TIDMONT
Oxford Nanopore Technologies plc
13 January 2022
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.
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:
https://www.nejm.org/doi/full/10.1056/NEJMc2112090
DOI: 10.1056/NEJMc2112090
Oxford Nanopore Technologies, the Wheel icon, EPI2ME, Flongle,
GridION, Metrichor MinION, MinKNOW, PromethION, SmidgION, Ubik and
VolTRAX are registered trademarks of Oxford Nanopore Technologies
plc in various countries. All other brands and names contained are
the property of their respective owners. (c) 2021 Oxford Nanopore
Technologies plc. All rights reserved. Oxford Nanopore Technologies
products are not intended for use for health assessment or to
diagnose, treat, mitigate, cure, or prevent any disease or
condition.
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