this project is a significant milestone in our journey.

“NVIDIA GPUs were instrumental in accelerating both base calling and variant calling with NVIDIA Clara Parabricks. Accurate, GPU-accelerated sequence analysis helped achieve this world record, which is monumental for quick identification of genetic variants linked to disease.”

Read the letter in the New England Journal of Medicine summarising this work

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DOI: 10.1056/NEJMc2112090

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