Oxford Nanopore Technolo... Share Discussion Threads

[bamboo2] 01/11/2023 15:52

74tom, there are additional significant costs associated with all the main SBS type suppliers, such as Pacb, ILMN etc,. For example, Andrew Beggs, working on cancer and infection genomes at NHS Birmingham, said that they had to have the floor strengthened to bear the weight of the new ILMN machine!

[74tom] 01/11/2023 14:21

Indeed, and I feel like things are rapidly picking up pace now that there seems to be widespread acceptance that cost is no longer a barrier? That <$1k genome figure was referenced by the FDA as justification for potentially employing long read techniques for monitoring.

I struggle to imagine a world where nanopore aren't generating >£1b in revenue come 2030, they are building a formidable moat & their balance sheet strength means that they can continue to expand as quickly as is technically feasible.

Ps. The latest reason why shares are under pressure from the shorts is Pacbio's Q3 results which were published on Monday evening, in it they referenced headwinds to their 2024 demand due to the global macro. Nothing at all to do with the fact their latest sequencer, 'Revio' is priced at $700k (and on which they make <30% gross margin)...

It was notable that whilst they managed to sell 52 Revio machines in Q3 for a total of ~$35m, their consumables sales only increased 5% vs Q3 2022. To me that suggests the new machines have simply cannibalized their previous devices (i.e. been bought by existing customers as replacements) rather than expanding their market share.

They certainly appear to have a huge competitive problem vs Nanopore devices with little apparent wiggle room if it's costing them $500k to produce each Revio...

[bamboo2] 01/11/2023 12:48

From yesterday...

Oxford Nanopore Technologies and Fabric Genomics collaborate to launch an integrated whole-genome sequencing solution to advance the future of paediatric patient care
Tue 31st October 2023

The partners will offer an integrated sample-to-report rapid nanopore sequencing analysis platform for neonatal/paediatric intensive care units to support clinicians in acute settings

Oxford Nanopore Technologies plc (Oxford Nanopore), the nanopore-sequencing company delivering unparalleled rich genomic data insights, and Fabric Genomics, the leading AI-driven analysis and interpretation software provider, today announced a new collaboration to develop a scalable software solution for the end-to-end analysis and clinical reporting of rich genomic data.

It is estimated that roughly 2.8 million children in the US reported a rare genetic disorder, according to data from the National Survey of Children’s Health. The joint solution, which will be commercially available for deployment in CLIA/CAP labs, will support use of nanopore sequencing in neonatal/paediatric intensive care units, bringing the benefits of richer data and faster insights to support rapid disease characterisation of babies and children with genetic disorders in acute settings.

"For this incredibly high-risk patient population, speed and data-rich insights matter,” said Gordon Sanghera, PhD, CEO of Oxford Nanopore Technologies. “We are excited to team up with Fabric Genomics to develop an end-to-end analysis tool for the clinical reporting of nanopore sequencing data in paediatric care settings that will make it easier for healthcare providers to leverage genetic insights and, in the future, support the health and wellbeing of children and families.”

The end-to-end workflow from sample to answer with push-button integration between Fabric Genomics and Oxford Nanopore will offer a simple solution for interpreting nanopore’s data-rich, any-length reads by integrating Oxford Nanopore EPI2ME™ software with Fabric’s software-as-a-service platform to provide analysis and clinical reporting. Clinicians and healthcare providers will also be connected to Fabric’s network of clinical geneticists, who will be on hand to help clinicians interpret their dataset. While initially focused on the highest complexity testing for paediatrics in the NICU, the partners expect to launch additional push-button solutions for late onset genetic conditions including cancer and cardiovascular disease at a later stage.

“We’re excited to partner with the fast-driving team at Oxford Nanopore to integrate our AI-driven whole-genome sequence solution with nanopore sequencing and help to accelerate the adoption of that technology in the clinic,” said Martin Reese, PhD, CEO and co-founder of Fabric Genomics. “Oxford Nanopore’s real-time genomic reading technology represents an important opportunity to speed critical analysis of children’s genomes in NICU settings and for all genomic medicine patients.”

The new platform, which is available now to customers on a limited basis and will be widely available in Q1 2024, will be powered by Fabric GEM, a novel artificial intelligence algorithm, to help healthcare providers sort through thousands of structural variants and potential pathogenic mutations and prioritise a short list of areas of interest, saving time and reducing costs.

Fabric Genomics has been working with NICU patients through its long-standing collaboration and partnership with Rady Children’s Institute for Genomic Medicine to accelerate the diagnosis of rare genetic diseases. Fabric Genomics and Rady Children’s Institute for Genomic Medicine have published results showing Fabric AI GEM to predict causative variants in genomes from previously diagnosed newborns and rare disease patients.

American Society for Human Genetics Annual Meeting November 2nd - 4th

Fabric Genomics and Oxford Nanopore will present initial results of their collaboration at the American Society for Human Genetics Annual Meeting in Washington D.C., including a presentation by Kamran Shazand, PhD, the Director of the Genomics Institute at Shriners Children’s Hospital. The CoLab session will be on Thursday, November 2nd at 4:30 p.m. ET. In addition, the partners will launch early customer availability at the meeting and showcase a workflow integration at Fabric Genomic’s booth #1215 on Friday November 3rd at 1.00 p.m. ET.

[bamboo2] 01/11/2023 12:43

74tom, thanks for sharing. There is literally a plethora of opportunities out there.

Another today,

Oxford Nanopore and Genomics England announce new strategic research project to resolve undiagnosed rare disease cases
Wed 1st November 2023

Oxford Nanopore sequencing technology will be used in a pioneering new collaboration with Genomics England, to sequence as many as 7,500 samples from participants of the landmark 100,000 Genomes Project with a range of genetic or suspected genetic disorders. The programme aims to improve diagnostic outcomes for participants with rare conditions, including those who have not yet received a diagnosis through short-read only sequencing methods. The programme will also further aim to develop an accredited lab workflow and data analysis pipelines to support the clinical use of human whole genome sequence data generated using nanopore sequencing.

The study will use nanopore whole genome sequencing for three distinct objectives: to uncover new diagnoses in participants who have yet to be diagnosed, to finalise genetic characterisation and heritability within families for partially diagnosed participants. And finally, to identify potentially missed variants and highlight improvements over other, short-read-only technology. The ultimate goal of this proof-of-concept study will be to generate datasets that characterise improvements in insights using nanopore sequencing. The dataset will also be of great value in any disease where genetics plays a role, including common diseases, enabling researchers to look easily in the one dataset to study how genetic variation can influence health and disease.

This project will be part of a wider multiomic study led by Genomics England – including genomic, transcriptomic, epigenetic, proteomic and metabolomic analysis - to support the understanding of multiomic research in rare cases that are difficult to resolve. Whole genome sequencing will be performed on all samples and a subset will also have full-length RNA sequencing, made possible by Oxford Nanopore technology’s ability to sequence fragments of any length. The sample cohort will be inclusive of singleton samples and duo/trio families.

Eurofins Genomics will be the service provider for the sequencing, in the UK. Eurofins Genomics brings a rich legacy of managing extensive population genomic initiatives across the globe, employing cutting-edge sequencing and predictive genomics methodologies. The incorporation of long-read, high-throughput capabilities will significantly expedite the integration of long-read technologies in both diagnostic and applied sectors. This advancement is set to be fortified by the commencement of procedures aimed at securing clinical accreditation for the pipeline.

The project will use Oxford Nanopore’s high-throughput sequencing device, the PromethION 48, which provides rapid characterisation of large genomes, delivering scalability for large projects with low infrastructure requirements. Combined with the latest “Q20+” chemistry, comprised of Kit 14 and R10.4.1 flow cells, Oxford Nanopore delivers complete and accurate genomic data, at scale.

Oxford Nanopore’s ability to sequence any DNA/RNA fragment length from short to ultra-long, allows for characterisation of more genetic variation that includes single nucleotide variants, insertions/deletions, complex copy number variations and structural variations. This has been highlighted in a recent Nature Methods paper, in which a team contributing to the National Institutes of Health (NIH) Center for Alzheimer’s and Related Dementias (CARD) shared an end-to-end pipeline for nanopore sequencing that produces comprehensive, state-of-the-art single nucleotide polymorphism (SNP), structural variant and methylation calls. In the paper, the team describe how this makes large-scale, long, native DNA sequencing projects feasible due to the lower cost and higher throughput of Oxford Nanopore’s PromethION when compared with alternative sequencing methods.

To date, methylation has not been characterised at a whole genome scale in rare disease cohorts and is often only analysed in targeted tests or EPIC arrays. This offers the first large scale database of rare disease patients that will be characterised epigenetically and will be made available to the research community to investigate the importance of methylation as a type of variation and to shed light on mechanism of action.

Once the project is complete, the data will be stored in the National Genomic Research Library, creating the world's largest global dataset with genetic and epigenetic profiling for rare disease.

Gordon Sanghera, CEO, Oxford Nanopore Technologies, commented:

“We are delighted to be extending our collaboration with Genomics England into rare disease research, in addition to our current cancer programmes. The combination of very high single-molecule accuracy with the ability to reach all parts of the genome and characterise all types of genetic variation, mean that nanopore sequencing can deliver comprehensive whole genome analysis and will reveal that what’s missing matters.”

Professor Matt Brown, CSO, Genomics England, commented:

“Over the last decade we’ve seen incredible technological and scientific advances across genomic research. This vast progress means we now have a wealth of tools at our disposal to study rare genetic conditions. We’re excited to work with Oxford Nanopore to explore the potential for long-read and epigenetic sequencing to improve our understanding of the causes of rare conditions and help us to build the world’s largest dataset with comprehensive genomic profiling to support diagnosis for patients and families affected by rare genetic conditions.”

[74tom] 01/11/2023 08:35

There was an FDA advisory meeting yesterday to discuss CRISPR gene editing technology & it's benefits vs risks

Part of the panel discussion focused on whether post market monitoring of the patient population could provide insights into what are known as 'off target' gene edits - i.e. unintentional changes made by the drug which could cause unwanted side effects for the patient.

At 6 hours 45 the FDA chair asks whether there is 'any emerging disruptive tech that would actually result in a step change in the evaluation of these off target edits?'



Professor Scot Wolfe name dropped Nanopore as a solution :)

Vertex, the company who will market the drug, have committed to a 15 year post approval monitoring program, so as with the dozens of other avenues disclosed on this BB, this appears to be a significant potential opportunity to apply Nanopore tech in a very positive way.

[bamboo2] 31/10/2023 10:30

74tom, I am almost certain that LR genomic sequencing of cancer will add hugely to the total number of metagenomic tests. Last year, a friend of mine had her SUP cancer sequencing done in the US, as we in the UK did not have the capacity.

Genomics England are are helping to lead initiatives to broaden access to cancer sequencing in the UK.

There is a lot of work going on elsewhere in the NHS, for example, Exeter Genome service has been expanding work on newborns with genetic conditions, and in London, NHSBT is moving forward with genetic testing and tissue typing for transplant recipients.

In the background of all this is the health economics justification for expanding and expediting LRS, eg reduced AMR, reduced time spent in critical care beds, and the real big one, lives saved.

[74tom] 31/10/2023 08:36

You know you've made it when Apple reference your technology in a press release!

Ps. Thanks for the continuous quality research Bamboo2, the synlab PDF in particular provides some really good insight into future potential.


"The aim now is to move nanopore sequencing through into a clinical service within five years. The commercialisation opportunity is significant since microbiology is still a culture based service but there is potential for up to 25% of samples to undergo initial same day sequencing before reflex culture of only a minority. Synnovis are at the forefront of this transformation. Target volumes each year at GSTT are 20,000 blood, 5,000 lower respiratory tract and 2,000 fluid/tissue samples [numbers are mean of actual 2019 and 2020 GSTT activity – and can be multiplied two or three fold for an ICS]. In addition, pure isolate sequencing from automated culture based on infection control or public health significance could add an additional 3,000 samples per annum."

So they are talking about 30,000 samples per annum @GSTT, but 60-90k for an ICS (Integrated care system). The key commercial question is what does the revenue model look like for ONT?

I'd presume they'll get a cut of each test cost, plus revenue from the consumables & hardware?

If they then roll that out across the NHS then ONT steadily becomes a beast over the next few years...

[bamboo2] 31/10/2023 07:26

Oxford Nanopore Technologies plc

Apple showcases Oxford Nanopore in M3 silicon chip launch

31 October 2023

Oxford Nanopore Technologies plc (LSE: ONT) ("Oxford Nanopore"), the company delivering a new generation of nanopore-based molecular sensing technology, was showcased in Apple Inc.'s global product launch on Monday. Apple positioned Oxford Nanopore's DNA/RNA sequencing technology as a companion platform that can run on Apple devices equipped with its new M3 silicon chips, supporting broad access to biological insights in scientific research, health, agriculture and industry.

In a blog post , Apple said that its latest M3 silicon chip is now even faster and more powerful to support improved nanopore sequencing, seamlessly integrating with Oxford Nanopore's onboard MinKNOW software to run and analyse DNA/RNA reads from the small-format Oxford Nanopore sequencing devices, the MinION and PromethION 2 Solo. Both products rely on external computing power to process the electrical signals from the nanopore platform.

The upgrade means that anyone with an M3-enabled Apple product, including the Macbook Pro(TM) and iMac(TM), will be able to access the same high-definition sequencing data with the MinION or P2 Solo alongside their Apple device. This further enhances the experience over M1 or M2 users and supports future improvements in nanopore sequencing data outputs. The sequencing data is then turned into usable insight through a range of software applications. Oxford Nanopore's higher-output devices that include onboard computing, including the GridION and PromethION 24 and 48, will continue to be powered by NVIDIA's A-series towers.

The new M3 chips' compute capacity can process thousands of inputs at once and in real time - similar to processing 6,000 conversations with Siri simultaneously. Pairing the M3 chip-enabled products with Oxford Nanopore's affordable and accessible MinION and P2 Solo sequencing devices has the potential to enable more global communities to access faster, richer biological data, powered by the latest machine learning technology.

Gordon Sanghera, CEO of Oxford Nanopore, commented:

"We are incredibly proud to be showcased by Apple as a complementary technology that can seamlessly integrate with Apple's new silicon chips, which is even faster and more powerful to support real-time nanopore DNA/RNA sequencing. Powered by Apple's M3 silicon chips, we are one step closer to achieving our vision of enabling the analysis of anything by anyone, anywhere by making it possible for more scientists around the world to access real-time, data rich DNA/RNA insights with only a MinION or P2 Solo and an iMac or Macbook Pro."

[bamboo2] 30/10/2023 08:55

The Combination of ONT's partnerships with bioMerieux, Synnovis and Mayo Clinic mean that we now have the local knowledge necessary to obtain fast track regulatory approval to take us into the EU, UK and US markets for diagnostics.

[bamboo2] 29/10/2023 22:40

I was looking to find out more about Jonathon Edgeworth's work with respiratory metagenomics and made a few notes about the future plans for the use of ONT's kit in the NHS.

The new pathology service for Guys and St Thomas is located at Blackfriars. It's forecast to begin operations in Spring 2024, and will be offering Oxford Nanopore sequencing services through a new organisation, Synnovis.

This is one of the public/private partnerships we read so much about. It has a 15-20 year contract.

Looking at the Synnovis RID strategy document, plans for the implementation of ONT's LRS start on page 11...



If all goes to plan, we are looking at a full LRS pathology implementation by 2025.

Further, "...Discussions are taking place with Oxford Nanopore technologies for creation of a formal
partnership through investment in the laboratory infrastructure to enable iterative high
throughput evaluation of their new technology advances and to provide information they
require for regulatory approvals and filing..."

[bamboo2] 28/10/2023 09:08

ONT currently supplies all its kit for experimental use only as this designation 'gets around' a forest of different standards around the world. As the product line matures, and new kit becomes available, it will be probably be necessary to get market approval. This is one of the reasons for the partnership with bioMerieux. ONT will benefit from their experience in translating new tech into everyday use.

As we know some of the tests produce results in a few hours, and I reckon this will be levered by bioMerieux in the fast tracking meaning market approval could be under six months.

[In order to qualify as a breakthrough device, the device must (1) provide for a more effective treatment or diagnosis of a life-threatening or irreversibly debilitating disease or condition and (2) meet at least one of: (a) represents a breakthrough technology; (b) no approved or cleared alternatives exist, (c) offers significant advantages over existing approved or cleared alternatives, or (d) device availability is in the best interest of patients.]

Further info on Fast tracking...
h ttps://biomedspecialist.com/fda-on-pace-for-a-record-number-of-breakthrough-devices-in-2023/

[bamboo2] 28/10/2023 08:54

bones698, I am certain we will be seeing an increase in costs over the next two to three years. There is quite a bit of new hardware and software to fund, and headcount will continue to increase for the foreseeable. Turnover will also increase, which along with the healthy bank balance, should mean that cash-burn is manageable.

Covid gave the co valuable experience adapting the kit towards clinical use in metagenomics, ie using the kit to id ALL the pathogens in a particular sample. This is essence of the work being done by Jonathon Edgeworth at Guys Hospital. The sequencing based test gives fast, precise results that hugely improve patient outcomes, saving lives, reducing time spent in acute care, and thus reducing costs. Secondary benefits include reduced AMR, and info on pandemic preparedness.

Two additional hospitals have started to use ONT kit, and there are current discussions on expanding this throughout the NHS.

It's likely that the kit, already in daily use for respiratory, will also be fast tracked for Sepsis.

Fast tracking the kit both here in the UK, the EU and US will also add to costs going forward, however it's the clinical market that will lead to huge growth over the next decade.

[bones698] 28/10/2023 02:38

Added this to my watch list . I'll keep an eye on it and wait for things to settle . Seems some hit with COVID kits etc . Losses are high but nice cash pile . Lot of early stage development . Think there is plenty of time to watch how this plays out yet . Chart doesn't look great longer term since float but bit of upside next few weeks i suspect . See where it is in 6 months maybe.
Not a fan of companies who jumped on the COVID bandwagon and seems these got caught out too . Rather focus on the other things in the pipeline .
They need to get costs under control and reduce cash burn that cash pule won't last forever and making 90m losses on 180m turnover isn't the best position to be in . Good luck

[bones698] 28/10/2023 02:34

Added this to my watch list . I'll keep an eye on it and wait for things to settle . Seems some hit with COVID kits etc . Losses are high but nice cash pile . Lot of early stage development . Think there is plenty of time to watch how this plays out yet . Chart doesn't look great since float . See where it is in 6 months maybe.

[bamboo2] 26/10/2023 19:51

1000 Genomes Project Oxford Nanopore Sequencing Consortium: understanding human genetic variation



Vid uploaded today by Danny Miller, who was one of the contributors on the Customer Panel at the CMD.

There's a bit of tech jargon, but not too bad.
The predictions at the end of the video are very interesting.

[bamboo2] 26/10/2023 11:06

CIT, Thanks, I have added your list to the bottom of post 1

Might be worth revisiting in some months to see if there are any changes of note.

[cousinit] 25/10/2023 19:38

and ONT:

IP Group PLC 9.71% 83,356,088 (6,056) 28/02/23
Image Frame Inve 7.35% 63,116,008 (40,136) 28/02/23
Biomerieux SA 6.88% 59,062,832 59,062,832 22/10/23
G42 Investments 5.17% 44,362,952 29,820 28/02/23
Baillie Gifford 4.86% 41,712,891 (7,689,429) 10/5/2023
GIC Private Limi 4.53% 38,910,524 26,156 28/02/23
Oracle Investmen 4.11% 35,275,568 (58,848) 28/02/23
Invesco Advisers 3.34% 28,666,566 28,666,566 28/02/23
Lansdowne Partne 3.26% 28,005,666 (228,846) 28/02/23
GT Healthcare Ca 2.88% 24,686,160 (6,653,266) 4/11/2022
Amgen Ventures, 2.25% 19,323,660 0 1/1/2023
The Vanguard Gro 2.13% 18,241,185 153,657 29/09/23
Odey Asset Manag 1.63% 13,954,795 7,965,241 29/06/23
Ip2ipo Australia 1.38% 11,812,440 0 1/1/2023
Elbrus Investmen 1.33% 11,428,560 0 1/1/2023
7-Main Ltd 1.32% 11,326,940 0 1/1/2023
Sanghera (Gurdia 1.21% 10,409,373 35,480 10/4/2023
Ag Sequencing Re 1.07% 9,198,820 0 1/1/2023

[cousinit] 25/10/2023 19:31

This is what FEVR looks like:

Lindsell Train L 15.09% 17,601,116 616 27/02/23
Capital Research 8.50% 9,919,569 136 27/02/23
Fundsmith LLP 7.63% 8,905,465 (3,785) 27/02/23
Nordflint Capita 5.08% 5,922,237 5,922,237 26/09/23
Rolls (Charles T 4.88% 5,688,308 2,380 27/02/23
Warrillow (Timot 4.78% 5,575,172 0 31/12/22
Baillie Gifford 3.89% 4,534,328 (60,051) 27/02/23
Ninety One UK Li 3.02% 3,519,237 (36,241) 31/12/22
Nuveen LLC 2.96% 3,454,161 (88,955) 9/5/2023
Invesco Advisers 1.74% 2,032,935 (1,117) 25/02/23
Walter Scott & P 1.49% 1,733,947 104,497 27/02/23
Manulife Investm 1.47% 1,720,330 180,080 28/02/23
BlackRock Instit 1.43% 1,666,841 358,265 14/07/23
Troy Asset Manag 1.36% 1,588,733 (485,228) 14/07/23
Epoch Investment 1.33% 1,548,204 341,794 23/02/23
M&G Investment M 0.84% 976,793 (24,587) 14/07/23

[bamboo2] 25/10/2023 15:12

CIT, does it look like they trawl through and cross reference any of the other [than INOV] Investment trust holdings?

I know of one US site that does do this, and it can be very interesting to take a snapshot every few months to see them change. I put their table into the FEVR header a while ago, if you want an example from a different stock.

[cousinit] 25/10/2023 14:37

I suspect they use similar info to the FT tearsheets. Seem to suggest Odey was in, out and is currently back in (which doesn't chime with the business basically winding DOWN! ). Also has lost the Schroder holding as below the notifiable level and they don't actually state the nominal held in any of the INOV reports.

[eeza] 25/10/2023 14:27

I would think they are in the Market today - sell bots unloading plenty.
Someone has to be taking the other side of the trade.

[bamboo2] 25/10/2023 14:15

bioMerieux holding 6.88% would mean that barring further dilution, they would only have to add approx 1,030,067 shares to trigger another TR-1

[bamboo2] 25/10/2023 14:07

CIT, I'd probably start with the free sign up.

Do they shed any more light on ONT's significant holders other than that is already in post 1? I'm always keen on attempting to keep up with a record of of changes.

I know the FT tearsheets are different, but I'm not convinced that the data they contain is complete or up to date.

[cousinit] 25/10/2023 13:58

No worries.

No BB - I think the majority of the user base is in the US.

Find it useful for research with the historic transcripts, forecasts and screening. Also has some useful shareholder register lists. Not comprehensive for UK small caps though but seems to have similar coverage in most mainstream markets globally.

Not sure what current offers are but do seem to have some early users who are able to provide discounted registration links.

[bamboo2] 25/10/2023 12:41

CousinIT, thanks. Will edit something together.

TIKR is new to me.
I will think about signing up.

I couldn't see a bulletin board. Do they offer one?