Oxford Nanopore Technolo... Share Discussion Threads

[csalvage] 12/8/2022 12:00

Share price being used by mm to scare people in to selling shares why.

[bamboo2] 11/8/2022 21:12

Illumina — Illumina slumped nearly 23% postmarket after the company missed top- and bottom-line estimates in the most recent quarter and issued disappointing guidance for the full year as it faces a troublesome macro environment.

[bamboo2] 09/8/2022 21:27

A brilliant discussion from Mark Akeson in the US

The Present and Future of Nanopore Sequencing - Mark Akeson Jul 20, 2022



This is part of the virtual symposium "Understanding Recent Advances in Genome Technology Development" supported by NHGRI, The Jackson Laboratory and Genome TDCC.

[bamboo2] 09/8/2022 10:11

Ilmn and pacb well off lows. Ont should follow.

[bamboo2] 07/8/2022 07:40

For info, Clive Brown, Tech Director at ONT, formerly held the same position at Solexa

[bamboo2] 07/8/2022 07:23

P1nk, thanks for posting.
Is he trying to raise awareness of the co for some reason?

A few paragraphs copied below. Use link for full article.




His commitment to backing British biotech is in marked contrast to some other chief executives, who have been only too happy to sell out to the highest bidder.

The weak pound has made innovative British companies tempting targets, particularly for US buyers. Sanghera, 61, and his fellow directors are, he says, 'likeminded that we are not for sale'.

Top shareholders include the IP Group, a UK-listed firm that invests in innovation, Tencent of China and Abu Dhabi's G42.

Neil Woodford, the disgraced fund manager, was an early backer of the business and US investor Acacia, which bought some of his holdings, still has a stake.

Sanghera says: 'Based on my outreach with investors, I believe most recognise there is value within the company that would not be realised in a near term-sale.'

Oxford Nanopore came to the stock market last year alongside a host of other debutantes, including take­away platform Deliveroo.

Lord Hill published a review in the spring of 2021 aimed at making the City more attractive for flotations. But the Ukraine war and rising interest rates have had a chilling effect so far this year, and Oxford Nanopore shares have dropped sharply.

'When we floated, the market was in a very different place to where it is today,' Sanghera says.

'Looking at the peer group on [US tech market] Nasdaq, some of them are down significantly more.'

The decision to float the company in London went against the prevailing trend for UK tech and biotech firms to list on Nasdaq.

Semi-conductor giant Arm is currently eyeing a flotation in the US while Cambridge biotech outfit Abcam is abandoning its UK listing on AIM and heading Stateside.

The stereotypical belief among tech company founders is that London is a second-class venue, with grudging investors who struggle to understand cutting-edge science and technology.

Sanghera is having none of it, saying: 'I want to demonstrate it can be done over here. People say we in the UK don't have the capital, we don't have the ambition, we don't have the expertise or the right people. I just don't think that's true.

'Somebody has to make a stand.'

He adds: 'Too many UK life science and tech companies are sold.' He cites the example of Solexa, a biotech firm set up by former Cambridge University scientists, that was bought by Illumina of the US for £600million in 2007.

It was a high price but the deal enabled the American company to become the world's dominant DNA sequencing business. Illumina is now worth $35billion (£29billion) even after heavy recent share price falls so, in hindsight, it looks as though Solexa was a bargain buy. And it shows how the UK missed the chance to develop a multi-billion pound British champion, enabling the US to reap the gains.

[p1nkfish] 06/8/2022 21:24

Good someone is making a stand for the UK.

[bamboo2] 29/7/2022 21:15

New vid, in Layman's terms. 3m26s long. Time well spent.

Nanopore sequencing: the most comprehensive insight into cancer genomes.

"Without nanopore sequencing, our work would not be possible"

[bamboo2] 28/7/2022 19:49

NIH Researchers Deploy Nanopore Sequencing for Large-Scale Alzheimer’s Study
Jul 27, 2022 | Huanjia Zhang

BALTIMORE – Researchers at the National Institutes of Health and their collaborators are exploring the use of nanopore sequencing to analyze thousands of brain samples as part of a study of Alzheimer’s disease and related disorders.

The long-read sequencing project, enabled by NIH’s recently established Center for Alzheimer's and Related Dementias (CARD), aims to build a framework for the large-scale application of nanopore sequencing while filling the knowledge gaps about genomic variation in Alzheimer’s disease and other neurological disorders.

Founded about two years ago, CARD is a collaboration between the National Institute of Neurological Disorders and Stroke (NINDS) and the National Institute on Aging (NIA), said Cornelis Blauwendraat, an NIA investigator who is involved with the CARD long-read sequencing project.

“One of the goals of CARD is to generate resources,” said Blauwendraat, adding that the long-read sequencing project, which is a collaborative effort between NIH and other academic scientists, intends to sequence around 4,000 brain samples to create a sequencing and bioinformatic resource for other researchers.

According to Benedict Paten, a professor at the University of California, Santa Cruz, who is part of CARD, the goal for the project is to create something similar to the Broad Institute’s Genome Analysis Toolkit (GATK), which offers tools for genome variant analysis that are mainly designed for Illumina data, but for nanopore sequencing. While there are other long-read sequencing modalities, such as the Pacific Biosciences HiFi sequencing, Paten said the team settled on nanopore sequencing for the project because of its cost advantage and scalability. “The [PacBio] HiFi is amazing technology, but right now, it is expensive and time-consuming to scale,” he said.

According to Blauwendraat, the roughly 4,000 samples included in the project will be frozen brain tissues, mostly obtained from biobanks in North America, that cover Alzheimer’s disease, Lewy body dementia, and other dementias.

While working with brain tissues may involve “a little bit more effort,” there are also added benefits to studying these samples, Blauwendraat said. For one, compared with other sample types, such as blood, the brain can offer direct insights into mosaic variation involved in neurological diseases. Additionally, nanopore sequencing can not only sequence the DNA in these samples but also find methylation signals.

Blauwendraat emphasized that the project is making an effort to include subjects of diverse backgrounds. “We don't just want to sequence a couple of thousands [of samples of] European ancestry and call it a day,” he said.

While the long-read sequencing project is still optimizing its workflow, Blauwendraat said that the wet lab protocols typically start with sectioning the frozen brain tissues into small pieces for DNA isolation once they arrive from the biobanks on dry ice.

However, given that the brain is a “fairly fatty” organ, Blauwendraat said the team had to optimize the DNA extraction protocol for different brain regions in order to achieve appropriate DNA yields for nanopore sequencing while preserving the integrity of the DNA molecules. “It's a very delicate process,” he explained. “We really want to preserve the long reads.”

After QC, the DNA will undergo shearing to obtain fragment sizes between 30 kb and 35 kb, which is optimal for nanopore sequencing for this study. The sheared DNA will then be turned into libraries and sequenced using the Oxford Nanopore Technologies PromethIon platform.

For this project, Blauwendraat said, the goal is to sequence one sample per flow cell to achieve 30X to 40X genome coverage and an N50 of about 30 kb. The team operates two Oxford Nanopore PromethIon 48 and one PromethIon 24 sequencers, he added.

In addition to sequencing, the project also aims to establish a computational infrastructure to achieve phased assemblies of nanopore sequencing data at scale. “Until recently, there was really no end-to-end pipeline to have phased assembly for nanopore [sequencing],” said Mikhail Kolmogorov, a National Cancer Institute investigator who is also part of CARD.

To address that, Kolmogorov said, the team has developed pipelines to achieve large-scale de novo genome assembly using nanopore sequencing data only. “We have been spending a lot of time making sure that the assembly is very accurate,” he said. “We want to produce the best diploid assemblies possible.”

According to Kolmogorov, the final analysis output of the project will include a collection of phased small and structural variants. In the end, all of the data from the samples — including the raw sequencing data, the alignment and assembly data files, as well as the methylation data — will be made “broadly available to any qualified researchers” through ​​AnVIL, an NIH-designated data repository platform, the group said.

Given the scale of this project, Blauwendraat said, the group had to overcome a few technical bottlenecks. One of them is to carry out the wet lab procedures at scale. To address that, the project has “invested heavily” in robotics, he said, and the team is currently testing out various automation platforms for sample preparation and QC.

Still, Blauwendraat said, the brain cutting step, which cannot be easily automated, presents a challenge and will remain more labor-intensive.

Another bottleneck is the large amount of data, given that every sample will generate about one terabyte of data. To overcome that, he said CARD has provided the project with fiber optics and high-speed internet to facilitate data transfer.

Regarding nanopore sequencing’s error rate, Paten said that for detecting single-nucleotide variants genome wide, nanopore sequencing currently outperforms Illumina sequencing based on Genome in a Bottle (GIAB) statistics. “There is a small deficit in precision [for nanopore sequencing], but it's made up for by the fact that you miss fewer variants, and there is more of the genome that ends up getting covered as a result,” he said.

However, “the homopolymers are a problem still” for nanopore sequencing, Paten said, adding that he thinks that it's “just going to be a work in progress.”

So far, the group has sequenced about 250 samples. While the researchers want to make sure that everything works well before starting to scale up, they are hopeful to release a preprint describing the methods used in the project toward the end of this year.

Eventually, the team is hoping to shed light on genomic variations pertinent to neurological diseases that were previously unattainable using short-read sequencing.

“I'm very interested in characterizing structural variants in the germline but also on the somatic and mosaic level,” said Fritz Sedlazeck, a researcher at Baylor College of Medicine and another academia collaborator of the CARD long-read sequencing project.

One reason for missing heritability of neurological disorders is the lack of knowledge about complex repeats within the genome, he said. With the nanopore long-read data generated in this project, researchers can now dive into these parts of the genome and identify variants that are potentially associated with Alzheimer’s disease and related disorders.

“I don't think anyone can claim that they're going to solve [these brain disorders] with 4,000 samples, but we're going to put up a fight and discover some new cool stuff,” Sedlazeck said.

[bamboo2] 18/7/2022 21:23

Twitter just now...

Researchers at UCSC have developed a method that can convert Illumina libraries with short DNA fragments into long DNA molecules optimal for sequencing with the nanopore MinIon platform.

This could "massively lower" the entry barrier for high-throughput sequencing. 🧬


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

BALTIMORE – Researchers at the University of California, Santa Cruz have developed a method that can convert Illumina libraries with short DNA fragments into long DNA molecules optimal for nanopore sequencing with the Oxford Nanopore Technologies MinIon platform.

The workflow, named "Illumina But With Nanopore" (IBWN), employs a strategy to circularize short Illumina library molecules and copy them by rolling circle amplification, resulting in long molecules with tandem repeats that enable MinIon sequencing for almost all Illumina libraries with comparable cost and accuracy to the Illumina MiSeq.

There were two main motivations behind developing the protocol, said Christopher Vollmers, a biomolecular engineering professor at UC Santa Cruz who presented the method, described in a preprint on BioRxiv last month, at the Advances in Genome Biology and Technology annual meeting in June.

For one, he said, like most small molecular biology labs, the lack of an Illumina sequencer on-site often means a turnaround time of several weeks to process sequencing samples with a genomic core facility. To reduce that wait time, the group sought to devise a way to sequence Illumina libraries using the Oxford Nanopore MinIon, which even a small lab like his can afford to purchase.

The other incentive for developing the method was to "massively lower" the entry barrier for graduate students to interact with high-throughput sequencing technology firsthand, Vollmers said. A lot of Ph.D. students in labs without Illumina sequencing platforms cannot get first-person experience with the technology, he said, adding that "we don't do anybody a favor if we give people molecular biology Ph.D.s, but they have never handled the Fastq files."

Mechanistically, Vollmers said, IBWN is built upon the Rolling Circle Amplification to Concatemeric Consensus (R2C2) method that was previously published and optimized by his lab for full-length cDNA sequencing.

"The idea is straightforward," he said, adding that the method leverages the fact that the vast majority of Illumina libraries have known adapters on their ends.

By targeting these double-stranded adapters, R2C2 can circularize short library molecules using Gibson assembly and copy them using rolling circle amplification with Phi29 polymerase, creating long, linear, double-stranded DNA pieces that contain multiple copies of the original Illumina library molecule's sequence. These long molecules can then be sequenced on the MinIon platform.

"Whatever you put on your Illumina sequencer, that's where we come in and convert," Vollmers pointed out. "You don't have to change the Illumina prep at all, [IBWN] just builds on top of it."

To analyze the data, the team also developed software called Concatemeric Consensus Caller with Partial Order alignments (C3POa), which can process the R2C2 nanopore data to generate consensus reads while demultiplexing the Illumina library indexes.

To test and benchmark the method, the team applied IBWN to RNA-seq libraries of the human A549 cancer cell line, Illumina ChIP-seq libraries of soybean samples, Illumina Tn5-based genomic DNA libraries of a Wolbachia-containing Drosophila melanogaster cell line, and Illumina Tn5-based genomic DNA libraries from lung cancer cell lines enriched for certain cancer-relevant genes.

Overall, the researchers found that the R2C2 method led to MinIon sequencing data with accuracy comparable to an Illumina MiSeq 2x300 bp run, independent of the read position. In particular, they reported that R2C2 RNA-seq data were "almost entirely interchangeable" with data produced by the Illumina MiSeq. Meanwhile, R2C2 library metrics from ChIP-seq and target-enriched Tn5 libraries were "very similar" to those generated by Illumina sequencers.

Beyond that, the group also sought to achieve real-time analysis of R2C2 libraries using nanopore sequencing. For that, they developed a computational pipeline called Processing Live Nanopore Experiments (PLNK), which can carry out basecalling, process raw sequencing data into R2C2 consensus reads, demultiplex the libraries, and align the demultiplexed R2C2 reads to a genome in real time.

In terms of cost, Vollmers said, without taking instrument cost into account, R2C2 sequencing with MinIon, which can generate up to almost 9 million reads from a single flow cell, is "about equivalent, maybe a bit more expensive" than traditional Illumina sequencing using MiSeq. However, he pointed out that for a small lab, the number one expense is often labor cost, and the fast turnaround afforded by R2C2 sequencing makes the method still cost effective. "If I have a grad student sitting around for a month waiting for data and having to work on something that's not the main project, that is a big loss for me," he said.

Continued...

[bamboo2] 13/7/2022 09:51

See how cancer research can benefit from accessible, targeted long nanopore reads which facilitate a comprehensive analysis of multiple variant types across genomics, transcriptomics, and epigenetics.

Sponsored research. Clearly written.

[bamboo2] 13/7/2022 09:47

Gap filled earlier this morning.
[Dated 6/7/2022 Measured 283-288]

[elsa7878] 13/7/2022 09:45

Ok thanks. Hard to find any research online (MIFID etc), so difficult to quantify the opportunity.

[bamboo2] 13/7/2022 09:39

elsa, I do not have an idea of where sales will be in three years.

If forecasts are realised and the installed user base grows, an increasing amount of revenue will be coming from licensing and consumables. The existing range of hardware will be maturing, with the incremental improvements in accuracy reaching a plateau. This will allow research efforts to broaden.

It is highly likely that new hardware and software products addressing both the personal genetic testing market, and proteomics will become available in this timescale.

Much depends on the way healthcare settings decide to implement the growing use of genomics in modern medicine. Historically, for numerous good reasons, centralisation of sequencing facilities has been the case. Now there is a choice. ONT allows for massive decentralisation, with local clinic based approaches. The reason that this is so compelling is the time and cash saving that decentralisation brings, it also saves lives.

[elsa7878] 13/7/2022 07:47

Bamboo - as the knowledge leader here - do you have any revenue expectations further out than the next 2 years. Figures I see indicate growth in revenue of circa 20-25% pa but continuing losses of around £80 million pa for this year and next.
Clearly heaps of cash but at some point it needs to turn a profit to justify the £2.5 billion market cap.
Thanks in advance.

[bamboo2] 13/7/2022 07:08

Results from first batch of Kit 12 are starting to appear.


TBLR reporting on Twitter... The new Kit 12 chemistry from @nanopore is amazing!

Sequencing bacterial genomes using MinION Mk1C produced a median value of raw read accuracy of 98.75% (simplex) and 99.63% (duplex). The genome assembled using trycycler was almost perfect (99.99995% identity vs. the reference)!

edit, TBLR typo[?] mentioned in the comments. The new kit is actually called V14, rather than 12.

[bamboo2] 12/7/2022 07:59

ONT cost summary, in USD

Oxford Nanopore Technologies’ sequencing costs are all available on their store website. Here’s a summary, to save you a bit of clicking:

[the lockkeeper] 11/7/2022 09:37

Think you are on the money there! Rate of growth will be phenomenal there are no comparators that can compete for sequencing.

[bamboo2] 11/7/2022 07:07

Ayl, could it also be recognition that one way or another the existing building will be too small in ten years?

[ayl30] 11/7/2022 06:28

Looks a good deal. In effect a fundraising without incurring dilution of equity or debt

[bamboo2] 11/7/2022 06:03

11 July 2022

Oxford Nanopore Technologies plc

("Oxford Nanopore")

Sale and leaseback of headquarters building to The Oxford Science Park

Oxford Nanopore Technologies plc (LSE: ONT), the company behind a new generation of molecular sensing technology based on nanopores, today announces that it has completed the sale of its interest in the Gosling Building (the "Property") to The Oxford Science Park (Properties) Limited ("TOSP") for GBP42.5 million.

On completion of the sale, TOSP will immediately grant Oxford Nanopore an occupational lease of the Property for 10 years; at a rent of GBP1.8 million per annum.

Tim Cowper, Chief Financial Officer of Oxford Nanopore, commented:

"We are pleased to have agreed the sale and leaseback of our headquarters building. The proceeds will be used for continued development of our core business."

[bamboo2] 11/7/2022 05:51

Illumina But With Nanopore
Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the R2C2 method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, as well as regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.