Oxford Nanopore Technolo... Share Discussion Threads

[bamboo2] 16/12/2022 11:56

p1nk, Assuming they are selling all and want the cash cleared by 31/12/2022, by my calcs, this could be the day we see the back of Acacia.

[p1nkfish] 14/12/2022 20:40

We need a larger market to dominate.

[bamboo2] 13/12/2022 11:54

edward, In the UK, Illumina have first mover advantage in lab based genomics. They have been established for around 14 years, compared to two or three years for ONT. They are good at short reads in bulk. They are not so good when it comes to longer reads and the more repetitive areas of the genome. I reckon it's quite likely that the two technologies will be used together, as has been the case in the recently completed T2T project in the US [Karen Miga & co].

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Looking at the recent volume, and the settlement period, I'm wondering if this week we will see the last of Acacia's sales? They are likely to want to get things done and dusted for their 31/12/2022 year end.

[edwardt] 13/12/2022 10:23

would be huge disappointment if not ONT

[edwardt] 13/12/2022 10:22

100,000 newborn babies set to have their DNA fully decoded
Genomics England programme aims to extend the number of treatable conditions detected to about 200


us or illumina win the contract??

[p1nkfish] 09/12/2022 12:12

Getting a clubbing.

[p1nkfish] 08/12/2022 10:26

Yes,that's my thinking too bb2. Possinlw flush coming this month.

[bamboo2] 08/12/2022 08:22

Acacia, who I estimate have less than 3m shares to sell, will likely be disappointed that there is no spike to sell into after the New York meeting and update. This means if they plan to sell all before their year end, we will likely see more price pressure until 31/12/2022 or whenever they are finished.

[bamboo2] 08/12/2022 08:09

The link in the above post takes you to the ONT website where there is a film of the presentation.

The past few months have seen a focus on the consolidation of accuracy improvements, with advanced plans to increase it further over the coming months, through various methods.

A new MinIon is in the offing, which can be paired with Apple tech.

A new device that removes the need for sample prep is in development.
A major step forward for those considering clinic/office/home/field based genomics.

The company is experiencing some very rapid technical development.

[bamboo2] 07/12/2022 18:07

Oxford Nanopore technology updates show consolidations and updates for a single, high-performance sequencing platform
Wed 7th December 2022

At the Nanopore Community Meeting, Rosemary Sinclair Dokos, Stuart Reid and Lakmal Jayasinghe showed how the Oxford Nanopore sequencing platform’s capabilities continue to be pushed. They provided a summary of the current platform, imminent platform developments, and the innovation pipeline. Multiple updates and consolidations to improve and simplify the platform were presented, showcasing a single, simple, high-performance sequencing technology.

The latest R10.4.1 flow cells in combination with Kit 14, for high-yield, high-accuracy (Q20+ single molecule) sequencing, are expected to move from ‘early access’ to ‘released’ status in the first quarter of 2023. This enables all users to generate highly accurate, information-rich data, in real time and from any length fragments of DNA/RNA, providing one platform for all users’ sequencing needs.

Updates were provided that included developments in platform chemistry, hardware, data analysis, preparation and product range:

Current platform status and imminent developments

Comprehensive, information-rich genomics

Low cost, high-yield accessible sequencing

Simple, versatile and consistent platform for end-to-end analysis

Simple pathways for assay developers: Project TurBOT and Q-Line

Unique platform features

Pipeline developments: Towards sequencing by anyone, anywhere




Oxford Nanopore sequencing today, and imminent developments
Comprehensive, information-rich genomics

Oxford Nanopore’s sequencing platform provides a comprehensive view of human, and any other genomes, with simple, scalable workflows. This is driven by the ability to sequence any-length DNA/RNA fragments and to sequence native molecules to elucidate methylation for free and in real time. Updates that enhance this include:

Sequencing with high-yield and high-accuracy Kit 14, in combination with R10.4.1 flow cells, will move from early access to general release in Q1 2023

The standard 400 bases per second (bps) conditions delivers >Q20 (>99%) single molecule, single-pass accuracy at high yields

The chemistry provides complete, continuous, accurate genomes, delivering a comprehensive picture of genomic variation from push-button analysis workflows

Simplex data – from single strands of DNA – is showing Q20+ (>99%) single molecule accuracy and, comprehensive high performance across all human genetic variation including SNP, SNV and methylation

Duplex sequencing – from complementary strands of DNA for higher accuracy – is now achieving Q30 (>99.9%) accuracy for more challenging applications. Enhanced rates of duplex data within runs can now be seen, for example >70% duplex rate was shown from an E.coli dataset. Flow cells are currently offered under a developer release

New compute performance: with the Dorado basecaller and NVIDIA’s PromethION A100 processor, high accuracy basecalling (HAC) results are available in real time during the 72-hour sequencing run. Dorado is expected to be introduced into the operating software, MinKNOW, in Q1 2023

Base modifications provide critical insights into many biological questions, including cancer research. Oxford Nanopore provides the most accurate and comprehensive technique for base modifications, offering 99.5% raw read accuracy for 5mC calling (2-way classification)

The Kit 14 and R10.4.1 model for 5mC base modification is available and integrated now

5mC and 5hmC model is available as a stand-alone now, with a goal of integrating into MinKNOW in Q1 2023 offering users unprecedented insights into methylation of their samples

Upgrades are largely delivered through consumables and software, so that users do not need to invest their research funds in new devices.

Low cost, high-yield, accessible sequencing

Users can access ultra-high yield sequencing data at competitive pricing. At 1-2 human genomes per PromethION Flow Cell today, this provides customers with the ability to sequence up to 9,984 whole human genomes per year at 30x coverage from $345 per genome, including library preparation costs. Further chemistry developments are in the pipeline designed to further extend the yield of PromethION Flow Cells.

Simple, versatile and consistent platform for end-to-end analysis

The Oxford Nanopore platform is versatile and can be tailored for a range of use cases, including whole genome sequencing, epigenetic analysis, transcriptomic and single cell approaches, and applications requiring both short (down to 20 bases) and ultra-long (over 4 million bases) fragments to be sequenced. Real-time data permits users to generate the answers they need, when they need them, even with targeted sequencing.



From sample preparation to analysis, platform improvements were shown that better support users with end-to-end analyses:

To support consistent high-yield performance and a new wave of PromethION users on the new PromethION 2 (P2), new end-to-end workflows are being introduced, initially focusing on human samples (cells, blood), which are supported by the expanding Oxford Nanopore field application scientist team. Users should expect to routinely achieve >100Gb per PromethION Flow Cell using these protocols with R10.4.1 flow cells and Kit 14

Protocols are being released that enable sample recovery after sequencing, designed to support users with particularly rare/precious samples so that they can drive for maximum data per sample, rather than per flow cell

The EPI2ME analysis platform provides simple, powerful analytical pipelines​ at the push of a button, from a comprehensive picture of human variation to metagenomics to single cell. EPI2ME labs enables local or distributed sequencing and GitHub for user defined workflows and analysis. An open data analysis ecosystem has now been created, to combine user workflows with the Oxford Nanopore platform. Users can run their own analysis pipelines from EPI2ME with simple point and click implementation. Register your interest here

Users can develop their own workflows in GitHub, increasing the reach of the simplicity of the product.

Enabling simpler pathways for assay developers: Project TurBOT and Q-Line

Oxford Nanopore has been investing in a range of ISO9001-qualified devices with locked-down, standardised format, that will integrate Q20+ chemistries in a controlled offering with fewer and more predictable releases with a refreshed launch of ‘Q-Line’

Project TurBOT integrates standard high sample-throughput liquid handling devices with sequencing devices such as MinION and P2 Solo to deliver sample preparation and analysis in a single device. Register your interest here

Unique platform features

Adaptive sampling, where users can use the software, MinKNOW, to select and enrich regions of interest for targeted sequencing, is a unique capability unlocked by real-time sequencing. This ‘intelligent’ method is being used in many ways, including focusing in on cancer genes in a human genome, or enriching pathogen DNA in a broader human/metagenomic sample.

Adaptive sampling is already built into MinKNOW, and has now been demonstrated on P2

Updating small, portable formats

MinION Mk1D is in development – the next generation of portable sequencing that is designed to be compatible with the new iPad Pro®. With USB-C connectivity, the Mk1D can utilise the power of M1/M2 Apple® silicon for basecalling whilst also combining simple sequencing with the market leading user interface. Those interested can now register their interest in Mk1D here.

Pipeline developments: Towards sequencing by anyone, anywhere
Oxford Nanopore integrates accessibility into its product design, in order to broaden access to genomics.

Research teams have been utilising machine learning to develop new enzymes that pass DNA through a nanopore faster. With greater speeds these have the potential to deliver 400Gb of sequence data, and as many as four human genomes from a single PromethION Flow Cell

Additional chemistry and basecalling developments aim to characterise more diverse base modifications including 8oxoG and ribo-bases in DNA

New nanopores are in development with almost double the length of reader head of R10.4,1 with a view to further improved homopolymer resolution

Only Oxford Nanopore offers direct RNA sequencing, including characterisation of base modifications. With new RNA-specific nanopores and faster enzymes, a threefold improvement in output with accuracy was shown, increased to 96%. In addition, an order of magnitude reduction in required sample input was shown, to 50ng. This is expected to be offered as a developer release early in 2023

Oxford Nanopore seeks to redefine the term “liquid biopsy”, showing R&D progress that offers the promise of sequencing native DNA/RNA directly from complex biological fluids – without the need for lab equipment – with the goal of broadening access to this important technique

A new method continues to be developed, with the goal of delivering unparalleled single molecule accuracy, including for low frequency (eg below 0.1%) genetic variants. By combining standard sequencing with ‘Outy’, a method of reversing the direction of sequencing through a single nanopore, it is possible to re-read a single molecule forwards-and-backwards through that nanopore. This can continue as many times as is required to reach the desired accuracy. Base modifications are also detected with high-accuracy by the Outy method.

[bamboo2] 07/12/2022 11:04

Sample prep free nanopore sequencing for liquid biopsy.

[bamboo2] 06/12/2022 16:24

Tech update imminent.

[bamboo2] 05/12/2022 16:53

Here, at Sanger, we are lucky to be working at the crossroads of innovation and have many role models who are paving the way toward a healthier, more sustainable future. Physilia Chua is one of them. She is a postdoctoral fellow leading the BIOSCAN flying insects project in the UK and her work documents UK insect diversity and the discovery of species interactions.

She is part of the Tree of Life Programme and her team has recently won a Translation Committee Fund from the Technology Translation team at Sanger with the aim of making sequencing more accessible. Her team is working to adapt three existing high-throughput DNA sequencing protocols to an ONT (Oxford Nanopore Technology) platform, which is a small, portable and affordable sequencing machine. This will open the door to sequencing anything, anytime, anywhere.

[ianood] 03/12/2022 17:16

Excellent call Bamboo

[p1nkfish] 03/12/2022 12:57

bb2, looks like you nailed the turn.

[bamboo2] 30/11/2022 19:57

p1nk, My chart suggesting a turn today or tomorrow.
Have added to trading account.

[bamboo2] 29/11/2022 10:44

p1nk, it should be obvious once the seller is finished. Millennium will likely have a plan!

[p1nkfish] 25/11/2022 12:11

Initial position, look to add when it breaks out whenever that is.
It does look like consolidation with volume and volatility dropping.
Question is whether a break up or down.
Weekly MACD and RSI upward, ADX down, trend losing steam. Needs some volume.
Thoughts?

[bamboo2] 24/11/2022 16:54

74tom, p1nk, good luck with the new positions!

[bamboo2] 24/11/2022 08:39

p1nk, Acacia year end is 31/12/2022.

I would guess that they will be finished selling by then as they will want to maintain their track record of profitability.

We probably won't know for sure until they report fourth quarter and full year in March 2023

ps, on 18/10/2022 5m were sold by unknown seller.
I think this was Acacia, as unaware of anyone else selling quantity.
If so, they have less than 2.9m to sell.
This matches the requirement of Millennium quite well.

[p1nkfish] 23/11/2022 20:51

Thanks bb2, I bought today.
CTO action is strange but at least his sales were absorbed without much impact.
Agreed, it's small vs Acacia.

[bamboo2] 23/11/2022 20:41

p1nk, Re catalysts, ONT will RNS the tech update at the start of December.

This will outline the tech releases for the period between now and early May 2023 when London Calling will take place. eg new hardware/chemistry/software

With regard to commercial catalysts, we are still waiting to see how Genomics England plan to implement the tech in the NHS. It's permanent inclusion next to the existing Illumina installation looks certain. This means manufacturing a considerable quantity of gear, just for the centrally placed Genomics labs. The unknown is the likely demand for locally based clinical and diagnostic sequencing. One major hurdle is the need for sample prep for DNA extraction, which is often a lab based job.

There are already a considerable number of pilot projects under way in the UK.