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[bamboo2] 30/6/2022 07:05

30 June 2022

Oxford Nanopore Technologies plc

("Oxford Nanopore" or the "Group")

Duncan Tatton-Brown appointed as Non-Executive Chair

Oxford Nanopore Technologies plc, the company behind a new generation of molecular sensing technology based on nanopores, is pleased to announce that Duncan Tatton-Brown will be joining the Group as Non-Executive Chair with effect from 1 August 2022. Duncan will succeed Peter Allen, who will retire from the Board on 31 July 2022.

Duncan brings extensive, relevant experience as an executive and Non-Executive Director of FTSE companies, growth and founder-led technology businesses, and, in particular, where UK-born businesses have grown to have a strong international commercial presence. He has had a distinguished career across a wide range of innovative businesses in the technology, retail and media sectors, including serving as Chief Financial Officer of Ocado Group plc from 2012 to 2020, during which time the business expanded from being a pure-play online grocer to a leading UK technology business serving clients around the world, with revenue growing 3.5 times and technology headcount growing 10-fold . He remains a Senior Advisor to Ocado and currently also serves on the Boards of Cazoo and Trainline.

Duncan holds a master's degree in Engineering from King's College, Cambridge.

Wendy Becker, Senior Independent Director at Oxford Nanopore, said : "We are extremely pleased to have appointed Duncan as the next Chair of Oxford Nanopore. Duncan's impressive track-record of working with FTSE companies that have grown internationally, and extensive board experience, means he is ideally placed to lead the Board as we continue to innovate and grow. On behalf of the Board, I would like to thank Peter for his enormous contribution to Oxford Nanopore and wish him all the best."

Duncan Tatton-Brown, incoming Chair, commented: "I am delighted to be joining Oxford Nanopore at such an exciting time in the company's journey. The company has already achieved a huge amount, and yet the company is in the foothills of its growth journey. The future opportunities for its sensing technology are immense, from the current scientific research community to future uses across health, agriculture, food or environmental applications. This potential is underpinned by its highly innovative and differentiated technology, fantastic team, strong business model and growing customer base. I look forward to working with the Board and the executive team to ensure the ongoing and long-term success of Oxford Nanopore."

Gordon Sanghera, Chief Executive Officer of Oxford Nanopore, said : "Duncan brings substantial board experience of supporting high-tech growth technology companies, critical to our long-term ambition of enabling the analysis of anything, by anyone, anywhere. I would like to thank Peter for his support and guidance over the years and very much look forward to working with Duncan as we enter the next phase of growth."

[bamboo2] 29/6/2022 14:55

New Kit 14 Chemistry available from today.

This improves accuracy still further for Q20+

[bamboo2] 29/6/2022 13:30

Small gap from 20/5/2022 now filled.

Added a trading tranche.

[bamboo2] 29/6/2022 11:55

Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic



In this study, the portable real-time ONT sequencer (MinION) was used for the first time to target and sequence the full MPXV genome from DNA isolated from a human clinical sample in the CAR. [Central African Republic]

Unlike PacBio, ONT sequencers, especially the MinION, are better adapted to field sequencing, because they are highly portable, being small in size and weight (under 100 g). In addition, library preparation is simpler than that used for SGS. All these technical advantages of TGS have made it possible to sequence genomes rapidly in regions with extreme climate conditions23,24.The most elegant demonstration of the usefulness of rapid MinION sequencing is that of the field for a rapid molecular characterization of Ebola virus during the last West African outbreak25. Real-time monitoring of the Ebola virus and the associated genomic analysis shed much-needed light on the spread of the virus and helped establish infection control strategies26. MinION sequencing has also been successfully used to study other viruses in epidemics, such as the Zika virus in South America, where MinION sequencing results helped link congenital malformations to Zika fever, or in the recent Lassa virus epidemic in Nigeria in 2019.

[bamboo2] 27/6/2022 18:29

eDNA. This allows us to track species of interest, in the wild, without the use of camera's. This short video explains the method currently in development. eDNA can also be found in the air, and on land, as well as in water. There are a great many possibilities opened up by this tech, such as species range, and calculation of numbers of viable populations.



Reindert Nijland
Endangered European sturgeon detection through non-amplified eDNA sequencing

The European sturgeon (Acipenser sturio) is critically endangered and no natural breeding population exists. Currently, a reintroduction program is running. We are developing environmental DNA (eDNA) based monitoring to track the reintroduction of the European sturgeon in the rivers and estuaries in the Netherlands. Supported by the ORG.one program, we sequenced the full genome of A. sturio. Initial experiments with eDNA from the tank, housing the sturgeon, demonstrated that this genome data enables direct, unamplified detection of sturgeon eDNA. Ultimately, we will create a biodiversity monitoring system based on eDNA sampling and real-time analyses, including in situ eDNA sequencing.

[bamboo2] 27/6/2022 18:03

More on using ONT for Liquid Biopsy.



Detection of cancer biomarkers from blood samples using nanopore-based DNA computing technology.

At the time of diagnosis, most bile duct cancers are typically already incurable. This is why methods for the early diagnosis of bile duct cancer are urgently needed.

Liquid biopsy, the sampling of non-solid biological tissue like blood, is gaining interest as a quick and non-invasive method for diagnosing cancers. Unlike traditional biopsies that require surgery and often general anesthesia, a liquid blood biopsy only requires a couple of milliliters of blood, with minimal harm to the patient.

After sampling, the blood is screened for specific markers indicating the presence of cancerous tissue. For example, specific patterns of microRNA (miRNA), short non-coding strands of RNA, are associated with different types of cancer and can be used to diagnose cancers from liquid biopsies with high precision. However, the low concentration of miRNA in the blood samples makes their detection challenging.

Researchers at the Tokyo University of Agriculture and Technology have developed a new method for the detection of cancer miRNA patterns based on DNA computing technology. The developed method shows potential as a promising tool for simple and early cancer diagnosis from liquid biopsies with low concentrations of target biomarkers. The findings were published in the peer-reviewed journal JACS Au on June 26th, 2022.

“DNA computing uses the biochemical reactions of the information-encoding DNA molecules to solve problems based on formal logic, in the same way that normal computers do,” said corresponding author Ryuji Kawano, professor in Tokyo University of Agriculture and Technology (TUAT) in Japan. “In this case, a diagnostic DNA molecule was designed to be able to bind five different kinds of miRNA associated with bile duct cancer. In the process of binding the miRNA molecules, the diagnostic DNA converts the expression pattern of the miRNAs into the information contained in the form of a nucleic acid structure.”

To read this information, the scientists use a method called nanopore decoding. In this method, the DNA is passed through a nano-sized hole, or “pore”. As the molecule transits the pore, it will obstruct the flow of electrical current through the pore. These perturbations in the current through the pore can be then measured and used to deduce the properties of the passing molecule. In the case of the diagnostic DNA, the bound miRNAs will be “unzipped” from the DNA, resulting in a current inhibition of characteristic amplitude and duration. Through statistical analysis of the unzipping data of the miRNA patterns, the scientists were able to recognize cancer-specific expression patterns even from clinical samples with extremely low concentrations of miRNA. This is a significant improvement in the field of nanopore diagnosis, as nanopore measurements have generally been considered unable to detect nucleic acids at such low levels, which has undermined the use of the technology in clinical applications.

For more information about the Kawano laboratory, please visit

[bamboo2] 24/6/2022 20:46

Published: 24 June 2022
Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic

[bamboo2] 24/6/2022 20:21

The frontlines of pathogen genomic surveillance with rapid nanopore sequencing
Offering comprehensive, real-time insights into infectious disease samples, nanopore sequencing delivers immediate access to the critical genomic epidemiology data required for effective control of infectious disease outbreaks.

Listen to these talks to find out how infectious disease experts are using nanopore technology.



Includes...

1. Monkeypox virus genome sequencing – first draft genome associated with the 2022 multi-country outbreak obtained using shotgun metagenomics in Portugal

2. Implementation of rapid, direct sequencing for poliovirus surveillance

3. Practical perspectives on laboratory support during initial activation of a High Consequences Infectious Diseases Unit

Topical, if you want it.

[bamboo2] 24/6/2022 07:08

New Technology Helps Reveal Inner Workings of Human Genome
JUNE 23, 2022

Weill Cornell Medicine and New York Genome Center researchers, in collaboration with Oxford Nanopore Technologies, have developed a new method to assess on a large scale the three-dimensional structure of the human genome, or how the genome folds. The genome is the complete set of genetic instructions, DNA or RNA, enabling an organism to function.

Using this method, the researchers demonstrated that cell function, including gene expression, may be affected by groups of simultaneously interacting regulatory elements in the genome rather than pairs of these components. Their findings, published May 30 in Nature Biotechnology, may help shed light on the relationship between genome structure and cellular identity.

“Knowing the three-dimensional genome structure will help researchers better understand how the genome functions, and particularly how it encodes different cell identities,” said senior author Dr. Marcin Imieliński, associate professor of pathology and laboratory medicine and computational genomics in computational biomedicine at Weill Cornell Medicine and a core member of the New York Genome Center. “The ways that we’ve had to study genome structure have given us amazing insights, but there have also been key limitations,” he said.

For example, previous technology to assess the genome’s three-dimensional structure has allowed researchers to study how frequently two loci, or physical locations on the genome, interact with one another. Traditionally, pairs of loci called enhancers and promoters—components in the genome that interact with one another to influence gene expression—have been observed.

Information about these pairings offers incomplete insight into genome structure and function. For instance, linking a folding pattern to how the genome encodes for a specific cell identity—like a liver, lung or epithelial cell—has been difficult, said Dr. Imieliński, who is also a member of the Englander Institute for Precision Medicine and the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine. Scientists have theorized that this folding influences gene expression. “But how cell types are encoded, particularly in the structure of DNA, has been a mystery,” he said.

Dr. Imieliński and his research team, including first author Aditya Deshpande, a recent graduate of the Tri-Institutional Ph.D. Program in Computational Biology & Medicine working in Dr. Imieliński’s lab, developed a new genome-wide assay and algorithm that allows them to study groups of loci, not just pairs.

They adapted a traditional technology, Hi-C (chromatin conformation capture), which assesses a mixture of DNA and protein to analyze three-dimensional genome structure, to nanopore sequencing, or the high-throughput sequencing of long, continuous strands of DNA molecules. The resulting assay, which the researchers called Pore-C, enabled them to observe tens of millions of three-dimensional locus groupings.

They also developed statistical methods to determine which locus groupings were important, based on whether they interacted cooperatively to affect gene expression. “Many three-dimensional interactions of the genome are not important,” Dr. Imieliński said. “Our analytic methods help us prioritize the group interactions that are likely to matter for genome function.” As a key finding of the study, the researchers found that the most significant cooperative groupings of DNA elements occurred around genes associated with cell identity.

Future experiments will explore which specific groupings of genomic components are essential for various aspects of cell identity. The new technology may also help researchers to understand how stem cells, the immature, master cells of the body, differentiate into different cell types.

In addition, researchers may be better able understand abnormalities in cancer cells. “In the future, this technology may be really helpful in understanding how cancer cell genomes are rearranged, and how those rearrangements drive the altered cell identities that enable cancers to grow and spread” Dr. Imieliński said.

[bamboo2] 23/6/2022 06:41

New Oxford Nanopore PromethION sequencer
June 23, 2022

Bragato Research Institute (BRI) has recently finished completed the new Canterbury-based Grapevine Improvement Laboratory with the installation of the first high-throughput third-generation sequencer in New Zealand. The ‘PromethION’ sequencer, supplied by Oxford Nanopore technologies, generates long-read data that is critical for understanding genetic differences among grapevines, as well as the impact that a vine’s environment has on its genetic traits.

The sequencer is already being put to work to decode the Sauvignon Blanc genome and will be a key tool for rapidly selecting vines with potentially useful new traits in the seven-year Sauvignon Blanc Grapevine Improvement Programme. Most of New Zealand’s Sauvignon Blanc vines are of the same variant, meaning a new pest, disease or environmental change that affects one Sauvignon Blanc vine would likely affect all of them.

The programme aims to make New Zealand’s wine industry more resilient and sustainable, by selecting new traits among spontaneous variants of New Zealand’s premier wine varietal and biggest export while maintaining the characteristic Marlborough Sauvignon Blanc wine flavour and aroma. Traits of interest include improved yield, more tolerance to fungal attack, frost, high temperatures and drought.

Like most plants, grapevines respond to environmental stress by increasing their genetic diversity. The research programme will use this natural response to produce a population of 12,000 entirely new variants of contemporary New Zealand Sauvignon Blanc. Applying the latest genome sequencing technology will BRI to identify plants that exhibit the most useful traits selected by the wine industry within this large population.

The Nanopore sequencer works by passing molecules of DNA or RNA through tiny pores in a membrane and measuring changes in the electrical current flowing through the pores. This allows much longer molecules to be read (up to a million bases and above), enabling the complex parts of genomes that frequently change in response to stress to be studied. The sequence data is generated in real-time and base modifications, which can play a role in regulating gene expression, can be included.

Principal Research Scientist Dr Darrell Lizamore says the PromethION sequencer is “a step-change in the type of DNA sequencing that was available up till now. For us, it’s a way of getting efficiency into the programme, allowing us to do some of the selection almost in parallel with the plant production.”

This capacity is available as a service, and BRI is already working with collaborators across NZ to bring this enabling technology to bear on diverse research challenges. BRI is also offering a limited number of flow cell grants to collaborators to help build NZ expertise with this technology. For more information, or to discuss potential projects, contact: [e-mail]

The programme is funded by MPI’s Sustainable Food and Fibre Future fund, NZW levy, and industry support from participating New Zealand wine companies.

[bamboo2] 22/6/2022 17:52

AGM tomorrow. Will we get an update?

[bamboo2] 21/6/2022 07:33

EVENTS/
The frontlines of pathogen genomic surveillance with rapid nanopore sequencing
Thu 23rd June 2022

Online
Join us at 3:00 pm (BST), to hear how a team released the first draft genome sequence of the monkeypox virus associated with the recent major outbreak. This will be followed by talks on rapid, direct sequencing for poliovirus surveillance and laboratory support during initial activation of a High Consequences Infectious Diseases Unit.

REGISTER HERE

[bamboo2] 20/6/2022 16:28

A few stories circulating that the co is having trouble keeping up with the demand for systems.
Slightly concerning until we get to know why. Probably more info later this week.

[bamboo2] 18/6/2022 14:23

Friday saw ath daily volume approx 37.7m, which is over 4% of the company traded.

Who is the seller?
Lansdowne Shareholders, with 37,991,000 or 4.78%
RM Special Holdings LLC, with 40,817,120 or 4.90%
GT Healthcare Shareholders with 31,404,260 or 3.95%

Should get some idea by Tuesday. If not I will contact IR at the co.

[bamboo2] 18/6/2022 11:12

The current gold standard PCR test for MPX takes between 3-5 days to give results and relies on calculated guesswork to decide for which pathogen to test. If it's not MPX, what is it? Chickenpox? Herpes simplex?

ONT's pathogen-agnostic test can offer confirmed results within 7 hours and can differentiate between different causes.

A significant benefit meaning earlier treatment.

Metagenomics relies on separating the host genome from that of the virus or bacteria, and has previously been used to great effect in determining Sars Covid 2 from other types of infection such as Flu, or common cold.

The main reason that this type of testing has not really taken off in the UK commercially, or in the NHS, is the reliance on large centralised labs doing traditional PCR type testing.

By adopting a more decentralised approach, the same ONT hardware used for Covid, could also be used to test for MPX, or any other pathogen.

[bamboo2] 17/6/2022 17:48

Nice bit of volume this afternoon.

Looking at approx 37.7m

Over 4% of the company.

[bamboo2] 10/6/2022 07:53

The first dedicated MPX Workflow for use with Oxford Nanopore [ONT] kit.

A number of these were developed for Covid, and it's possible that others will appear for MPX, with the most effective becoming the industry standard.


Monkeypox (MPX) is a double-stranded DNA virus. There is an ongoing outbreak of the West African clade of the virus in multiple countries. Data has been generated for a number of these cases using Oxford Nanopore Technology sequencing and here we describe wf-mpx, a decentralised workflow to analyse this data on device, anywhere.

Data Analysis
A dive into the many excellent community posts on virological.org indicated that:

people were mapping to existing references,
creating a consensus based on this mapping,
or they were creating de novo assemblies;
and in either case, performing some manual review.

We wanted to empower those users who perhaps are keen to sequence MPX using Oxford Nanopore Technologies devices but don’t have the expertise or resources to throw together an analysis workflow. We have therefore released wf-mpx. By releasing this workflow in it’s nascent state anyone with ONT Monkeypox data, be it metagenomics or something more targeted can get a draft consensus using EPI2ME Labs.



ONT used for sequencing MPX

[bamboo2] 08/6/2022 16:50

Re post 350, AGBT meeting currently in Florida.

I have been following some of the notes that have made it onto Twitter, but have now lost count of the sheer number of references to Nanopore by various speakers and attendees. It's worth a search on Twitter to get a flavour of the general level of positivity and excitement amongst the sequencing community.

[bamboo2] 06/6/2022 11:55

During his talk at London Calling 2022, Miten Jain discussed the latest nanopore sequencing chemistry, Kit 14 with R10.4.1 Flow Cells, as well as why he believes “phased, Q40+ accuracy de novo assemblies may be achievable” soon.

Video here,

[bamboo2] 06/6/2022 10:42

Cihan Erkut, working with ONT kit at Division of Applied Functional Genomics, DKFZ and NCT Heidelberg, Heidelberg, Germany.

Describes on Twitter...

"We used Oxford nanopore sequencing to get a glimpse of the transcriptomes of tumor samples, which were already deep sequenced with Illumina within the framework of our precision oncology program. We found that our "shallow" sequencing approach, thanks to the long-read technology, estimates gene expression levels fairly as good as Illumina sequencing."



Shallow nanopore RNA sequencing enables transcriptome profiling for precision cancer medicine.

[bamboo2] 06/6/2022 09:36

The Genome Partnership

The Genome Partnership has been proudly organizing The Advances in Genome Biology and Technology (AGBT) meetings since 1999. The Genome Partnership is a not-for-profit organization and its mission is to advance research, promote education, and expand commerce in genome science and technology.

AGBT is the world-renowned not-for-profit provider of three prestigious conference and networking events for the leading luminaries and change-makers of the life sciences and global biotech community.

AGBT delivers a trifecta of preeminent conferences and networking events for the world’s top genome science and technology researchers, leaders, and innovators to share the latest advances, discoveries, and breakthroughs with influential peers and key decision-makers.

By providing opportunities for the global scientific community and technology industry to gather and collaborate in casual, intimate settings, AGBT functions as a key player in advancing DNA sequencing technologies, driving novel applications, and furthering experimental and analytical approaches for genomic studies in the public and private sectors.

Among our attendees are heads of internationally regarded labs and institutions, C-suite executives of life science companies, Wall Street analysts, and media representatives.