Oxford Nanopore Technolo... Share Discussion Threads

[brucie5] 27/3/2024 09:59

Just another 20% to drop, by the looks of.
😏

[brucie5] 25/3/2024 16:38

Blimey. New low. Not far to go now?

[p1nkfish] 24/3/2024 10:42

Tax losses might be a thing too. Crystallising those for use elsewhere.

[bamboo2] 24/3/2024 10:37

Brucie, hope the share price stabilizes soon!

We have at least one seller, INOV, [with the dregs of the former Woodford Patient Capital holding] they report 28/3/2024, so we will get more idea of their position.

GIC, the sovereign wealth fund of Singapore, was also selling recently.
[02/02/2024 TR-1 reduced to 3.976561% or 34,177,560]

Unfortunately many of the international institutional holders are below the 5% reporting threshold, meaning it's hard to keep tabs.

Ironically, the larger holders of shares that were fighting to get their allotments during the flotation now seem content to sell at any price!

This is despite the fact that the intended growth led objectives of the flotation, such as increases in headcount, and accuracy improvements are nearing completion.

[brucie5] 23/3/2024 12:39

Bamboo thank you. I. for one, am most appreciative of your ongoing commentary and undoubted expertise here. It's far too complex for me to understand in any detail, so you help me to see the wood for the trees.

I am looking for a bottoming pattern of the kind I believe we are currently seeing at OXB; and I suspect it won't be until we descend to the £1 level like a plane coming down to land. There may be bumps but eventually I expect a round of applause from the passengers who remained seated.
;)

[bamboo2] 23/3/2024 12:01

Price action is far from ideal.

This is a weak sector at present. Hopefully it should change at some point, as massive expansion of sequencing around the world is forecast. The UK market is discounting many growth and tech stocks, and analysts have taken against ONT management and their attempts to be realistic in the face of unexpected problems, such as the ban on export of devices containing NVDA chips to China.

On the positive side, ONT has almost completed the planned increases of staff in technical, manufacturing and sales functions. Naturally, this should increase turnover. Accuracy continues to improve and customer sentiment is at all time highs. The new ASIC should get an airing in May 2024.

Management have so far made no attempt to extend the life of LAT shares that expire in June 2024, which means takeover potential could lift the valuation. There are a large number of organisations around the world that could currently buy the whole company for pocket money.

I find ONT one of the most exciting companies in the UK, and despite a losing position at present will continue to hold for the long term.

[takeiteasy] 23/3/2024 11:08

Brucie, not just ONT, this part of biotech is in a major downtrend..including the highest beta type stocks in the ARK genomics fund...hot happy 5 year charts at all :(

dyor etc

[brucie5] 23/3/2024 09:57

I think bamboo offers us understanding of the huge story developing at ONT, independent of the plunging share price It may or may not be a great investment. My feeling is, it will come very good, in time; though at this rate £1 might soon reached.

[minsky] 22/3/2024 16:53

x = ONT share price;
while x > 0 {
bamboo2 posts article about ONT success;
x = x-2;
}

[bamboo2] 22/3/2024 13:53

A new National Academies of Sciences, Engineering, and Medicine [NASEM] report calls for a focused, large-scale effort to accelerate technological innovation to harness the full potential of RNA modifications to address pressing societal challenges in health, agriculture, and beyond.

The report is available to read free online,


ONT are currently the leaders in the study of raw RNA. Pacb have a system, but like their other products, it relies on SBS which means the sample to be sequenced has to undergo treatment before processing. This treatment can add errors.

Chapter 5 contains considerable info on Nanopore.

[bamboo2] 22/3/2024 11:52

Wasatch Biolabs Bets on Nanopore Sequencing for Clinical Testing, Research Services

Mar 21, 2024 | Huanjia Zhang



NEW YORK – Wasatch Biolabs is eyeing to become a high-throughput nanopore sequencing service provider for both research and clinical customers, exclusively using platforms from Oxford Nanopore Technologies.

Last month, the Brigham Young University spinoff launched one of its first commercial offerings — a targeted DNA methylation sequencing service that is based on proprietary molecular enrichment technology developed by company cofounders Tim Jenkins and Jonathon Hill, who are both professors at BYU.

"We started this company roughly two and a half ago with the goal of creating a high-throughput lab based off nanopore [sequencing]," said Wasatch CEO Chad Pollard, another company cofounder who is also currently a Ph.D. student in Jenkins' lab.

The targeted DNA methylation sequencing service enables researchers and clinicians to analyze epigenetic signatures of samples while avoiding PCR amplification biases and harsh bisulfite conversion, he said.

Jenkins, who also serves as the company's VP of research and discovery, said the workflow involves a proprietary hybridization method to pull down genomic regions of interest, which are then sequenced using the Oxford Nanopore platform.

It can currently target about 2,000 regions of interest across the genome, which typically span 1 kb to 2 kb in length. While the company offers pre-designed probes, customers can also develop their own probes with the company.

After target enrichment, sequencing libraries are prepared using Oxford Nanopore Ligation Sequencing Kit V14 protocols, followed by sequencing.

The raw data are processed using Oxford Nanopore's standard pipeline for basecalling and methylation analysis, which can detect 5mC, 5hmC, and 6mA.

For research use, the per-sample list price for the service ranges from $266 to $2,525, depending on batch size, according to the company's website.

Unlike in the traditional bisulfite sequencing approach, samples don't undergo harsh chemical treatment, which can damage them, said Hill, who now serves as Wasatch's VP of science and technology. In addition, the method requires no PCR amplification, which can be prone to errors and biases.

Besides methylation information, the service also offers insights into ​​copy number variations (CNVs), structural variations (SVs), single nucleotide polymorphisms (SNPs), and indels, Hill added.

Compared with existing target selection schemes for nanopore sequencing, such as CRISPR-Cas9-mediated approaches or adaptive sampling, Hill said the company’s method leads to "much higher enrichment" — typically in the range of 400-fold to 2,300-fold.

One application of the company's methylation assay is infertility testing, Pollard said, where it can detect the presence or absence of certain rare sperm in a sample by looking for specific DNA methylation signals.

The firm is also developing an assay to capture epigenetic signatures of neuron-derived cell-free DNA in blood as a predictor for the early onset of neurodegenerative diseases, he noted.

In general, the company wants to apply its enrichment method "in any way that's clinically impactful," Jenkins said, such as to sequence difficult regions of the genome, including pseudogenes or areas with high GC contents. Pollard said the company is in discussions with Oxford Nanopore about potentially developing the technology into a kit.

In an email, an Oxford Nanopore spokesperson said there is no partnership between the company and Wasatch at this point. She did not comment on any potential interest in commercializing Wasatch's target enrichment method.

In order to be able to offer high-throughput nanopore sequencing as a clinical service, the company is currently building out a 20,000-square-foot CLIA lab in Salt Lake City.

Wasatch also plans to move its headquarters to Salt Lake City from its current location in Heber City, Utah, where it operates an R&D sequencing lab that also offers nanopore research sequencing services, such as whole-genome sequencing and RNA-seq.

Currently, Wasatch employs 12 full-time employees and plans to expand its workforce to 40 by the end of this year. It is completely privately owned, and the only ongoing relationship with BYU is a sponsored research agreement, under which the company helps fund relevant research projects within Jenkins' and Hill's labs.

The firm has licensed its founding technologies from BYU, according to Pollard, who noted that it is working on six other patents.

To date, Wasatch has raised $11 million in Series A funding, supported by its parent company Renew Biotechnologies, a biotech incubator.

While Wasatch is betting on nanopore sequencing for methylation analysis, other companies have also been making strides on alternatives to bisulfite sequencing, using short-read sequencing platforms.

New England Biolabs, for instance, recently launched the NEBNext Enzymatic 5hmC-seq kit that promises to detect 5hmC at single-base resolution. The kit follows the company’s existing NEBNext Enzymatic Methyl-seq (EM-seq) product, which can analyze both 5mC and 5hmC but does not distinguish between them. By subtracting E5hmC-seq data from EM-seq, researchers can now determine individual 5mC and 5hmC sites, according to the company.

Additionally, Cambridge, UK-based Biomodal also recently launched a new version of its epigenetic sequencing and sample prep kit that enables researchers to achieve single-base resolution sequencing of the four standard DNA bases, 5-methylcytosine (5mC), and 5-hydroxymethylcytosine (5hmC) from the same DNA molecule and in the same workflow.

With limited benchmarking data publicly available, it remains to be seen how Wasatch's workflow will fare against other players in the space.

Still, with the data quality of nanopore sequencing continuing to improve, Wasatch management thinks the opportunity is ripe for the company to venture into the nanopore clinical sequencing service market, which is vastly untapped at this point.

"If we tried this a couple of years ago, it would not have been ready, and I think if we waited a couple more years, then others would have beat us to it," Hill said. "We're trying to catch that wave just right, where the technology is just getting to the point where it's ready for prime time."

[bamboo2] 20/3/2024 13:42

New study results from Norway confirming and bettering those at Guy's Hospital.

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

Nanopore sequencing can potentially be an effective tool in the future for clinical diagnostics



Nanopore sequencing can overcome most of the limitations current blood culture diagnostic methods face. It offers several advantages, like low cost, portability, real-time sequencing and data analysis, easy library preparation protocols, and a wide variety of sequencing kits. The cost of the ONT starter pack is $1999, which includes the MinION device, sequencing kits, and two flow cells (hxxps://store.nanoporetech.com/minion.html). In our experiments, we used the rapid barcoding and ligation sequencing kits (coupled with barcode expansion), which allowed us to run multiple samples in one sequencing run by barcoding them, thus further reducing the costs. Using this methodology, we estimate the cost per sample to be ca. $40, including the costs of culture media, DNA extraction kit, library preparation kit, and flow cell. Also, sequencing costs are gradually decreasing, and different flow cells (MinION, Flongle, and PromethION) are available per user needs.

[brucie5] 18/3/2024 11:44

Bamboo, did you see the recent IC coverage on Ont?
Perhaps counterindication of the perfect time to buy in..?
;)

[bamboo2] 18/3/2024 08:20

This is a significant milestone in the development of ONT's tech. Many of the leading US scientists in the field of genomic sequencing have had involvement.

" The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and has the potential to provide a single-instrument solution for the reconstruction of complete genomes."

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

[bamboo2] 15/3/2024 08:58

Customer comment on twitter today,

"I assembled the sup simplex reads, and the result is so absurdly accurate that I don't even need to use the famous duplex reads that I so desperately wanted..."



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So far this year, the concentration of Nanopore days has increased around fivefold. Judging by the pictures online, these are standing room only events. I hope this leads to increased adoption of ONT kit.

[74tom] 13/3/2024 12:54

This will be interesting to monitor;

"Rumour that Roche are revealing a Nanopore system on May 22. mid throughput, using the expandamer technology. Launch 2025+."

[32v31today] 11/3/2024 12:14

Very interesting announcement. This is another hot area- producing data is one thing, interpreting it is another. Lots of little (and larger) companies competing for this and will be fundamental going forward. It's much harder than everyone thinks. Interesting they teamed up with a relatively (but fast moving) unknown that raised Eur20m series A in 22. Most relevant Biomerieux backed, so stakeholders obviously getting themselves organised to move forward. Very good.

[ih_828197] 11/3/2024 11:03

hxxps://www.businesswire.com/news/home/20240311144269/en/Oxford-Nanopore-Technologies-and-SeqOne-Partner-to-Support-Interpretation-of-Nanopore-Sequencing-in-Clinical-Use

[bamboo2] 08/3/2024 18:17

Management buying 57,960 more.
£80k or so

[ih_828197] 07/3/2024 11:15

One of the biggest indicator that's making me bullish is the fact that everyday i keep seeing more and more papers pubblished on nanopore sequecing (see twitter), that's the best type of publicity that no marketing department can match.

[32v31today] 07/3/2024 10:50

I know the feeling. Managed to top up a little but not at these prices. I suspect the train is leaving the station. Looking forward, hopefully the LAT shares expiring, decreasing interest rates and (hopefully) LS tools market turning will mean a good run up to and through the summer. Some helpful commercial announcements from the company will also help build momentum. By the end of the year, hopefully we could then have steadily increasing confidence over timing of ebitda be, which is a game changer. Plus hopefully the large, less supportive, holders will be/ are sold down and no longer be a pressure on price. Apols, don't mean to sound like I'm ramping. Still a volatile run up to BE.

[apple53] 07/3/2024 10:10

anyone good on the technicals/fibs? Resistance levels? There could still be frustrated shareholders who missed out selling on the way down and who may throw in the towel prematurely on the way back up.

Thanks tom for very interesting analysis vs pacbio.