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[bamboo2] 04/10/2023 08:18

mRNA vaccine technology wins 2023 Nobel Prize, highlighting importance of RNA research
Mon 2nd October 2023

On Monday, the 2023 Nobel Prize in Physiology or Medicine was awarded to Katalin Karikó and Drew Weissman for their contributions to the field of mRNA vaccines – pioneering work that underscores the increasingly popular field of RNA research.

Their work focused on discovery of the nucleoside base modifications that enabled the unprecedented development of effective mRNA vaccines against COVID-19. This prestigious recognition highlights the transformative potential impact of RNA biology, an emerging application area that Oxford Nanopore is uniquely positioned to help advance.

With nanopore sequencing, scientists can analyse native RNA of any fragment length - including full length isoforms - and electronically analyse RNA modifications ‘at the source’.

It has been exciting to see many scientists investigate the biological implications of this feature. For instance, BASE researchers at the University of Queensland are using nanopore sequencing to optimise vaccine performance, and to reduce the time needed to measure mRNA vaccine quality attributes. Oxford Nanopore takes great pride in its unmatched position at the forefront of this rapidly developing industry.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented: “Congratulations to Katalin Karikó and Drew Weissman for their remarkable achievement in advancing the field of mRNA vaccines. As we look to the future of vaccine development, RNA modification is an area of exciting potential and one the Oxford Nanopore scientific community is increasingly focused on. With the only technology currently available to accurately read native, full-length RNA, Oxford Nanopore is proud to be in a position to support research and development in this fast-moving space, helping unleash new potential for RNA-based therapies and vaccines.”

Libby Snell, Principal Scientist, Sample Technology, Oxford Nanopore Technologies, commented: “It is wonderful to see that the work of Katalin Karikó and Drew Weissman on RNA modifications has been recognised with such a highly deserved honour. We congratulate them for all their contributions leading to this achievement. This is undoubtedly a very exciting time for RNA science, especially within the field of RNA therapeutics and mRNA vaccines. We are excited to continue developing Oxford Nanopore’s unique ability to accurately read modified bases using long-read direct RNA sequencing – and support RNA research and biopharma manufacturing as these burgeoning fields advance.”



Further information:

Oxford Nanopore’s direct RNA sequencing kit (SQK-RNA004) is sensitive to a variety of RNA modifications and stands alone as the sole sequencing platform capable of accurately reading native full-length modified RNAs.

[bamboo2] 03/10/2023 07:44

Oracle Second-Generation Cloud Delivers Clinical Sequence Analysis in Under an Hour
September 13, 2023



Ruzhu Chen
Master Principal Cloud Architect

Dan Spellman
Director of AI/ML, Healthcare & Life Sciences (NACT)


Using its Second Generation cloud offering, Oracle Cloud Infrastructure (OCI) has reached new heights for Ultrarapid Nanopore Sequencing Analysis. This speed and compute performance is another delivery of Oracle’s support for fast and accurate genome analysis for healthcare and researchers, which can help save lives.

In 2022, NVIDIA released an Ultrarapid Nanopore Analysis Pipeline (UNAP) capable of running an Oxford Nanopore germline workflow for small and structural variants of a 55x coverage sample in just 4 hours and 10 minutes on an NVIDIA DGX A100. In collaboration with NVIDIA, Oracle Cloud engineering has deployed a new workflow featuring upgrades to both software and hardware, including replacing Guppy with the new Dorado basecaller, the latest NVIDIA Parabricks DeepVariant v1.5 and the latest NVIDIA H100 Tensor Core GPUs.

UNAP analysis was processed on an OCI computing environment containing a single node of eight H100 GPUs, each with 80GB memory. On OCI, the workflow benefits from bare-metal GPU compute, an industry-leading 61.44TB of included NVMe storage and time-to-market advantages OCI customers can realize with deep ongoing engagement from Oracle’s world-renowned engineering organization.

Record-setting benchmark results
Utilizing all eight NVIDIA H100 GPUs in a single node, Oracle completed the entire UNAP workflow — including basecalling and alignment as well as multiple variant calling — in just 57.44 minutes. This performance represents a 4.3x speedup compared to the previous workflow on DGX A100.

By combining industry-leading performance for genome analysis with OCI’s lower, simpler and more predictable pricing, Oracle can help organizations deliver better and faster genomic analysis -at a lower cost.

[bamboo2] 01/10/2023 13:27

Happy second birthday.

Capital Markets Day - 19th October 2023

Major convention in US early November 2023

Next NCM Boston 6 December 2023 [Replaces NY]

[bamboo2] 29/9/2023 07:27

Update from the Applications Team
From Singapore 2023 earlier this week

[bamboo2] 29/9/2023 07:01

R&D Update from Oxford Nanopore Technologies
From Singapore 2023 earlier this week

[minsky] 28/9/2023 17:54

is that a gap or a hairline fracture?

[bamboo2] 28/9/2023 17:50

Gap 200-201.6 dated 30/3/23 filled today.

[bamboo2] 27/9/2023 08:23

MinIon mk1 D is on show in Singapore.
Also T2T full human genomes sequenced using only ONT gear.
Tech update in progress. Should be a recording available later.

The event is so popular that for some of the sessions eg RNA, there is simply not enough room!
Search Twitter for #nanoporeconf

[eeza] 26/9/2023 19:38

Yes, the tech side is firing on all guns, all very encouraging, but the stock market side is in the toilet. AT sell bot hammered away all day long. Going sub 200p, imo.

Double-bottom around 190p?

[bamboo2] 26/9/2023 18:46

eeza, let's hope it picks up over the next few days.

Certainly on twitter Clive Brown has been making some interesting noises recently about new developments.

[eeza] 26/9/2023 16:46

Unfortunately, I averaged down Last week & yesterday - and no spare funds left available.

[bamboo2] 26/9/2023 16:41

eeza, 210 gone on the daily. Cest la vie. I will use the op to average down.
I have done quite a bit of this over the last few years!

Second birthday on Friday.
Just one more year to go before management are forced into a decision about dual structure.

ps, how much more Odey stock is there to work through??

[eeza] 26/9/2023 13:08

Not much resistance to gravitational pull, tho.

Down 10p and looking to test 200p.

[bamboo2] 26/9/2023 12:48

I am basing support on daily charts, I normally use eod closing price to determine busted support.

Valid point ont' intraday though!

[eeza] 26/9/2023 09:42

"210 support level nearby for those looking for a trade."


In the rear view mirror.

[bamboo2] 25/9/2023 20:57

Nanopore sequencing and DNA barcoding method gives hope of personalised medicine

by Hayley Dunning

25 September 2023



With the ability to map dozens of biomarkers at once, a new method could transform testing for conditions including heart disease and cancer.

Currently, many diseases are diagnosed from blood tests that look for one biomarker (such as a protein or other small molecule) or, at most, a couple of biomarkers of the same type.

The new method, developed by scientists at Imperial College London in a research collaboration with Oxford Nanopore Technologies (Oxford Nanopore), can analyse dozens of biomarkers of different types at the same time. This would potentially allow clinicians to gather more information about a patient's disease.

For example, current tests for heart failure look for a couple of common proteins to tell whether the condition is present. The new method was able to additionally detect 40 different types of miRNA molecules, which have the potential to be used as a new class of biomarkers. It can simultaneously examine proteins, small molecules like neurotransmitters, and miRNA from the same clinical sample, providing comprehensive data for a more precise diagnosis.

The results of using the new test in this way with the blood of healthy participants, for a proof-of-concept study, are published today in Nature Nanotechnology.

Co-first author Caroline Koch, from the Department of Chemistry at Imperial, said: "There are many different ways you can arrive at heart failure, but our test will hopefully provide a low-cost and rapid way to find this out and help guide treatment options. This kind of result is possible with less than a millilitre of blood. It's also a very adaptable method so that by changing the target biomarkers it could be used to detect the characteristics of diseases including cancer and neurodegenerative conditions."

Co-first author Ben Reilly-O'Donnell, from the National Heart and Lung Institute at Imperial, added: "The ability to monitor different types of molecules at the same time, in the same sample, offers a distinct advantage over traditional analysis methods."

DNA barcoding
The test works by mixing the blood sample with DNA 'barcodes'. These are small tags made of short DNA sequences, each encoding a unique probe designed to attach to a different biomarker. Once the sample and barcodes have been mixed, the resulting solution is injected into a low-cost handheld device previously developed by Oxford Nanopore – the MinION.

The Oxford Nanopore device holds a flow cell, containing an array of nanopores – very small holes – that are able to read the electrical signature from each DNA barcode that passes through them. The complex electrical signal the device produces is interpreted by a machine-learning algorithm to identify the type and concentration of each biomarker present in the sample.

The DNA barcodes used for each test can be made to order, specifically for the biomarkers that need to be analysed to characterise the disease being tested for. Using DNA barcodes also removes the need for complex and time-consuming sample preparation, which can also introduce sample bias.

Lead researcher Professor Joshua Edel, from the Department of Chemistry at Imperial, said: "Working with Oxford Nanopore Technologies, we have been able to take their existing platform and innovate how it can be used, with the addition of DNA barcodes and machine learning to understand the results."

Co-lead researcher Dr Alex Ivanov, also from the Department of Chemistry at Imperial, said: "In principle, we are close to enabling a technology being suitable for clinics, where, in the long run, we hope it could provide a wealth of individualised information for patients with a range of conditions."

Future directions
After showing that this method can successfully measure 40 miRNA molecules in healthy patient blood, the team are now working with clinical samples from heart failure patients to validate the results. Regular testing like this could also help clinicians establish their individual patient baselines for common blood biomarkers.

The method may be useful for speeding up diagnosis in two ways: as well as measuring more biomarkers at once, it can also help find new biomarkers. While currently only a handful of biomarkers are validated for diagnosing heart disease, by measuring 40 miRNA types of interest simultaneously, the team could also see which of these are relevant and could be validated with more testing.

[bamboo2] 25/9/2023 15:40

Bought some trading stock at 211.2

[bamboo2] 25/9/2023 09:54

210 support level nearby for those looking for a trade.

[p1nkfish] 24/9/2023 15:48

Thank you bb2.

[bamboo2] 24/9/2023 13:56

p1nk, with the advent of R10.4.1, the pore size/length has changed.

This enables all sorts of new features, as standard. eg accuracy above 99%, Read Until [real time data allows the user to stop sequencing the moment enough data is generated], Full Duplex etc

All new Flowcells come with the light shield as standard.

Market size will not increase imo, but this will help lead to further improvements in sequence quality, and therefore a broader acceptance of the tech.

High Duplex cells are now arriving at early access sites.

It is these that will mean at last we see ONT based reference genomes become much more common. At the moment ONT often provide a 'skeleton' reference, with detail added using Illumina.

[p1nkfish] 24/9/2023 13:25

Will these findings increase available market size?

If not, is there a way improved performance from using a light shield can be monetised, perhaps charging more for light shields?

[p1nkfish] 24/9/2023 12:59

Re-looked at it - and yes I am wrong and this is very interesting & potentially impactful.

Should have spent a little longer looking at the comparatives, benefit of light shield with the older R9.4.1 vs increased benefit with new R10.4.1. Appears substantial.

[p1nkfish] 24/9/2023 12:47

Lets hope so bb2.

The old flow cells also benefit from shielding from light, more pronounced on the new but the need for the shield is not new, nor the benefit of it. How sensitive the new is appears to be the shocker. Let's hope it results in a better accuracy than was expected or originally specified - that would be really good news.

My scepticism comes from seeing stuff go viral in the past for the benefit of a few savvy traders at the cost of the majority of the herd. It doesn't do most any good (nor the company concerned) unless info is based on truthful measurable benefit - TBD imho.

I want to be proven a miserable, stale b'stard.

What does bother me is the dismissing of Ox Nano by the deep pockets in NY that don't understand that the world doesn't revolve around the USA. Would love to see Pac Bio and Ilumina have their apple carts tipped over big time.

[bamboo2] 24/9/2023 08:48

p1nk, with respect, I think you are wrong to dismiss the light shade concept. The thread has gone from about 10 posts, to 50 overnight!

The effect is particularly strong on MinIon using the new R10.4.1 Flowcells.

These have only been on sale for a few months, so have only just made their way into general use, therefore it is new to the majority of users.

[p1nkfish] 24/9/2023 00:26

Below is on youtube, ONT mention about 33-35 mins in. Would love to see Ox Nano upset the applecart big time.

Global X analyst. Is she as up to date as she thinks she is?

"Big Data in Healthcare: Nvidia Set to Revolutionise MedTech’s Future? | Arelis Agosto"