Oxford Nanopore Technolo... Share Discussion Threads

[papillon] 29/11/2023 20:40

Why the big drop in the share price since it listed just over 2 years ago, bamboo2?

advfn give the Mkt Cap as £1.65 billion. Is that correct?

[bamboo2] 29/11/2023 16:19

Oxford Nanopore and WeNou announce a partnership to develop and commercialise the first rapid and portable food authenticity sequencing test to detect food fraud
Wed 29th November 2023

Oxford Nanopore’s sequencing devices and kits with WeNou’s expertise will be used to develop a validated food authenticity workflow to meet industry standards

Oxford Nanopore Technologies (Oxford Nanopore) and WeNou, a company providing innovative services based on DNA analysis for the food and feed sectors, today announce a collaboration that will bring to market the first industry-accepted, simple and rapid test using nanopore sequencing to accurately determine critical adulterants and composition of food samples. Using an ‘untargeted’ approach, the collaboration will result in a single DNA sequencing-based analysis for identification of multiple species in a sample that is more cost effective and faster compared to current methods.

With fraud accounting for 5 - 25% of all globally reported food safety incidentsi, food manufacturers and retailers typically perform spot-tests on their raw materials to verify the safety of their food products. However, current analytical methods for spot-testing either require multiple targeted tests and/or large capital investment for testing. This partnership aims to develop and commercialise a validated, fit-for-purpose test using Oxford Nanopore-based sequencing to identify multiple species present in different food sample types, including unprocessed, highly processed or complex.

As experts in food authenticity testing with a track record for innovation, WeNou compared nanopore sequencing with the traditional sequencing workflow commonly used in the food industry. This preliminary work showed equivalent and highly reproducible results. In addition, turnaround time was faster when used for meat and fish identification across multiple retail food samples including canned, fresh, frozen and other. The portability of nanopore sequencing created efficiencies through more decentralised sample testing.

The collaboration will expand on the preliminary study by optimising the workflow using the latest sequencing chemistry from Oxford Nanopore. In addition, the ability to identify shellfish, plants, and insects from highly processed and complex food samples will be assessed in the collaboration. After validation, the test will be suitable for service providers to obtain industry accreditation to assess food and feed authenticity.

Sandra Chaves, CEO, WeNou, commented:

“We are thrilled to reach agreement with Oxford Nanopore on this collaboration to provide access to the latest technologies suitable for highly reliable testing services to the food and feed sectors. The features of the platform will allow WeNou to offer cost effective, rapid turnaround species identification testing for authenticity assessment. I’ve been working in this area for a long time and there is no existing product that addresses increasing demand for this type of cutting-edge solution. Through this collaboration, we will be able to validate a test that will meet the industry’s expectations and needs. Although there are currently no established guidelines in this sector, those guidelines are coming, and we believe this solution has the potential to support better regulation in this field.”

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“We’re delighted to partner with WeNou to develop the first rapid and portable food authenticity sequencing test. Combining Oxford Nanopore technology with WeNou’s expertise, this collaboration will result in the sector’s first single test for the identification of multiple species in one food sample, detecting food fraud using a method that's more cost effective and faster compared to current time-consuming tests.”

[bamboo2] 27/11/2023 19:32

TraxIon

This is a "Sample-to-answer" device
The closest thing yet to a real Tricorder.

[bamboo2] 24/11/2023 16:18

Oxford Nanopore - Futures of Genomics

New introductions from existing clients.

[bamboo2] 24/11/2023 16:05

If you have been following 'nanopore' on Twitter over the past six months you can't help but notice the number of photo's of jam-packed rooms and halls around the globe holding seminars, workshops, teach-ins, meetings, and events.

These are typically hosted for scientists and clinicians etc, by ONT, our partners, Universities, labs and hospitals etc. They are dedicated to broadening the knowledge base for users and would be customers. 2023 reaches a climax with a number of US based conferences over the next three weeks. More details to follow.

[bamboo2] 24/11/2023 15:03

A new, mostly layman accessible blog from ONT.

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Blog: A new benchmark: discussing telomere-to-telomere assemblies with the founder of GrandOmics
Fri 24th November 2023

Wonder (Depeng Wang) is the founder and CEO of GrandOmics, a leading sequencing provider in China. Read on to discover more about their pioneering work on telomere-to-telomere (T2T) assemblies, why they are using nanopore sequencing to resolve complex regions, and how GrandOmics are supporting academics to achieve their research goals...

[bamboo2] 23/11/2023 11:30

eeza, hi, needs eod close above yesterdays close to confirm the turn. [upwards, I hope]

Agree it doesn't look good a the mo. Shorts have control as not enough buyers.

[eeza] 23/11/2023 10:45

"Chart tells me we are turning today."

Looks to be downwards.

[bamboo2] 22/11/2023 21:17

Chart tells me we are turning today.

[bamboo2] 22/11/2023 20:13

For info HLA is tissue testing to check a good match between donor and patient.

Illumina currently takes a minimum of 36-48 hours to provide results.
ONT takes 20-60 minutes. Needless to say, donor material has a finite shelf life and needs to be transplanted asap.
Another thing against using Illumina for this purpose is the fact that processes must be batched in order to make them economic.

Approval timelines suggest that this clinical use will be commercially available in Q1 2024

Afaik HLA tissue typing is already in use on ONT kit by NHSBT in London

[bamboo2] 22/11/2023 20:08

MDx Firms Bet on Nanopore Sequencing for HLA Transplant Diagnostic Tests
Nov 22, 2023 | Huanjia Zhang

NEW YORK – As nanopore sequencing continues to advance into the clinic, next-generation sequencing assay makers are starting to harness the technology to develop transplant diagnostic products that promise to have a fast turnaround and are cost-effective.

Last month, Hungarian molecular diagnostics firm Omixon released a new single-locus human leukocyte antigen (HLA) typing kit called NanoType Mono that uses nanopore sequencing. Meanwhile, Dutch company GenDx, which is part of Eurobio Scientific, launched NGS-Turbo, an assay also designed for high-resolution HLA typing using Oxford Nanopore Technologies platforms.

While the new assays are currently for research use only (RUO), both Omixon and GenDx said they are working to obtain regulatory approval for their clinical use under the EU’s In Vitro Diagnostic Regulation (IVDR).

Encoding proteins that play a significant role in the immune response, the HLA system "is the most diverse set of genes in the human genomes," said Omixon Founder and CEO Attila Berces. "It has a very diverse set of polymorphisms, and it has specific challenges, both for the wet lab as well as for the bioinformatics."

Previously, the company developed short-read sequencing-based HLA typing products using the Illumina platform, based on technologies licensed from Children's Hospital of Philadelphia. While Illumina sequencing has improved the resolution of HLA typing in recent years compared with other molecular techniques, such as Sanger sequencing and PCR, turnaround time and cost still remain a challenge for certain users, Berces noted.

To that end, nanopore sequencing has "tremendous benefits" for HLA typing, said Omixon VP of Product Innovation Gregory Werner. In addition to low upfront instrument costs, the long reads allow for HLA genes to be sequenced in full, leading to better phasing and typing with higher resolution.

Moreover, the real-time sequencing capability of nanopore sequencing can lead to a faster turnaround time of just hours, Werner said, which can be crucial for rapid HLA typing of organ donors in time-sensitive cases. In contrast, an HLA typing test on an Illumina platform typically runs more than a day, he noted.

Omixon first launched its nanopore sequencing-based HLA typing assay in September of 2022. Named NanoType, the kit is compatible with blood DNA samples and can amplify all 11 HLA loci — HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1, HLA-DRB1, HLA-DRB3, HLA-DRB4, and HLA-DRB5 — in a single tube using long-range multiplex PCR before nanopore sequencing.

According to Omixon’s website, customers using NanoType have the option to run up to 12 samples at a time. In that case, the turnaround time, from sample to result, is 16 hours, including less than five hours on the nanopore sequencer and about two hours of hands-on sample prep time.

Alternatively, users can use NanoType for single-sample urgent typing, which promises to deliver results in about five hours, including less than four hours for sequencing and a 50-minute hands-on prep time.

The difference between NanoType and the more recently launched NanoType Mono products is that the latter allows labs to perform HLA typing on an individual gene locus as needed, Berces said. The starter kit of this product line, dubbed NanoType Monoall, includes separate tubes for each of the 11 HLA loci and is configured to accommodate 24 samples. Meanwhile, customers can also purchase NanoType Mono kits, configured for 24 or 96 samples, for individual gene families.

According to Omixon, when running 24 samples on the HLA-B NanoType Mono kit, the turnaround time from sample to results is about six hours, including an hour of hands-on time. Additionally, Werner said, the long-read data is analyzed using the company’s proprietary NanoTyper software, which specifically caters to nanopore-based typing.

Given the RUO status of the company’s kits, they are currently only marketed for research applications. However, Werner noted that the company has submitted an application for the NanoType kit in July for clinical clearance in the EU and is "on the fast track" with the notified body to obtain CE-IVD marking under the IVDR.

The long-term goal of the company is to transition from the Illumina sequencing-based kit, which is named Holotype HLA and has been CE-IVD marked in Europe, to the nanopore sequencing products, Berces said.

Additionally, clinical labs in the US have the possibility to develop and validate their own laboratory-developed tests (LDTs) using the NanoType kits, he said. Omixon currently has no plans to seek FDA approval, he noted, though it is "always thinking about it."

"Proper characterization of the [HLA] genes is challenging, and next-generation sequencing platforms have proven particularly helpful to this challenge," said Dimitri Monos, director of the immunogenetics laboratory at CHOP whose lab developed the technologies that were licensed to Omixon. "Unless you have an accurate and thorough characterization of the genes, you cannot define with precision what is the allele you have in your patients or in your donors."

Monos said his team started to develop NGS assays in the early 2010s and subsequently licensed a subset of primers for Illumina sequencing-based HLA typing to Omixon in 2014.

Recognizing some of the inherent limitations of short-read NGS, the group later started to explore the utility of nanopore sequencing in HLA typing, he said. In 2020, he and collaborators published a proof-of-concept study demonstrating the ability of nanopore sequencingto characterize 11 HLA loci rapidly and comprehensively.

According to Monos, Omixon’s most recent licensing agreement with CHOP covers additional primers for more HLA genes, as well as the workflow that enables HLA typing using the Oxford Nanopore platforms. In addition, the team has signed a collaborative research agreement with Omixon to further develop nanopore-based HLA typing tests.

Despite the ongoing partnership with Omixon, Monos said the company’s product is not exactly the same as what is currently used by his team, and the lab is not obligated to use Omixon’s products. His group is actually independently developing and optimizing its own nanopore-based HLA typing assays, with the goal of deploying the method for clinical use down the road.

Two of the areas that his team is continuing to improve, for instance, are speed and turnaround time. In the case of a newly-deceased donor, the optimal time to complete the typing is less than five or six hours in order to preserve the integrity of the organ, Monos pointed out.

Omixon is also not the only company betting on nanopore sequencing for HLA typing in the market. Shortly after the company launched the NanoType Mono products, Dutch diagnostic firm GenDx released a nanopore-base HLA typing kit named NGS-Turbo. It remains to be seen how the two companies’ products will compete with each other moving forward.

Similar to Omixon, GenDx also previously developed an Illumina sequencing-based HLA test, named NGSgo, which features multiplexed HLA amplification of 11 loci for sequencing and has already been approved for clinical use under IVDR.

According to GenDx Chief Marketing Officer Hanneke Merkens, one of the main selling points for the company’s nanopore kit is speed. "Twenty-four hours is the absolute bare minimum you need with the Illumina kit," Merkens said. "Normally, the turnaround time is one and a half days to two days." In contrast, NGS-Turbo promises to achieve high-resolution HLA typing in as little as three hours, from blood sample to result.

NGS-Turbo is designed to work with Oxford Nanopore’s MinIon and GridIon sequencers and includes two workflow components: NGS-TurboAmp and NGS-TurboPrep. Specifically, NGS-TurboAmp can achieve multiplexed rapid amplification of all 11 HLA loci within 90 minutes.

After that, users can run NGS-TurboPrep, a single-tube library preparation process that can be performed at room temperature in 30 minutes and is designed "as dummy-proof as possible," Merkens said.

Nanopore sequencing takes from 20 minutes to 60 minutes, and the data are analyzed directly with GenDx’s proprietary NGSengine-Turbo, which is designed for analyzing Oxford Nanopore long reads.

Similar to Omixon’s products, NGS-Turbo is also currently marketed as an RUO assay. While IVDR compliance is "definitely the route" the company is taking for the product, Merkens said, FDA approval is "not on the agenda yet," given the possibility of developing the kits into LDTs.

At the moment, NGS-Turbo is designed to analyze one sample at a time. The next version of the product will allow customers to type one to 96 samples in one go, Merkens said.

[bamboo2] 17/11/2023 21:49

DZD, report. A bit more on Sepsis sequencing...

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Day Zero Diagnostics and Oxford Nanopore today announced a collaboration to develop a solution for diagnosing bloodstream infections.

Boston-based Day Zero Diagnostics develops diagnostics utilizing whole-genome sequencing and AI to combat antibiotic-resistant infections. Oxford Nanopore offers a new generation of nanopore-based molecular sensing technology. They seek to enable early detection to combat bloodstream infections as they are a leading cause of sepsis.

The companies plan to integrate and optimize a diagnostic system for use in clinical settings like hospitals. They aim to offer same-day identification and genomic-based antibiotic susceptibility profiling without the need for blood culture. According to a news release, the companies plan to pursue regulatory approvals, including with the FDA, down the line.

In the collaboration, the companies intend to combine Day Zero Diagnostics’ ultra-high enrichment sample preparation technology and its AI-drive Keynome microbial identification and antibiotic susceptibility pipeline with sequencing reads from Oxford Nanopore’s high-throughput, small-format PromethION 2 Solo.

The companies target a fully automated sample processing and sequencing workflow fitting the needs of clinical hospital labs. Oxford Nanopore brings to the table real-time, scalable features and advances in single-nucleotide sequencing accuracy. This makes it “ideal” for rapid and cost-effective characterization of pathogens in clinical samples, the companies said.

“We are pleased to launch this collaboration with Oxford Nanopore that integrates nanopore sequencing innovations with Day Zero Diagnostics’ platform technologies to develop a first-of-its kind diagnostic solution for sepsis,” said Jong Lee, CEO and co-founder of Day Zero Diagnostics. “Culture free, same day, organism identification and antimicrobial susceptibility profiling directly from native samples will be a game changer for infectious disease diagnostics, directly enabling early, targeted life-saving treatment for patients.”


More details of the Day Zero Diagnostics-Oxford Nanopore collaboration


In addition to combining diagnostic systems, Day Zero Diagnostics agreed to offer ONT-based sequencing and analysis commercially.

The company currently offers a family of lab services under its epiXact brand. This utilizes proprietary technologies to help healthcare and life science organizations track and manage infection outbreaks. It also enables the characterization of organisms of interest for research purposes and high-impact R&D decisions.

Day Zero Diagnostics now offers ONT as a sequencing platform on which such services can be provided.

“We are excited to partner with Day Zero Diagnostics to bring the benefits of nanopore sequencing to fight bloodstream infections,” said Gordon Sanghera, CEO of Oxford Nanopore Technologies. “Our hope is that the rapid results, high accuracy and accessibility of the Oxford Nanopore system, combined with DZD’s expertise and workflow, will make it possible for more people to access a solution that’s fast and effective in the fight against bloodstream infections.”

[bamboo2] 14/11/2023 14:13

eeza, it's being shorted by those that think that irrespective of the potential, non-profit making UK companies do not deserve a premium valuation.

The shorts think that companies like ONT have no business listing in the UK in the first place and should be sold abroad at the earliest opportunity.

At times of reduced buying pressure they will likely influence downward movement in the share price

[eeza] 14/11/2023 14:01

It's a pity the share price is illiterate.

[bamboo2] 14/11/2023 13:54

Sepsis requires immediate treatment to prevent serious life changing illness or death. There simply isn't any time to lose when looking to ID particular causative pathogens, which means that culture based processes are not fit for purpose.

Hence ONT's next diagnostic collaboration with DZD

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


OXFORD, England and BOSTON, Nov. 14, 2023 /PRNewswire/ -- Oxford Nanopore, the company delivering a new generation of nanopore-based molecular sensing technology, and Day Zero Diagnostics (DZD), an infectious disease diagnostics company harnessing the power of whole-genome sequencing and AI to combat the rise of antibiotic-resistant infections, today announced a collaboration to develop an end-to-end solution for the diagnosis of bloodstream infections, a leading cause of sepsis.

The companies will collaborate to integrate and optimize a diagnostic system for use in clinical settings, such as hospitals, that will provide same-day identification and genomic-based antibiotic susceptibility profiling without the need for blood culture. The companies plan to pursue regulatory approvals, including with the FDA, in the future.

According to the World Health Organization (WHO), there are 11 million sepsis-related deaths every year, accounting for one in five deaths worldwide. Early and effective treatment is paramount in a severe infection because the risk of mortality can increase by the hour. However, current culture-based diagnostics can take days to return a result, including for antimicrobial susceptibility.

Long turnaround times have also severely limited the role of diagnostics in standard of care therapy, leading to both damaging overtreatment and deadly undertreatment when antibiotic resistant organisms are involved. There is a critical need for rapid diagnostics that can deliver both organism identification and antimicrobial susceptibility test results in hours to guide therapy.

"We are pleased to launch this collaboration with Oxford Nanopore that integrates nanopore sequencing innovations with Day Zero Diagnostics' platform technologies to develop a first-of-its kind diagnostic solution for sepsis," said Jong Lee, CEO and co-founder of Day Zero Diagnostics. "Culture free, same day, organism identification and antimicrobial susceptibility profiling directly from native samples will be a game changer for infectious disease diagnostics, directly enabling early, targeted life-saving treatment for patients."

The diagnostic system will combine DZD's ultra-high enrichment sample preparation technology and its AI-driven Keynome® microbial identification and antibiotic susceptibility pipeline with sequencing reads from Oxford Nanopore's high-throughput, small-format PromethION 2 Solo. The collaboration is targeting a fully automated sample processing and sequencing workflow that fits the needs of clinical hospital labs. The unique real-time, scalable features and advances in single-nucleotide sequencing accuracy of the Oxford Nanopore platform make it ideal for the rapid and cost-effective characterization of pathogens in clinical samples.

"We are excited to partner with Day Zero Diagnostics to bring the benefits of nanopore sequencing to fight bloodstream infections," said Gordon Sanghera, CEO of Oxford Nanopore Technologies. "Our hope is that the rapid results, high accuracy and accessibility of the Oxford Nanopore system, combined with DZD's expertise and workflow, will make it possible for more people to access a solution that's fast and effective in the fight against bloodstream infections."

In addition to the diagnostic system collaboration, DZD has also signed an agreement to offer ONT based sequencing and analysis for commercial customers. DZD currently offers a family of lab services under its epiXact® brand that utilizes proprietary technologies to help healthcare and life science organizations track and manage infection outbreaks, characterize organisms of interest for research purposes, and make high impact R&D decisions. ONT will now be a sequencing platform on which these services can be provided and DZD has recently announced the launch of epiXact® ID, a rapid turnaround service that provides high resolution organism ID and deep characterization of a sample using nanopore whole-genome sequencing.

About Oxford Nanopore

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. Oxford Nanopore Technologies products are intended for molecular biology applications and are not intended for diagnostic purposes. www.nanoporetech.com

About Day Zero Diagnostics

Day Zero Diagnostics, Inc., based in Boston, is pioneering a new class of infectious disease diagnostics using whole-genome sequencing and artificial intelligence to revolutionize how the world fights the growing threat of antimicrobial resistance. The company's mission is to change the way infectious diseases are diagnosed and treated by rapidly identifying both the species and the antimicrobial susceptibility profile of severe infections directly from a clinical sample without the need for a culture. Day Zero also offers a family of lab services under the epiXact® brand that utilize proprietary technologies to assist healthcare organizations manage infection outbreaks, investigate organisms of interest, and make high-impact decisions. Day Zero Diagnostics was founded in 2016 by a team of clinicians and scientists from Harvard University and the Massachusetts General Hospital. The company has been recognized as a leading innovator by CARB-X, UCSF Health, American Association of Clinical Chemistry, MedTech Innovator, TedMed Hive, HealthTech Arkansas, and MassChallenge HealthTech. Follow DZD on X (formerly Twitter) and LinkedIn.

[eeza] 14/11/2023 13:46

Trade vol suddenly got a boot up the behind.

[bamboo2] 13/11/2023 23:29

Oxford Nanopore to participate in upcoming investor conferences

13 November 2023

Oxford Nanopore Technologies plc (LSE: ONT) ("Oxford Nanopore"), the company delivering a new generation of nanopore-based molecular sensing technology, today announces that management will be participating in the following upcoming investor conferences:

-- Canaccord Genuity MedTech, Diagnostics and Digital Health & Services Forum on Thursday, 16 November 2023 in New York, USA

-- J.P. Morgan UK Leaders Conference on Tuesday, 21 November 2023 in London, UK

-- Berenberg European Conference on Thursday, 7 December 2023 in Surrey, UK

Gordon Sanghera, Chief Executive Officer, will participate in an analyst led fireside chat at the Canaccord Genuity MedTech, Diagnostics and Digital Health & Services Forum on Thursday, 16 November at 11:00am ET/ 4:00pm GMT.

A live webcast of the event can be accessed at the company's investor relations page at:



A replay will be available via the same link following the event.

[bamboo2] 13/11/2023 17:54

Another day, another international collaboration deal. This time it's with MATRIX, the Norwegian Centre for Clinical Cance Research. The hope is that all hard to treat cancer patients will receive sequencing to ID tumor type.

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Oxford Nanopore and MATRIX, the Norwegian Centre for Clinical Cancer Research, collaborate to advance precision cancer medicine research
Mon 13th November 2023

MATRIX’s first official research collaboration will explore the clinical value of Oxford Nanopore’s DNA and RNA sequencing technology in precision cancer medicine

Oxford Nanopore Technologies plc (Oxford Nanopore) and the Norwegian Centre for Clinical Cancer Research - MATRIX - today announce a research collaboration to explore the clinical value of nanopore sequencing in precision cancer medicine.

The agreement between Oxford Nanopore and MATRIX will initially focus on tumours of the central nervous system and be conducted at Oslo University Hospital (OUH) under the direction of Professor and senior physician Hege Russnes, who leads the national precision diagnostics in cancer programme in Norway (InPreD) in close collaboration with neuropathologist Pitt Niehusmann. This collaboration will focus on DNA methylation-based classification in central nervous system (CNS) tumours, detection of somatic and pathogenic copy number variants and tumour heterogeneity of gene expression, mutations and fusions at a single cell level.

Nanopore sequencing is uniquely positioned to enable methylation and copy number variation through sequencing the native DNA and long-read fragments respectively, providing unparalleled richness of biological content in real time and reducing the turnaround time for clinical tests. All of these insights are provided in a single sequencing run, enabling the streamlining of certain cancer indications, such as brain tumours, where methylation-based tumour classification is important in both diagnosis and treatment of these tumours.

Hard-to-treat cancer patients in clinical trials based on advanced molecular diagnostics is rapidly moving towards routine clinical care in Norway. Sequencing DNA and RNA from patients' tumours can reveal a number of genetic abnormalities that subsequently has the potential to open up more precise treatment opportunities, using targeted drugs.

Cancer patients in Norway who may benefit from experimental treatment can be offered molecular genetic analyses of the tumour tissue. Integration into the public health system of established diagnostics and experimental treatment is supported by the health authorities. Since InPreD was launched in April 2021, more than 1200 patients have had such examinations and approximately a third of these patients have been offered experimental treatment in clinical trials. The clinical trial centre MATRIX will test diagnostics and novel trial designs that have a potential for implementation in InPreD.

The collaboration will use Oxford Nanopore’s PromethION 24 device, which provides 24 independently addressable, high-output flow cells. Nanopore sequencing provides scalable platforms, and this technology could potentially be deployed across the different hospitals in Norway, ensuring that sequencing is performed close to the patients and clinical reports can be returned quickly.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“We are really excited to be collaborating with MATRIX to explore the clinical value of nanopore sequencing technology in precision cancer medicine. By reading the native DNA, nanopore sequencing can deliver richer insights into cancer genomics than ever before, through areas such as methylation. Together with the ability to sequence any-fragment-length of DNA, we expect to reveal new biological insights that have not been possible with other sequencing technologies. We look forward to seeing the outcome of this work and the future potential to improve precision cancer medicine.”

Professor Åslaug Helland, Director MATRIX, commented:

“MATRIX continuously tests and develops new, ground-breaking molecular, functional and clinical analyses that will shape next-generation trials in precision cancer medicine. In this context, we are very pleased to enter into a research collaboration with Oxford Nanopore Technologies to test out their sequencing technology within this field".

Professor Hege Russnes, MATRIX and Head InPreD, commented:

“The ability to test the technology and assays developed by Oxford Nanopore through these projects is very exciting for us. It is important to be able to utilise instrumentation both for research and diagnostics as it enables us to move knowledge and assays into routine use when feasible. The increasing need for genome information, that includes epigenetics, demands tailored solutions”.

MATRIX is the latest addition to the Norwegian ecosystem within precision cancer medicine, which in addition to InPreD also includes IMPRESS-Norway, a national researcher-initiated clinical trial opened in April 2021, which contributes to targeted cancer treatment based on precision diagnostics. Altogether, 17 hospitals in Norway with cancer departments participate in this trial in addition to CONNECT, a public-private partnership driving the implementation of precision cancer medicine.

[p1nkfish] 13/11/2023 09:31

Once through this rotation in sequencing leadership there is a very high probability Ox Nano will be further up the list in terms of impact and investor focus.

Leaders don't go down easy or often and it takes time for the new leaders to emerge in the wake of the old.

I think that rotation is taking place.

[eeza] 13/11/2023 08:54

Flirting with the lows, once again.

[bamboo2] 10/11/2023 08:56

This paper goes a long way to explaining why the ongoing UK clinical trial of Illuminas GRAIL should be shown the door, because it is ineffective, slow, expensive and outdated compared with ONT's long read capability.

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


Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing.

The paper explained

Problem

Current sequencing methods based on short-read technologies to analyze cell-free DNA (cfDNA) as a liquid biopsy in cancer patients have limitations. These include a bias toward shorter cfDNA populations and long waiting times for data. The Oxford Nanopore Technologies (ONT) platform offers a portable and fast alternative, capable of sequencing any length of cfDNA fragment. However, its potential for analyzing cfDNA from cancer patients remains underexplored.

Results

Plasma and urine samples from lung and bladder cancer patients, as well as healthy controls, were sequenced with a MinION ONT and compared to a short-read sequencer. The ONT platform successfully retrieved cfDNA somatic copy number aberrations within 24 h of sampling, and with comparable sensitivity to short-read technologies.

The study also demonstrated that ONT sequencing could recover long cfDNA fragments in both plasma and urine samples, contrary to the canonical belief that cfDNA is predominantly short and fragmented. The presence of tumor-derived signal in these long fragments is confirmed in not only humans but also using a xenograft model. In addition to the size profile, other fragmentomic features could be retrieved from the cfDNA data.

Impact

In conclusion, the ONT sequencing provided a fast and accurate analysis of cfDNA from liquid biopsy samples. It allowed the detection of copy number aberrations, estimation of tumor fraction, and recovery of long cfDNA fragments. The ONT platform's deployability and short turnaround time make it a promising tool for liquid biopsy analysis.

[bamboo2] 08/11/2023 19:43

Thinking about the acquisition of the Solid state nanopore maker this week, perhaps the Canadians had been in a position to release something new, that maybe would have possibly infringed an ONT copyright, therefore it was seen as mutually beneficial to join forces? Pure speculation btw.

[bamboo2] 08/11/2023 15:16

Agenda for Houston meeting, 6/12/23



If you haven't already seen it, TURbot/TraxIon should be discussed a bit more in the update at the end of the day.