Oxford Nanopore Technolo... Share Discussion Threads

[bamboo2] 28/1/2022 09:28

Ayl, There are some significant developments on the technical side, with the Flowcell/Chemistry/Software that mean that later this year ONT kit will match the basic accuracy of Illm and Pacb, and bring superior detail, alongside all the other benefits, such as Raw reads, Real time results, Low costs, etc. The kit is already in use by early adopters in the community.

Following this weeks FoG meetings and presentations, I am hopeful that we will see the NHS making much more use of ONT kit. The other area where we should see evidence of growth is in the area of Metagenomics. [Environmental genomics]

[bamboo2] 28/1/2022 09:01

Ayl30, that is probably not going to happen for a few years as management have a golden share, that until 2023 can veto takeovers. This was one of the potential weaknesses for the share price discussed around the time of the listing. Management were particularly keen to avoid another Solexa type situation, where for peanuts, Illumina walked away with tech that became the foundation of their business.

Twitter is an interesting read at the moment as we have the juxtaposition of the Scientific community finding the ONT kit so good that they are buying the shares, while retail shorters, emboldened by success in bringing down other recent listings, are taking a punt.

[ayl30] 28/1/2022 08:36

At this rate if the price reduces much further it will be a candidate for a US takeover

[bamboo2] 25/1/2022 18:16

Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?



This mini review will be focused on the ONT MinION as a platform for microbiome analysis due to its low cost and portability. Recent summaries of capital/reagent costs indicate most second-generation sequencing platforms and the PacBio system range from $80 000 to $800 000 (Loman et al. 2012; Quail et al. 2012). In contrast, the ONT MinION is available for $1000, but requires a separate computer for data collection (bringing the capital cost to $3500–$5000). A new version of the ONT sequencer [the MK1C] combines the computer, a touch screen, 1 TB SSD drive, a 6-core CPU and a 256-core GPU in a single, handheld unit for the same capital costs. Nanopore sequencing is low cost because it is predicated on measuring the electrical conductivity of individual DNA strands translocating protein pores in a semiconductor membrane (Schneider and Dekker 2012). For the ONT system, each DNA molecule has an adaptor ligated to one end that interacts with a docking protein and binds to the nanopore. This docking protein regulates the speed by which the DNA molecule traverses the membrane (initially 50 bp/s; now 450 bp/s for each active pore). The DNA sequence is then determined on 5 bp segments (k-mers) by measuring the change in electrical conductivity across the membrane as the DNA flows along each individual channel. The basecalling is done using hidden Markov or recurrent neural network models to convert the electrical ‘squiggles’ into the various nucleotides.

Overall costs to perform a MinION sequencing run are modest. For example, a MinION flow cell costs $900 (if bought individually), a sequence reaction is $100, while additional enzymes/reagents for PCR/end-repair/library preparation/washing are ∼$200. If 40 barcodes are used per sequence run and each flow cell can be used at least twice (with washing), costs are ∼$1200 per 80 samples, which comes to $15 per sample. Furthermore, the newer MinION chemistries are providing >2 million reads within 24 h in many laboratories. This yield is roughly 50 000 raw reads per sample, providing up to 30 Gb per flow cell. Given the cost of the hardware is small, the required reagents are modest and a service contract or dedicated technician is not required, the MinION system is the first widely affordable sequencing system for virtually any laboratory.

[rogerc1985] 25/1/2022 09:34

Is the advfn Mcap wrong hereMust be

[bamboo2] 24/1/2022 07:53

G42 Healthcare’s Biogenix Labs becomes the first certified high throughput lab in Middle East to conduct sequencing of the SARS-CoV-2 virus, for COVID surveillance and the identification of new variants, using Oxford Nanopore technology



Abu Dhabi, January 23rd, 2022: Biogenix Labs, the UAE’s first COVID-19-accredited large-scale testing laboratory and part of Abu Dhabi-based leading health tech company, G42 Healthcare, has received certification for the use of Oxford Nanopore sequencing technology to conduct SARS-CoV-2 sequencing for COVID-19 surveillance and variant detection.
With this, Biogenix Labs becomes a Certified Service Partner for Oxford Nanopore and the first lab in Middle East to be certified for providing cost-effective, high accuracy sequencing for genomic epidemiology for COVID-19 strain surveillance in RT-PCR positive cases with a quick turnaround time.
The protocol is highly scalable and can be deployed on Oxford Nanopore’s range of sequencers such as the MinION, GridION and PromethION depending on the sample volumes and turnaround time. This capacity and volume of samples sequenced at Biogenix Labs positions it as a preferred referral lab for COVID-19 epidemiology through genome sequencing.
The ARTIC Midnight protocol uses overlapping PCR amplified targets across the viral genome, giving the advantage of whole genome surveillance rather than focusing only on the gene that codes for the viral spike protein. The barcoding capacity which ensures thousands of samples in a single sequencing run per instrument coupled with a rapid analysis pipeline post sequencing, makes the setup key in a pandemic situation, allowing scientists and healthcare workers to have up to date variant information for disease management.
Nanopore sequencing and ARTIC Midnight Kit can achieve higher coverage with a lower number of reads, producing less ambiguous base calls, and is affordable when compared to alternative approaches (reference).
Dr Fahed Al Marzooqi, Chief Operations Officer, G42 Healthcare, said: “We are delighted with this certification and the opportunity to enhance rapid insights that can be swiftly actionable for public health policy. As the UAE’s first COVID-19 accredited large-scale throughput testing laboratory, Biogenix Labs upholds the safety of communities and we have so far carried out more than 2.5 million RT PCR and saliva tests that have enabled safe return to work, seamless travel and helped children go back to school.”
He added: “The ARTIC Midnight Kit will allow us to deliver high-quality SARS-CoV-2 genomic sequencing faster, with more flexible workflows and cost optimization. In the long term, Oxford Nanopore sequencing unlocks many possibilities for the analysis of other pathogens, microbial surveillance, and larger public health impact that we look forward to exploring.”
Set up in only 14 days to cater to the urgent scale-up for COVID-19 testing in early 2020, Biogenix Labs have played a crucial role in the 4Humanity Phase III inactivated vaccine trials and is a frontrunner in diagnostics and viral genome sequencing in the UAE and region. The laboratory has now extended its offerings to facilitate molecular and genomic diagnosis that will provide insights into rare disease treatments.
The role of genomic epidemiology is important in the successful control and prevention of the COVID-19 pandemic. Oxford Nanopore sequencing technology has been used in more than 100 countries around the world throughout the pandemic to enable precise tracking of pathogen evolution, provide detailed insights to inform pandemic decision-making and the management of future outbreaks.
Dr Gordon Sanghera, Chief Executive Officer, Oxford Nanopore commented, “It’s great to see nanopore sequencing being provided as a service by the G42 Healthcare’s Biogenix Labs to enable rapid scale up of their SARS-CoV-2 sequencing efforts. The team have already made a huge contribution to the pandemic response and this certification will enable them to continue to gain rapid insights to inform public health decision makers.”
The ARTIC Midnight Kit, enabled by Oxford Nanopore sequencing, promises rapid turnaround of tens to thousands of samples and the scalable nature of the technology has minimal hands-on time, facilitating automation and high throughput, thereby making it cost optimal. The ARTIC classic method has been used extensively to support public health through the pandemic.

[bamboo2] 23/1/2022 11:10

FoG 2022, 25/2/2022 Greg Elgar will be joined by Andy Beggs and Sue Hill

Info is a little thin on the ground but it looks like some sort of announcement about the increasing role of third generation sequencing and PromthION in the NHS. As I have mentioned before, in Genomic England's video's, Elgar, Beggs and co can barely disguise their excitement and enthusiasm for the use of this kit instead of the SBS based platforms [Illumina/Pacb] they have used previously.



[Professor Dame Sue Hill OBE PhD DSC CBiol FRSB Hon FRCP Hon FRCPath is the Chief Scientific Officer for England – providing expert clinical scientific advice across the health system and head of profession for the healthcare science workforce in the NHS and associated bodies – embracing more than 50 separate scientific specialisms.

Sue is the Senior Responsible Officer for Genomics in NHS England, leading developments in this area, having previously established the NHS Genomic Medicine Centres and led the NHS contribution to the 100,000 Genomes Project. She is a respiratory scientist by background with an international academic and clinical research reputation.]

[bamboo2] 21/1/2022 16:30

Tuesday next week sees Greg Elgar present his plans at FoG for Nanopore sequencing in the NHS. The focus will be on the new pipeline that Genomics England are working on to sequence cancer genomes using 3rd generation nanopore sequencing technology.

[thefartingcommie] 21/1/2022 11:26

re...ONT potential 'liason' with Apple

Oxford Nanopore Technologies Provides Tech Updates, Inks ...
hxxps://www.genomeweb.com › ... › Sequencing
2 Dec 2021 — The firm is also working on an update to the MinIon Mk1C portable sequencing platform that will be based around the Apple iPad Pro. "The P2 Solo ...

Oxford Nanopore announces technology updates at Nanopore Community Meeting

Wed 1st December 2021

[bamboo2] 20/1/2022 12:07

Looking into the WGS [Whole Genomic Sequencing] of new-borns, in association with the Ultra-rapid sequencing work done recently in Santa Cruz, and surrounding areas, is fascinating.

In the UK, Genomics England have embarked on a major consultation that could lead to routine screening of all new-borns.



Whilst a broad base of systematic evidence is still being accrued, some reporting has become available since about 2018.

There are a number of concepts behind the push towards a more precision medicine based approach. These are based around sound common-sense and health economics.

Number one has to be improved outcomes. In 2018 it would typically take 24-48 hours to organise WGS, with a diagnosis in 3-12 days. In a large number of critical care situations this will lead to unnecessary suffering, and poorer prognosis. Faster diagnosis can allow for life-saving intervention.

It is easy to see why there is so much excitement about a diagnosis in under five hours.

Due to the lack of evidence [in practice, WGS has only been around a few years] and the wide variety of different conditions treated, it is hard to be specific about cost savings [Genomics England has some info in a post above this one], but there are a number of estimates. In the US there is an insurance based system of healthcare which has covered a few cases. Savings of $800,000 per case is seen as an average. Some estimate as high as $1.2-2.0m per case.

[bamboo2] 19/1/2022 12:04

Forthcoming news. PNAS January 25, 2022

Activity on Earth BioGenome Project and affiliated initiatives due to ramp up considerably in 2022

The Earth BioGenome Project (EBP), a global effort to map the genomes of all plants, animals, fungi and other microbial life on Earth, is entering a new phase as it moves from pilot projects to full scale production sequencing.





"...Importantly, new instruments from both Pacific Biosciences and Oxford Nanopore mean that the per assembled gigabase cost is now very reasonable..."

[bamboo2] 18/1/2022 07:46

New report recently published.

As part of the decentralised C-19 surveillance effort, ONT kit is increasingly used, and accounts for 20-25% of all uploads [approx two million] to the database. The report discusses how the massive amount of data has been organised, and is being used.

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"...Most existing public health sequencing initiatives are built around whole genome sequencing capacity afforded by facilities in large hospitals and public laboratories. However, with the emergence of lower capital cost sequencing instruments such as Oxford Nanopore platforms, genomic sequencing is now available to smaller regional hospitals and academic laboratories, vastly expanding the sequencing capacity for a hypothetical surveillance network. Such technology is small and cost-effective enough to conduct sequencing of small pathogen genomes in the field, in the clinic and in the classroom. However, with this democratisation of sequencing technologies, a new challenge emerges in how data generated across many different laboratories can be collated, compared and analysed to support outbreak/pandemic response simultaneously at local, regional, national and global levels..."

CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.



More info on COG

[bamboo2] 14/1/2022 09:01

What kind of savings are possible, if instead of trial and error, precision medicine is used?

Genomics England, through their 100,000 Genomes Project provide quite a large number of examples on their website and in their video's. eg

"...a 10-year-old girl whose previous seven-year search for a diagnosis had multiple intensive care admissions over 307 hospital visits at a cost of £356,571. Genomic diagnosis enabled her to receive a curative bone marrow transplant (at a cost of £70,000). In addition, predictive testing of her siblings showed no further family members were at risk."

Owen's story is interesting as had multiple hospital visits and treatment. After genomic testing was found to have a thyroid defect. Thyroxine once a day seems to be curative.


More here...

[tonsil] 14/1/2022 08:52

Top ten genomics companies reviewed First one up is Oxford Nanopore. hTTps://youtu.be/dd6MBI7EvPg

[bamboo2] 13/1/2022 18:54

Even more compelling, this work at Stanford was done prior to the recent upgrades in Flowcell/Chemistry/Basecalling. Speed and accuracy would be even better with the upgrade.

======================================================================================
Kishwar Shafin, [writer of PEPPER-Margin-DeepVariant basecaller s/w] replies to question, "Was this using the new Q20?"

No, this is nanopore R9.4.1 Guppy 4.2.2 HAC reads + PEPPER-Margin-DeepVariant r0.4.

Guppy 5 "SUP" with PEPPER-Margin-DeepVariant r0.7 would require much less coverage so will provide a turnaround time of <5h.
======================================================================================

Interview with Euan Ashley on NBC


"Looking forward to teaching other hospitals and labs how to do it"

[bamboo2] 13/1/2022 09:11

Ayl30, market not seeing the significance of this, yet!

This explains so much, the partnership with Oracle and NVIDIA for example, and Illumina's hasty move into their version of 'long sequencing'.

Illumina and Pacb can't compete with this. I don't know of another company that can.

Looking at this from a health economics perspective, the potential savings to be had are huge.
Genomics England has confirmed this in recent studies.

[ayl30] 13/1/2022 07:56

Good news, should help to drive sales line

[bamboo2] 13/1/2022 07:43

Worth repeating in the RNSNON

Oxford Nanopore Technologies plc Fastest human genome sequence uses Oxford Nanopore
13/01/2022 7:00am
RNS Non-Regulatory

TIDMONT

Oxford Nanopore Technologies plc

13 January 2022

Scientists describe new approach in NEJM, using Oxford Nanopore DNA sequencing technology to improve prognosis in critically ill patients, in less than 8 hours

Oxford Nanopore worked with a team led by Stanford University School of Medicine in a research study to develop a rapid, whole genome sequencing approach, that:

-- Improves prognosis in critically ill patients and guides clinical management at least as well as current short read technologies.

-- Reduces the time to identify disease-causing genetic variants - to as little as 7 hours and 18 minutes, a world record.

-- Provides the potential to identify large and complex disease-causing variants, missed by previous approaches, while enabling phasing and detection of epigenetic markers, which are known to have clinical impact.

Traditionally, rapid characterisation of variants that cause genetic disease, from whole human genome sequencing, has been challenging. Whole genome sequencing enables better detection of such variants but has typically taken days or weeks to return a result. This timescale can be particularly problematic in time-critical contexts, such as identification of suspected pathogenic variants in a critically ill patient.

Scientists from Oxford Nanopore Technologies, NVIDIA, Google and others worked with a research team led by Euan Ashley, MB ChB, DPhil, professor of medicine, of genetics and of biomedical data science at the Stanford University School of Medicine, to develop a whole genome nanopore sequencing approach that can characterise pathogenic variants in as little as 7 hours and 18 minutes - faster than any previously published approach in clinical samples.

Prioritising time to result

The team used PromethION 48 - Oxford Nanopore's highest-throughput sequencing device, capable of running up to 48 flow cells at once - to sequence 12 unique research samples from patients aged 3 months to 57 years. Each PromethION Flow Cell has the capacity to sequence at least one whole human genome on its own, but when multiple flow cells are used concurrently to sequence one genome, the time taken to complete the whole genome sequence is significantly reduced.

The team were able to take advantage of this and prioritise time to result, to generate a whole human genome and list of variants in as little as 5 hours and 2 minutes - a new Guinness World Record. Manual review of this list of variants that followed enabled disease-causing variants to be identified in 7 hours and 18 minutes.

A pathogenic or likely pathogenic variant was identified in five of the 12 samples analysed as part of the research. According to the study authors, this "informed clinical management (including sympathectomy, heart transplantation, screening, and changes in medication) for each of the five patients or their family members."

Each genome was sequenced to a minimum of 173Gb, with a mean read N50 of 25kb. Variant calling resulted in a median of 4,490,490 small variants, and 22 prioritised structural variants per sample. The base calling was accelerated using NVIDIA V100 and P100 GPUs.

Gordon Sanghera, CEO, Oxford Nanopore Technologies commented:

"Genomic information can provide rich insights and enable a clearer picture to be built. A workflow which could deliver this information in near real time has the potential to provide meaningful benefits in a variety of settings in which rapid access to information is critical.

"We designed PromethION to be able to prioritise time-to-result by using multiple flow cells together, just like cluster computing. We're delighted to see the research team demonstrate the real life potential of Nanopore technology through their research. I look forward to seeing the impact of real-time sequencing technology in the clinic in the near future."

Speed is of the essence

This new approach for rapid whole genome analysis using nanopore sequencing enabled insights from whole genome sequencing data to be gained within hours and not days or weeks, which could provide real benefits if applied in the clinic in the future. Further to this, nanopore sequencing enables a more comprehensive genetic picture to be built because of the technology's ability to generate very long reads, which can span large and complex disease-causing regions.

The Oxford Nanopore team worked with researchers at the Stanford School of Medicine to modify library preparation for optimum time efficiency and maximum yield. They also helped establish the framework for the cloud-based analysis and introduced a washing step that removed the need for barcoding, significantly reducing the cost per sample whilst retaining the rapid turnaround time.

These research findings point to the potential utility of validating a rapid whole genome sequencing platform for management of critically ill patients. This rapid whole genome sequencing approach was developed by a large group of contributors, including scientists from UCSC, Google and NVIDIA - who optimised and accelerated the small variant pipeline and cloud analysis - and Baylor College of Medicine, who contributed the structural variant pipeline.

Kimberly Powell, Vice President of Healthcare, NVIDIA commented:

"NVIDIA and Oxford Nanopore Technologies have a longstanding partnership in accelerating real-time genomic sequencing, and this project is a significant milestone in our journey.

"NVIDIA GPUs were instrumental in accelerating both base calling and variant calling with NVIDIA Clara Parabricks. Accurate, GPU-accelerated sequence analysis helped achieve this world record, which is monumental for quick identification of genetic variants linked to disease."

Read the letter in the New England Journal of Medicine summarising this work:

[bamboo2] 12/1/2022 23:38

News this evening from the US.

Eric Topol,
=========================================================================
"This is the future. Happening NOW.
Sequencing the genome of critically ill patients at the point of care with the diagnosis made as rapidly as <8 hours"
=========================================================================


Fastest DNA sequencing technique helps undiagnosed patients find answers in mere hours
share
A research effort let by Stanford scientists set the first Guinness World Record for the fastest DNA sequencing technique, which was used to sequence a human genome in just 5 hours and 2 minutes.

January 12, 2022 - By Hanae Armitage



...""To achieve super-fast sequencing speeds, the researchers needed new hardware. So Ashley contacted colleagues at Oxford Nanopore Technologies who had built a machine composed of 48 sequencing units known as flow cells. The idea was to sequence just one person’s genome using all flow cells simultaneously. The mega-machine approach was a success — almost too much. Genomic data overwhelmed the lab’s computational systems.

“We weren’t able to process the data fast enough,” Ashley said. “We had to completely rethink and revamp our data pipelines and storage systems.” Graduate student Sneha Goenka found a way to funnel the data straight to a cloud-based storage system where computational power could be amplified enough to sift through the data in real time. Algorithms then independently scanned the incoming genetic code for errors that might cause disease, and, in the final step, the scientists conducted a comparison of the patient’s gene variants against publicly documented variants known to cause disease.

From start to finish, the team sought to hasten every aspect of sequencing a patient’s genome. Researchers literally ran samples by foot to the lab, new machines were rigged to support simultaneous genome sequencing, and computing power was escalated to efficiently crunch massive datasets. Now, the team is optimizing its system to reduce the time even further. “I think we can halve it again,” Ashley said. “If we’re able to do that, we’re talking about being able to get an answer before the end of a hospital ward round. That’s a dramatic jump.”

Long-read sequencing
Perhaps the most important feature of the diagnostic approach’s ability to quickly spot suspicious fragments of DNA is its use of something called long-read sequencing. Traditional genome-sequencing techniques chop the genome into small bits, spell out the exact order of the DNA base pairs in each chunk, then piece the whole thing back together using a standard human genome as a reference. But that approach doesn’t always capture the entirety of our genome, and the information it provides can sometimes omit variations in genes that point to a diagnosis. Long-read sequencing preserves long stretches of DNA composed of tens of thousands of base pairs, providing similar accuracy and more detail for scientists scouring the sequence for errors.

“Mutations that occur over a large chunk of the genome are easier to detect using long-read sequencing. There are variants that would be almost impossible to detect without some kind of long-read approach,” Ashley said. It’s also much faster: “That was one of the big reasons we went for this approach.”

Only recently have companies and researchers honed the accuracy of the long-read approach enough to rely on it for diagnostics. That and a drop from its once-hefty price tag created an opportunity for Ashley’s team. To his knowledge, this study is the first to demonstrate the feasibility of this type of long-read sequencing as a staple of diagnostic medicine.""...

[bamboo2] 12/1/2022 19:33

Wittenberg, plant biologist at Keygene in the Netherlands is first off the mark with initial comparative findings using ONT's new 10.4 pore.

Shows ONT as a standalone sequencer is equivalent or better than both Pacb and Ilmn [comparing with recent sequencing results]. With the improvements that are planned over the next few months, we should be seeing more and more evidence of ONT's tech outperformance.



Conclusion & perspectives

We generated and released datasets and assemblies of two plant species based on the latest Oxford Nanopore technology and chemistry, that are comparable or better than public releases but with less effort in data generation and computational time. Data generation and analysis were completed within a week after high molecular weight DNA isolation. The KeyGene STL de novo assembler is significantly faster compared to most state-of-the-art assemblers. This is in strong contrast to public, consortium-based assemblies that have taken many years and large investments to be completed.

Raw read accuracies of Oxford nanopore reads have significantly increased in the past few months using the latest chemistry and R10.4 pore type in combination with a plant-trained basecalling model.

[edwardt] 11/1/2022 21:12

Anyone listen in?

[the lockkeeper] 11/1/2022 16:58

Wish I had bought today as opposed to yesterday ?Oh the joys of sharedealing...

[bamboo2] 11/1/2022 16:52

Link to this evenings presentation at 8pm GMT



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tonsil, no not a pro, just a keen private investor. I really like this kind of tech, and think these small decentralised sequencers will revolutionise healthcare in a way that can't easily happen with the larger, lab based systems. I have done some online courses to get a better understanding of NGS, but my technical knowledge is quite limited.

[tonsil] 11/1/2022 10:42

Thanks for your watchful eye on this. Are you a med research pro?

[bamboo2] 11/1/2022 10:00

JPM Virtual Healthcare conf this evening 8.00pm gmt.

I think the presentation from Gordon Sanghera, CEO, and Tim Cowper, CFO, will be more investor focussed than the recent technical update at the community conference. There may be some surprises.

Illumina used their presentation yesterday to announce some good sales figures, and a new attempt at longer reads. There is some interesting comment from the users and scientists on twitter. Illumina have called it Infinity but read length looks to be limited, unlike ONT, which is normally only limited in read length by sample strand length, as far as I understand it. Consensus seems to be that Pacb is the likely loser.