RCS - Oxford Nanopore Tech - ONT releases Remora:most comprehensive methylation

Oxford Nanopore TechnologiesAnnouncement

26/05/2022 07:00

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RNS Number : 8443M  Oxford Nanopore Technologies plc  26 May 2022

Oxford Nanopore integrates "Remora": a tool to enable real-time, high-accuracy
epigenetic insights with nanopore sequencing software MinKNOW

Oxford Nanopore has today released Remora, a high-performance tool for
methylation analysis, into its operating software, MinKNOW, broadening access
to direct, PCR-free nanopore sequencing that captures methylation across the
whole genome.

From today, Oxford Nanopore users have easy access to precise whole genome
methylation detection from PCR-free nanopore sequencing using Remora. By
integrating Remora into MinKNOW the analysis of epigenetic modifications
becomes seamless as it now runs in parallel to standard basecalling. This
release complements the simplicity of native DNA sample preparation, which can
be done in just 10 minutes using the same run, so at no additional cost.
Nanopore sequencing is now the most comprehensive technology for
characterising  methylation, with the first releases aimed at targeting all
CpG areas.

Native sequencing for greater epigenetic insight

Methylation detection has traditionally been dominated by using bisulphite
treatment with short-read sequencing. Whilst this method has opened up the
discovery of methylation sites, it also has limitations, increasing the cost
and complexity of sequencing, owing to the requirement to repeat the run for
essential comparison. Bisulphite cannot easily differentiate between
methylation types such as 5mC/5hmC, or indeed add the detection of other
modification types such as 6mA.

The Oxford Nanopore solution for detecting CpG methylation provides a number
of advantages. No additional, complex sample preparation is required and
epigenetic modification analysis can be performed across the whole genome
during the experiment. Therefore, no additional toxic chemistry is needed, and
the phasing of base modifications is put in genomic context with the ability
to sequence long fragments of DNA. Nanopore technology enables
base-modification analysis to be performed alongside nucleotide sequencing on
a single read basis, so without the need to repeat the run.

Remora models demonstrate improved performance from a significantly simplified
machine learning training process and they improve signal scaling which
results in higher detection accuracy and quality filtered calls achieving
99.8% accuracy for 5mC in CpG contexts. This means that Remora delivers
industry-leading methylation detection accuracy from a single read and
provides biological insight into eukaryotic samples at only 20X coverage.
Nanopore sequencing opens up the possibility of looking at methylation
directly on individual DNA molecules, therefore representing how the DNA
strands were in the cell, potentially the best and "most true" way of looking
at DNA.

Marcus Stoiber, Senior Data Analyst, Oxford Nanopore commented:

"Detection of methylation from raw nanopore signal is an incredible strength
of nanopore technology, but it has long been a cumbersome task to extract this
information at the highest accuracy. Remora changes this and delivers
epigenetic modifications at the same time as the highest accuracy canonical
basecalls. As part of the team who developed Remora, we are delighted that it
is now fully integrated and accessible to all Nanopore users and we're very
excited see how the research community puts it to work in their groundbreaking
research efforts."

Nanopore sequencing provides one platform for all your biology

These new tools will enable users to choose to sequence short fragments of DNA
and perform methylation analysis of those fragments in real time for greater
insights. DNA methylation is a process by which a methyl group is added to the
DNA molecule, thereby modifying its behaviour but not altering the sequence.
This modification of the DNA and its genetic expression is studied in
epigenetics. The greater epigenetic insight that methylation analysis reveals
is enabling discoveries across a breadth of genomic applications. Here are two
examples from the Nanopore community; for further examples please visit the
Resource Centre on at nanoporetech.com:

Ian Henderson, University of Cambridge, and his research group investigated
Arabidopsis thaliana (a small flowering plant) centromeres and found a
'striking suppression of recombination around the centromere, as well as
enrichment of epigenetic marks, like DNA methylation'. This was remarkable as
it's only been since the advent of long-read sequencing that the centromeres
can be studied in detail; previously, these regions have been too repetitive
to sequence using short-read sequencing. Full presentation here
(https://nanoporetech.com/resource-centre/video/ncm21/the-genetic-and-epigenetic-landscape-of-the-arabidopsis-centromeres)
.

Luna Djirackor, Oslo University Hospital, used nanopore analysis to show the
future potential to classify brain tumours using methylation in as little as
91 minutes - quick enough for results to be returned to the operating table
during brain surgery. Strikingly, in 60% of the samples sequenced in the
study, the information obtained would have altered the pre-planned surgical
strategy, demonstrating how this approach has the potential to significantly
improve surgical outcomes in future. Full presentation here
(https://nanoporetech.com/resource-centre/video/lc21/intraoperative-dna-methylation-classification-of-brain-tumors-impacts-neurosurgical-strategy)
.

Remora can be accessed here (https://community.nanoporetech.com/downloads) and
a dataset is available in EPI2ME labs for users to download here
(https://labs.epi2me.io/gm24385-5mc-remora) .

-end-

 

Further information from Marcus Stoiber, Senior Data Analyst, Oxford Nanopore
Technologies:
https://nanoporetech.com/resource-centre/video/ncm21/nanopore-methylation-better-way-mods

 

Direct DNA and RNA sequencing for methylation analysis with nanopore
sequencing (animation):
https://www.youtube.com/watch?v=7PraIiiN_Gc&list=PLxpxXZj-IgXyR0it4QjoBETC5JeEanW-o&index=17
(https://www.youtube.com/watch?v=7PraIiiN_Gc&list=PLxpxXZj-IgXyR0it4QjoBETC5JeEanW-o&index=17)

About Oxford Nanopore Technologies

Oxford Nanopore Technologies' goal is to bring the widest benefits to society through enabling the analysis of anything, by anyone, anywhere. The company has developed a new generation of nanopore-based sensing technology for real-time, high-performance, accessible and scalable analysis of DNA and RNA. The technology is used in more than 120 countries to understand the biology of humans and diseases such as cancer, plants, animals, bacteria, viruses and whole environments.

 

 

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