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[bamboo2] 05/11/2024 16:41

New strategic partnership between UK Biobank, Genomics England, NHS England and Oxford Nanopore
05 Nov 2024

New strategic partnership between UK Biobank, Genomics England, NHS England and Oxford Nanopore designed to:
Advance biomedical research and translate discoveries for improved patient care

Improve health outcomes by targeting novel genomic and epigenomic discoveries in cancer, human genetic disease and infectious disease

Initial programme: to create an ‘early warning system’ for future pandemics across as many as 30 NHS sites, to support improved biosecurity nationwide

Oxford Nanopore’s high-performance genomics technology to provide richer genomic data, faster, more accessibly and more affordably.

Oxford Nanopore, the company delivering a new generation of nanopore-based molecular sensing technology, today announced a landmark strategic partnership with the UK Government. This partnership brings together the UK’s world-class scientific organisations Genomics England, UK Biobank and NHS England, alongside Oxford Nanopore, to support the government’s vision to build an NHS “fit for the future" by enabling genomics-based translational research and accelerating the development and adoption of Oxford Nanopore’s ground-breaking genomics technology in the NHS.

By utilising Oxford Nanopore’s richer genomic insights, rapid, scalable and affordable sequencing technology, the initiative aims to deliver transformative improvements in patient care and foster economic growth in the UK’s thriving life sciences sector.

Oxford Nanopore CEO Gordon Sanghera, commented:

“The UK has a remarkable genomics ecosystem, and we are delighted to be innovating more collaboratively through this partnership. Genomics England and UK Biobank have led the way in scaling genomics discovery and translating these advances into patient impact. NHS England, through its Networks of Excellence and advancements developed by the Genomic Laboratory Hubs (GLHs), has been instrumental in adopting these innovations into national healthcare strategies. By working alongside our partners on shared goals of improved patient outcomes - whether in cancer, human genetic disease or infectious disease - we believe we can deploy our unique DNA/RNA sequencing technology in ways that are most impactful for the people of the UK.”

Health and Social Care Secretary Wes Streeting, commented:

“If we fail to prepare, we should prepare to fail. Our NHS was already on its knees when the pandemic struck, and it was hit harder than any other comparable healthcare system.

“We cannot let history repeat itself. That’s why this historic partnership with Oxford Nanopore will ensure our world-leading scientists have the latest information on emerging threats at their fingertips.

“As we embrace the technological revolution, our 10 Year Health Plan will shift the NHS away from analogue to digital, saving countless more lives.”

Science and Technology Secretary Peter Kyle, commented:

“During the Covid pandemic we saw the power of the UK life sciences sector very clearly – from the Oxford-Astra Zeneca vaccine that saved so many lives, through to operating one of the world’s most effective Covid surveillance systems, which spotted several emerging variants of the disease.

“This partnership will build on that expertise to monitor emerging diseases as they arise, putting our scientists and decision-makers one-step ahead and providing the information they need to make informed decisions.

“Together with the ability to better diagnose cancers and rare diseases, we are leveraging UK life sciences to protect the public and ultimately save lives.”

Professor Susan Hopkins, Chief Medical Advisor at UK Health Security Agency, commented:

“Early detection is absolutely crucial in enabling us to respond effectively to any emerging pathogen. The UK already has a wealth of expertise in genomic surveillance, and this programme will build on that expertise and enable us to bring our resources and capability to tackle developing threats at greater speed. Enhancing the capacity for the NHS to determine new and emerging pathogens causing severe acute respiratory infections will improve the detection and emergence of infections.

“As part of the 100 days mission, this will enable the development of effective diagnostics for novel pathogens and enhance our pandemic preparedness.”

Professor Ian Abbs, Chief Executive of Guy’s and St Thomas’ NHS Foundation Trust, commented:

“We’ve been working on the respiratory metagenomics programme for over four years and have clearly seen the benefit to our patients. It’s a momentous day now that we can ensure other hospitals, and more patients, can also benefit from faster and more accurate treatment for severe respiratory conditions thanks to new genomic technology.”

Advancing the understanding of genomics, for future disease prevention and personalised medicine
Oxford Nanopore’s partnership with Genomics England and UK Biobank is aimed at translating research-based discoveries from the lab into clinical settings, benefiting UK healthcare. Priority areas include cancer, where genomic insights (the analysis of DNA) can help identify personalised treatment options and enhance early detection, and rare disease characterisation, where information-rich genomic and epigenetic analysis – changes to DNA that contribute to disease – can improve diagnosis and inform targeted therapies. This partnership presents a further opportunity to collaborate on broader emerging applications, which in the future could include newborn screening, where genomics can enable early identification of genetic disorders for prompt intervention, and pharmacogenomics, where genetic insights guide safer and more effective medication choices tailored to an individual's genetic profile.

Creating a world-first pathogen surveillance system in the NHS
As a key part of the partnership, the UK will establish the first real-time, pathogen-agnostic biosurveillance system across as many as 30 hospitals in NHS England—a crucial early warning framework to detect and respond to emerging pandemics and biological threats. Building on successful NHS England Network of Excellence pilots led by Guy’s and St Thomas’ NHS Foundation Trust (GSTT), this system will expand the NHS Respiratory Metagenomics programme to enable rapid pathogen identification across the UK. This data will be provided by the NHS to the UK Health and Security Agency, allowing potentially quicker decisions on emerging diseases to be taken and bolstering national biosecurity as set forth in the UK Biological Security Strategy. This project is expected to start in 2025 and will continue over multiple years.

In addition to providing biosecurity capabilities, the expanded respiratory metagenomics programme will deploy Oxford Nanopore’s sequencing technology to support infectious disease management in the critical care setting. This rollout is designed to provide a groundbreaking, six-hour timeline for fully characterising respiratory diseases including drug (antimicrobial) resistance, an essential leap forward in patient care. By rapidly transitioning NHS diagnostics from analogue to digital, the programme’s goal is to enable quicker, targeted care for patients and reduce hospital strain, advancing the ambitions set out in the Government’s 10-Year Health Plan.

Translating genomics into enhanced NHS patient care
The integration of Oxford Nanopore’s innovative sequencing technology will enable the NHS to explore further this technology to characterise diseases including cancer and rare genetic conditions with greater speed and precision. With potential for collaborative development of rapid and improved diagnostic tools, Oxford Nanopore’s technology has the potential to enable patients across the NHS to benefit from earlier, more accurate disease detection and treatment pathways.

Driving economic growth and workforce development in life sciences
This work will not only enhance patient outcomes but also position the UK as a global leader in genomic research and innovation, further strengthening the nation’s biosecurity and healthcare resilience. By accelerating pathways for life sciences innovation into the NHS through globally recognised research programmes, this collaboration enhances the UK’s position as a global biotechnology hub, supporting economic growth and creating high-value jobs in the life sciences ecosystem. As part of this initiative, NHS staff and researchers will gain access to relevant training and support to advance a skilled workforce ready to harness the potential of genomics and personalised medicine.

[p1nkfish] 05/11/2024 13:06

Have a listen to founder podcast on Oracle and Ellison. Some background on personality etc.

More than one episode.

[trickydicky1] 05/11/2024 10:41

Not sure on ILMN.

I thought consumables were well ahead of expectations with an ongoing sharp shift to NovaSeqX+ on the back of clinical adoption which surely bodes well for us? Suspect the woke workforce has been carted out? Big falls in S&M & SG&A expenses => EPS well ahead of expectations.

Can't see them remaining independent much longer (ILMN that is).

[takeiteasy] 05/11/2024 08:53

On another topic, almost nothing to report back over the Illumina results last night - they did not have that much to say tbh.

[cousinit] 05/11/2024 08:35

I would have thought that if the holdings positions were combined that the chain of ownership would also need to show the Oracle holding. This makes me suspect that they are separate and combine to 9%. But I do see the need to treat these announcements with a dose of scepticism!

There seem to be quite a few core positions building again which might mean stock isn't particularly loose for when the FTSE index inclusion should arrive next month.

[bamboo2] 05/11/2024 07:45

TD1, having checked it does seem that way. Well spotted.

We are talking about...

TR-1 09-Aug-2024 Oracle Corporation 3.75%
TR-1 04-Nov-2024 EIT Oxford Holdings, LLC 5.3046%

I had assumed they were effectively the same holder. ie a concert party?

Perhaps this possible Party holding be recognised if both exceed the foreign holdings minimum notifiable threshold of 5%?

[trickydicky1] 04/11/2024 21:47

If the TR-1s are accurate and the assumptions of both Delphi/Oracle and EIT/Ellison being “controlled221; by Ellison, then yes.

I suppose there may be some who may argue that he doesn’t ‘control’; Delphi/Oracle.

[bamboo2] 04/11/2024 18:39

TD1, for something that ought to be relatively straight forward, these TR-1 holdings notices are notoriously difficult to read.

Are you sure Ellison is controlling 9%?

[trickydicky1] 04/11/2024 09:19

Sorry, Larry Ellison moves to 9% (5% via EIT and 4% via Oracle/Delphi) and no-one cares? What am I missing here?

Like, he's only far more influential than the usual names, Zuck, Bezos, etc. But just a bit quieter.

[bamboo2] 03/11/2024 09:52

National Geographic covers the clinical use of ONT in the operating room, identifying brain tumours in real time using nanopore sequencing.

[bamboo2] 02/11/2024 10:17

Wasatch BioLabs and Oxford Nanopore Team Up to Accelerate Methylation Sequencing Towards Clinical Use

News provided by Wasatch BioLabs
Nov 01, 2024, 14:45 ET


SALT LAKE CITY and OXFORD, United Kingdom, Nov. 1, 2024 /PRNewswire/ -- Wasatch Biolabs (WBL), a disruptive R&D and high-throughput clinical laboratory, today announced a collaboration with Oxford Nanopore Technologies (ONT), the company delivering a new generation of nanopore-based molecular sensing technology, to develop a Direct Whole Methylome Sequencing product that addresses key limitations associated with traditional bisulfite sequencing and methylation microarrays.

WBL develops proprietary methylation and genomic assays for mass-market research and customized clinical applications incorporating Oxford Nanopore's rich genomic insights and rapid, accessible, and affordable sequencing technology. This collaboration is designed to build on Wasatch BioLab's existing proprietary methylation assays and create market-leading offers to drive innovation in genomic and epigenomic analysis, accelerating breakthroughs in research and clinical applications.

"Through this collaboration, we are utilizing Oxford Nanopore's industry-leading sequencing technology and additional technological expertise to accelerate product development and bring groundbreaking innovations to market faster," said Chad Pollard, CEO and Co-Founder of Wasatch BioLabs. "These products are poised to redefine the standard for epigenetic research and revolutionize the field."

New Product Announcement: Direct Whole Methylome Sequencing

Following Wasatch BioLabs' recent release of a cell-free whole genome methylation sequencing assay that significantly improves sensitivity and data quality in assays targeting highly fragmented cfDNA, WBL is excited to announce their latest product: Direct Whole Methylome Sequencing (dWMS). This innovative technology addresses key limitations of traditional methods, such as bisulfite sequencing and methylation microarrays.

By eliminating DNA damage from harsh chemical treatments, sequencing biases from PCR amplification, batch effects, and restricted genomic coverage, dWMS offers comprehensive genome-wide coverage, capturing up to 98% of the 28.1 million CpG methylation sites in the human genome. It delivers precise single-molecule resolution and enables the simultaneous detection of DNA sequence, methylation, and hydroxymethylation patterns.

"We're excited to work closely with the Wasatch BioLabs team to help facilitate a paradigm shift in methylation research," said Kathleen Barnes, SVP of Population Health and Precision Medicine at ONT. "Together we will co-develop products that will replace conventional technologies such as sequencing arrays and bisulfite sequencing and reshape how methylation is incorporated into clinical research and diagnostics."

ASHG 2024 Speaking Event Announcement

From Arrays to Sequencing: Enhancing Methylation Analysis for Biomarker Discovery and Clinical Applications

WBL will discuss this product and other key developments in a joint WBL and Oxford Nanopore CoLab session at the upcoming American Society of Human Genetics (ASHG) Annual Meeting, held November 6th-8th in Denver, CO. The presentation will unveil key product details, including more robust details of MethylSeqR, a proprietary analysis package designed to provide researchers with the tools to perform complex analyses on robust native-read DNA output in minutes.

Date and time: Nov 6th at 12pm MT
Location: Colab: Theater #1

About Wasatch BioLabs
Wasatch BioLabs (WBL) is a leading R&D laboratory and next-generation sequencing service provider dedicated to advancing scientific discovery and clinical epigenomics. Headquartered in Utah, WBL specializes in developing innovative methylation-based technologies and delivering custom assays built for scalability, precision, and impactful results. WBL's offerings empower researchers and other clients with unprecedented insights into the genome. With a focus on collaboration, adaptability, and excellence, Wasatch BioLabs is a trusted partner for academic, biotech, and pharmaceutical industries worldwide. To learn more, visit www.wasatchbiolabs.com.

[bamboo2] 30/10/2024 20:29

The world is changing rapidly, and with it, our understanding of the molecular building blocks of life. Apple's recent announcement at their "Scary Fast" event introduced the power and speed of M3 silicon chips, and spotlighted Oxford Nanopore DNA/RNA sequencing devices as a companion technology that naturally partners with the new Macbook Pro™ and iMac™, enabling anyone anywhere to quickly uncover new insights about living systems.



Vid

[bamboo2] 23/10/2024 19:18

Nottingham leads the way with Nanopore: DNA sequencing technology.

A team spanning neuropathologists, scientists, neurosurgeons and researchers at Nottingham University Hospitals NHS Trust (NUH), the University of Nottingham and colleagues in Germany is developing a nanopore sequencing-based approach that has the potential to transform the diagnosis of tumours.

The Nanopore sequencer, in use as a research tool at present, enables a radical new pathway where brain tumours can be diagnosed within just two hours of a biopsy being taken from a patient.

Dr Simon Paine, Consultant Neuropathologist at NUH, and one of the team developing this technology, explains about the potential of this research breakthrough, and the work underway to get this approach into clinical practice in future.

[bamboo2] 21/10/2024 10:12

Results from new benchmarking of ONT's R10.4.1 MinION flow cells better than Illumina.

This study presents a comprehensive benchmarking of variant calling accuracy in bacterial genomes using Oxford Nanopore Technologies (ONT) sequencing data. We evaluated three ONT basecalling models and both simplex (single-strand) and duplex (dual-strand) read types across 14 diverse bacterial species. Our findings reveal that deep learning-based variant callers, particularly Clair3 and DeepVariant, significantly outperform traditional methods and even exceed the accuracy of Illumina sequencing, especially when applied to ONT’s super-high accuracy model. ONT’s superior performance is attributed to its ability to overcome Illumina’s errors, which often arise from difficulties in aligning reads in repetitive and variant-dense genomic regions.

[bamboo2] 16/10/2024 11:11

Precision genomics: the future of food safety.
[Layman accessible]

FDA adopting GridION for genomic sequencing needs.

[brucie5] 16/10/2024 07:44

I think your knowledge here is far above mine.
;)

[bamboo2] 15/10/2024 19:07

Tricky/Bruce, I have only just had time to have a quick look.
Oracle have ended up with quite a few more shares.

At their last holding TR-1 they reduced their holding.

20 Aug 2024 "TR-1 Oracle, aka Larry Ellison etc

Reducing from 3.75% [35,294,117] to 3.004100% [28,265,044]"

===================================

Now holding 4.200100% [39,542,200]

They added 11,277,156 shares.

===================================

I'm always grateful for others to check maths and facts. Let me know if you think this is incorrect.
[edited for clarity]

[brucie5] 15/10/2024 12:52

Looks like it. But I'm sure Bamboo will advise.

[trickydicky1] 15/10/2024 08:34

Have Oracle just increased their position by 5m shares from the LTIP vesting tap?

[p1nkfish] 12/10/2024 20:00

ILMN has also been interesting on the weekly at 52wk high and interest shown.

[bamboo2] 12/10/2024 13:45

takeiteasy, I find it hard to believe this individual contract is alone responsible for a 20%+ rise in the PACB share price They are in a fairly dire financial position. More likely t/o speculation might cause the rise.

[takeiteasy] 12/10/2024 12:45

PACB up 27pc late last week - their share price analyst target is many times the current share price showing just how much the sector fell out favourWould ONT have been competing against PACB for the contract PACB announced that got the share price response?nai etc

[bamboo2] 11/10/2024 07:48

09 October 2024
20 years of Nature Methods: how some papers shaped science and careers



Section 7 Direct to RNA with nanopores

DNA is quite hardy, so if it’s left out on a bench, it can still be analyzed. RNA, on the other hand, is best kept in a minus –80 °C freezer, says Libby Snell, an RNA biologist at Oxford Nanopore Technologies (ONT). RNases that degrade RNA are everywhere, and thus, when working with RNA, “you have to be very meticulous,” says Snell, who co-developed direct nanopore-based RNA sequencing (RNA-seq)12. A peek at ONT’s RNA lab reveals how fastidious Snell’s team is about clean surfaces and pipettes. RNA has long held her interest, given how it informs on events in a cell or organism. ONT application scientist Daniel Garalde, the paper’s first author, calls the work “one of the highlights of my career.”

RNA sequencing long involved a proxy: analysis of cDNA, which requires an extra step of reverse transcribing RNAs into complementary DNA sequences. This changed with the advent of direct RNA sequencing using nanopore sequencer arrays, developed at ONT. Snell enjoys seeing the many ways the method is being used. Its potential reaches to RNA modification analysis and perhaps mRNA vaccine quality control.

“I’m really proud of it and I have a framed copy of the Nature Methods cover on my wall,” says Daniel Turner.

Daniel Turner, the paper’s last author, used to be at ONT and is now chief scientific officer at Cambridge, UK–based Enhanc3D Genomics. The idea of direct RNA sequencing was, he says, ambitious and challenging. The direct RNA-sequencing project helped to shape his career. Moreover, he says, “it’s not easy to figure out the potential value of something that just doesn’t exist,” and he appreciates how the company had “faith in the vision.” Turner says of the paper12, “I’m really proud of it and I have a framed copy of the Nature Methods cover on my wall.”

Garalde, who co-developed direct nanopore RNA sequencing, now works in ONT’s business division in California with a focus on emerging techniques. He had joined ONT with a background in computer engineering from the University of California, Santa Cruz. He considered a postdoctoral fellowship with Hagan Bayley at the University of Oxford, one of ONT’s founders, but decided to join the company instead.

In nanopore sequencing, a polynucleotide moves through a nanopore that spans a membrane in a volume of salt buffer. The readout is an electrical signal that provides information about what just traveled through the nanopore. Software converts the signal to a base sequence. Working on RNA meant re-engineering much of the technology used to sequence DNA, says Garalde.

The voltage that runs across the nanopore accelerates the passage of DNA through the nanopore. Garalde and his colleagues worked on ways to slow this down, but the helicases that work with DNA didn’t work with RNA. They needed to get an RNA signal readout in the sensors. After Garalde left for California, Snell led next versions of the direct RNA sequencing chemistry up to the latest release. “It’s just tremendously better,” Garalde says.

The team developed the method’s aspects in parallel, says Turner. For library prep, they worked on affixing adapters to RNA so that the nanopores would process it; they needed to assure RNA didn’t degrade in the flow cell; the right motor protein had to control the speed with which RNA passes through the nanopore; and they sought a signal readout and software for base-calling. The sequencers were not as accurate and fast as they are today, he says, but the sequencing hardware itself—the MinION sequencer—existed.

In Snell’s academic training at the Universities of Oxford and Reading, she used cDNA sequencing to study ancient cell lineages and the relatedness of organisms in the eukaryotic tree of life. She was intrigued about working in industry when she came across ONT, then a startup. Its long-read DNA sequencing promised to avoid needing to put together genome assemblies piecemeal from short DNA sequences. She also knew that it would be good to avoid the use of reverse transcriptases and polymerases to make cDNA, which can bias sequencing. Among the challenges with RNA, says Snell, were finding ways to keep RNA molecules intact.

The work on direct RNA sequencing began around 2013 and the paper was published in 2018. At the time, it was not yet clear how scientists might apply the method but, says Snell, “I was always super excited by it,” she says. Projects like her academic ones would benefit greatly from such a capability.

The team hoped the same motor protein that threads the DNA molecule through the nanopore would work for RNA. But a DNA-specific motor protein disengages from RNA, she says. After screening a variety of motor proteins, they decided on a motor protein called M1. The one they now use, M2, is RNA specific, says Snell. It does not work on DNA, just as the DNA one does not work for RNA. They explored pore modifications, too. They would set up flow cells and then wait. “Sometimes it would work and sometimes it wouldn’t,” she says. They decided to not only work with RNA-specific motor proteins but also thread RNA not from the 5′ to the 3′ end—as with DNA—but from the 3′ to the 5′ end. “That just sort of cracked it all open at that point,” she says. The motor still needed an adaptor, but this shift simplified sample prep and made it easier to get signals to train a base caller that would read out the sequence.

Turner enjoys the fact that no other technology can sequence RNA directly and that a cDNA step is no longer needed with nanopore sequencing. One “gets so much closer to the action,” he says: actual RNA strands from the organism touch the nanopores during sequencing.

Currently, says Snell, the nanopore sequencers read RNA at 120 nucleotides per second with a pore optimized for RNA and the RNA-specific motor protein. “We’re at about 98.8% accuracy.” When training researchers, she relishes how excited they are to sequence RNA directly. It’s normal to her, but “it’s still pretty amazing, right?”