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[bamboo2] 23/2/2023 21:56

Slow Move from Culture Towards WGS Diagnostics?
Feb 21, 2023

Time for a change of pace. We usually talk about hospital acquired infections in our Lab Services Blog, but a recent blog article from Eric Topol asking why whole genome sequencing isn’t used for infectious disease diagnostics got us talking. Sequencing-based diagnostics have become almost standard of care in areas like prenatal testing and oncology in recent years, but have yet to make a dent in hospital infectious disease testing. For example, did you know there is currently no sequencing-based diagnostic for infectious disease that is cleared by the FDA?

Why has the move from traditional culture-based diagnostic methods to sequencing-based diagnostics been so slow? The article points at the lack of technical maturity, cost feasibility, and faulty financial incentives. All true. But, we at DZD believe the next 3 to 5 years will be a transformative period for sequencing-based diagnostics, and that FDA grade clinical applications will start to enter the micro lab within this window of time. Here’s why:

Rapid sequencing technologies have just hit clinically viable accuracy.

Illumina revolutionized the world by introducing high accuracy, high throughput sequencing technology. However, the problem with severe infections is a problem of time. If you are going to affect treatment, the diagnostic has to work on the scale of minutes to hours, not days. Unfortunately, traditional sequencing requires batch processing of many samples to be cost-effective, and overnight runs to get results. For most severe infections, the results take too long and the costs are too high to serve as an alternative to culture.

Rapid sequencing technologies like those from Oxford Nanopore Technologies (ONT) have always been appealing because of their speed, yet suffer from lower data yield and accuracy – but the pace of improvement has been remarkable. Over the last 5 years, raw read accuracy for the ONT platform has gone from below 85% to over 99%. At DZD, we are now seeing enough data with just an hour or two of sequencing to enable downstream analysis with accuracy rates high enough to make clinical grade calls.

Sequencing costs for single sample testing continue to fall dramatically.

You’ve all seen the charts, sequencing costs have fallen dramatically over the last decade. But those charts gloss over the fact that the majority of cost reduction comes from being able to multiplex increasingly more samples on ever larger machines. What if you just want to sequence one sample and do it quickly?

The cost for single sample sequencing is still prohibitively expensive. With some of the latest advances coming from the sequencing world, and process optimizations of the kind we are working on, we anticipate that microbial sequencing costs for single samples will drop by 90% over the next 3 to 5 years, enabling cost competitive sequencing for one patient sample at a time.

The road ahead…

Sequencing capabilities and costs aren’t the only barriers to moving away from culture-based diagnostics. To replace culture, any solution also has to think about how to isolate and retrieve low-abundance pathogen signals from complex samples, the analysis pipeline for making reliable organism ID calls, and how to profile antibiotic susceptibility without culture. These are being worked on by us and others.

However, sequencing is reaching a new level of technical maturity which suggests that we are in an exciting time for infectious disease diagnostics. The next 5 years will be different than the past 5 years and we can’t wait to see the impact it will have on our field. If you would like to hear more about our thinking on the evolution of this space, please reach out and let’s get talking.

Jong Lee
CEO & Cofounder
Day Zero Diagnostics

[bamboo2] 17/2/2023 21:44

Not certain, but think this could be very useful/pivotal for ONT.

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National Institutes of Health researchers have developed and released an innovative software tool to assemble truly complete (i.e., gapless) genome sequences from a variety of species. This software, called Verkko, which means “network” in Finnish, makes the process of assembling complete genome sequences more affordable and accessible. A description of the new software was published today in Nature Biotechnology.

Verkko grew from assembling the first gapless human genome sequence, which was finished last year by the Telomere-to-Telomere (T2T) consortium, a collaborative project funded by the National Human Genome Research Institute (NHGRI), part of NIH.

“We took everything we learned in the T2T project and automated the process,” said NHGRI associate investigator Sergey Koren, Ph.D., who led the creation of Verkko and is senior author on the paper. “Now with Verkko, we can essentially push a button and automatically get a complete genome sequence.”

The T2T consortium used new DNA sequencing technologies and analytical methods to generate and assemble the remaining 8-10% of the human genome sequence. However, the researchers assembled those fragments manually — a process that took this massive and highly skilled team several years to complete. Verkko can finish the same task in a couple of days...cnt'd



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Found the 'paper'. This is very interesting, but the detail is behind the wall. :o(

[bamboo2] 17/2/2023 15:07

Genomeweb report on 'All of us' paper.



..."Oxford Nanopore was probably further behind three years ago," Elgar said. But its accuracy has improved, and its platform for whole-genome sequencing is now "fully mature." Moreover, the PromethIon is the only instrument other than Illumina's NovaSeq that can offer the scale required by population sequencing programs, he said. PacBio is catching up, though — especially with Revio — "but not in the same ballpark," he said.

Elgar suggested that short read sequencing is "just not equipped" to handle some applications, such as complex rearrangements in cancer genomes.

"I think people will start making choices in the future," he said. "Long reads will not necessarily diminish the short-read market, just expand the range of applications for whole-genome sequencing. The great thing about Oxford Nanopore and PacBio is, you get that for free."

However, "cost is still an issue, and it still drives a lot of decision making," he added.

In the meantime, Sedlazeck said, large-scale, clinically focused long-read sequencing projects will continue to pump out data. The NIH's Center for Alzheimer's and Related Dementias (CARD), for instance, will be sequencing about 4,000 brain samples with Oxford Nanopore sequencers. In addition, the Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) consortium is analyzing hundreds of unsolved Mendelian disease cases with long reads. And, of course, there's All of Us.

"There will be more and more long-read data coming out of All of Us this year," he said.

[bamboo2] 13/2/2023 16:50

At last, the first PromethION device in a NHS lab.

ExeterGenomes@ExeterGenomes

Today we have welcomed a PromethION 24 to the Exeter genomics Laboratory - exciting new tech to help us to make more diagnoses for acutely unwell children
@SWGenomics...@nanopore

[bamboo2] 10/2/2023 20:04

Karen Miga has uploaded the slides from her 2023 AGBT T2T presentation.

[bamboo2] 09/2/2023 21:48

Some good reports starting to make their way out of AGBT23.

"During her talk at #AGBT23 Karen Miga showed the first whole human genome assembly using a combination Oxford Nanopore Technologies' ultra-long and Duplex sequencing reads. She shared how Oxford Nanopore data alone results in extremely high quality #T2T chromosome assemblies."

"The assembly was generated from ~30x Duplex (35-40kb+) and, 30X Ultra-Long (100kb+).

"Karen also discussed Duplex's clear progression & how it delivers extremely high (#T2T) quality, the longest continuous read lengths, & the most complete genome assemblies"

Karen concluded by sharing why nanopore sequencing is the only platform that is able to independently produce complete #T2T genome assemblies.

Enabled by Duplex nanopore sequencing provides industry leading and the most complete T2T assemblies."

[bamboo2] 04/2/2023 09:13

I'm certain 'All of us' will be getting much attention at next weeks AGBT23 in Florida.

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Separately, sometime over the next few weeks it looks like John Gorzynski and his team will be making a new attempt on the sequencing world record using PromethIon.



Nice timing if we get headline figures shortly after AGBT.

[bamboo2] 30/1/2023 23:52

Dr. Steven Salzberg is a Johns Hopkins University researcher and director of the Center for Computational Biology at Hopkins. I spoke with him about genomics, about long-read sequencing, about human biology and human diversity, about funding, technology choice, about complete and incomplete genomes, about jobs in bioinformatics. He described his technology choices and about the choices one has to make in small labs. He shared his thoughts about the trend toward pangenomes and graph genomes. And he described how technology has changed and how happy that makes him. Teeny reminder, Steven Salzberg headed bioinformatics at TIGR, the Institute for Genomic Research run by J. Craig Venter. It was part of the venture to determine the sequence of the human genome. And yes, there were human genome assemblies based on teeny tiny read lengths.
[transcript available]


"...there's currently only one technology on the market. And that's nanopore..."

[bamboo2] 30/1/2023 20:52

Article on Illumina's uncertain future.

Illumina’s Sorrow and DeSouza’s Woes

[bamboo2] 30/1/2023 00:32

Healthcare’s standard genome is mostly based on one American.

[bamboo2] 19/1/2023 17:08

Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.

Quite few mentions in this paper. Some interesting cost comparisons.

[cerrito] 17/1/2023 10:55

While for me the TU was respectable I was looking for something more and can intuitively understand the weakening of the sp

[bamboo2] 17/1/2023 10:26

Anastrophe, I am slightly disappointed that there is no detail in the outlook.

We need to start to see some of the pilot project work that has been ongoing in the NHS and elsewhere in the world come to fruition in the form of new business.

[anastrophe] 17/1/2023 10:07

I don't see why there's been such a bad reaction to the trading update - did we expect more from the Abu Dhabi deal?

[bamboo2] 17/1/2023 07:26

17 January 2023

Oxford Nanopore Technologies plc

Trading update

-- Total Group revenue for fiscal year 2022 is expected to be approximately GBP199 million
-- Core Life Science Research Tools revenue is expected to be approximately GBP147 million during the period

-- Life Science Research Tools revenue is estimated to have grown by approximately 15.7% on a reported basis and by approximately 25% on an underlying basis(1)

Oxford Nanopore Technologies plc (LSE: ONT) ("Oxford Nanopore" or "the Group"), the innovator and provider of a new generation of molecular sensing technology based on nanopores , today provides a trading update, ahead of reporting its annual results in March.

Performance for the year ended 31 December 2022 is expected to be in line with the Life Science Research Tools ("LSRT") revenue guidance set out in the Group's 2021 annual results, on 22 March 2022.

The Group expects to report LSRT revenue for the year ended 31 December 2022, of approximately GBP147 million compared to LSRT revenue of GBP127.0 million for the year ended 31 December 2021, representing annual growth of approximately 15.7% on a reported basis and approximately 25% on an underlying basis, excluding the impact of FX, revenue from COVID-19 sequencing and revenue from the Emirati Genome Program.

The Group expects to report total revenue of approximately GBP199 million, for the year ended 31 December 2022, which includes non-recurring revenue of GBP51.8 million following the conclusion of the Group's COVID-19 testing contract with the Department of Health and Social Care, compared to total revenue of GBP133.7 million in 2021.

Gordon Sanghera, Chief Executive Officer, commented:

"Oxford Nanopore continues to demonstrate strength and resilience with strong core revenues driven by growth across all customer groups in 2022. This reflects an increase in global demand for our DNA/RNA sequencing technology across many areas of scientific research. Our latest technology improvements have propelled this growth, enabling our customers to generate highly accurate, high-yield, information-rich data, in real time and from any length fragments of DNA/RNA, from short to ultra-long.

"The 2022 launch of the high-yield, highly accessible palm-sized PromethION 2 (P2) Solo device was well received and is further expanding our growing PromethION(2) user base. This launch coupled with our Q20+ chemistry continues to establish Nanopore as a highly accessible, accurate, information rich platform at any scale.

"With a single high-performance technology for all users' sequencing needs, we enter 2023 with good momentum as we continue to invest in our operational expansion alongside our innovation."

Notice of results

The Group is planning to report annual results for the year ended 31 December 2022 on 21 March 2023 and publish its Annual Report shortly thereafter.

[bamboo2] 16/1/2023 20:12

...Usually, there’s a hierarchy of tests. By the time you reach the most complex – which might be sending a sample to Finland to look for genes associated with epilepsy – weeks can be lost, Bloomfield says.

“It delays diagnosis and therefore potentially treatment, and it’s obviously difficult for the family and whānau [extended family] as they don’t know what’s going on with their baby.”

Which is why the Liggins Institute is importing PromethION machines to provide rapid sequencing in New Zealand...

[bamboo2] 16/1/2023 19:17

More fantastic reports reaching twitter. eg

New paper out January 15, 2023.

Long-read sequencing technologies substantially overcome the limitations of short-reads but to date have not been considered as feasible replacement at scale due to a combination of being too expensive, not scalable enough, or too error-prone. Here, we develop an efficient and scalable wet lab and computational protocol for Oxford Nanopore Technologies (ONT) long-read sequencing that seeks to provide a genuine alternative to short-reads for large-scale genomics projects. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the NIH Center for Alzheimer's and Related Dementias (CARD). Using a single PromethION flow cell, we can detect SNPs with F1-score better than Illumina short-read sequencing. Small indel calling remains to be difficult inside homopolymers and tandem repeats, but is comparable to Illumina calls elsewhere. Further, we can discover structural variants with F1-score comparable to state-of the-art methods involving Pacific Biosciences HiFi sequencing and trio information (but at a lower cost and greater throughput). Using ONT based phasing, we can then combine and phase small and structural variants at megabase scales. Our protocol also produces highly accurate, haplotype-specific methylation calls. Overall, this makes large-scale long-read sequencing projects feasible; the protocol is currently being used to sequence thousands of brain-based genomes as a part of the NIH CARD initiative. We provide the protocol and software as open-source integrated pipelines for generating phased variant calls and assemblies.

[p1nkfish] 14/1/2023 12:09

Thank you bb2. It's looking better and will feed through to IPO too in time.
Reminder of significant investor dates is always useful.

[bamboo2] 14/1/2023 11:18

Knock out performance from the recent Flowcell and chemistry upgrades continues to be reported by Scientists and other customers on Twitter, eg

Luke Blagdon Snell@lukebsnell

Have to see it to believe it. @nanopore R10 flow cells, v14 kit chemistry, SUP basecalling, duplex reads. Median quality score= 30. Significant number Q>40. Seq game changed...

...Ecstatic! We are going to move all bacterial isolate sequencing over to this strategy next week. Now a firm believer in this...

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Oscar Gonzalez-Recio @OscarGenomics
Impressive performance of duplex basecalling from @nanopore
KIT14 and R10.4.1 with accuracy mode of 99.96% and median of 99.3%. #developeraccess

This is a new era.

[bamboo2] 14/1/2023 11:13

Full year results and update this Tuesday.

For info, this was the outlook from 13 September 2022

Guidance

Trading year to date is in line with expectations and we continue to expect full year 2022 LSRT revenue to be in the range of GBP145 million to GBP160 million.

Full year 2022 LSRT revenue guidance accounts for an expected tapering of COVID-19 sequencing revenue in the second half of 2022 and expected EGP revenue of GBP15 million to GBP20 million, lower than previously anticipated. Full year 2022 revenue reflects the continued growth and diversification of the broader user base.

Over the medium term, we continue to anticipate revenue growth at a compound annual growth rate of more than 30% and gross margins greater than 65%.

In the shorter term, we remain vigilant regarding the current macroeconomic environment. For full year 2023 we continue to expect LSRT revenue to be in the range of GBP190 million to GBP220 million. Our full year 2023 gross margin target of greater than 60% also remains unchanged.

The Company is in a strong financial position, with GBP602.6 million of cash and cash equivalents and treasury deposits at 30 June 2022. We are still targeting a breakeven adjusted EBITDA by 2026.

[bamboo2] 14/1/2023 11:11

Key Financial dates for 2023 added to header a few days ago.

17 January 2023
Full year 2022 trading update

21 March 2023
Full year results for the year ended 31 December 2022

12 June 2023
Annual General Meeting

July 2023
Half year 2023 trading update

6 September 2023
Half year results for the six months ended 30 June 2023

[bamboo2] 13/1/2023 07:43

Following the above Nature article, a Gordon Sanghera/Clive Brown interview

When scientists want to know about genes, chances are they use instruments called sequencers. Some of them can generate long-reads, which helps with analysing genomes. The method of the year according to Nature Methods is: long read-sequencing. For a story I chatted with scientists at companies and in academia about long-read sequencing and did some podcasts, too. This episode is with Dr. Gordon Sanghera, CEO of Oxford Nanopore Technologies.

[bamboo2] 12/1/2023 19:56

Method of the Year 2022: Long-read sequencing

ONT feature prominently in the article and seem to come out on top!

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To the delight of scientists across the life sciences, reads, which are the output of sequencing instruments, have been getting longer. Reads might be sequenced DNA or RNA and could one day routinely be entire genomes, transcriptomes and epigenomes at high throughput and accuracy, and maybe even the amino acid sequences of proteins.


Academics have happy tales about how long-read technologies have empowered their genomics projects. A few companies have facilitated this journey, notably Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). Of late, other firms presenting long-read approaches include Element Biosciences, Illumina and MGI. Ultima Genomics and others have plans in this area.

Long reads have buoyed numerous findings in individual labs. In larger ventures, among the celebrated achievements are those in the Vertebrate Genomes Project (VGP) and the Telomere-to-Telomere Consortium (T2T)1. A set of papers and news features related to the T2T Consortium can be found as a Nature Collection online. During the T2T project, says Adam Phillippy, a researcher at the National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI) who co-leads the T2T Consortium, the longest read he and his colleagues handled had one million base pairs. Long-read sequencing is being used by the Human Pangenome Reference Consortium (HPRC)2,3,4. The HPRC teams want to assemble the human genome at the T2T level of completion and capture a “better spectrum of humanity in terms of how they represent allelic diversity,” says University of California Santa Cruz researcher Karen Miga, who co-leads the T2T Consortium with Phillippy and is part of the HPRC.

Population-level data from diverse populations are needed, says Heidi Rehm, who, among other appointments, is the chief genomics officer at Massachusetts General Hospital’s department of medicine and medical director of the clinical research sequencing platform at the Broad Institute of MIT and Harvard. She and her colleagues have found instances in which Black people received information about risk of a heart condition without sufficient evidence on genetic variants to support it5. Population data had been lacking about these variants, and such data are still limited, says Rehm.

One population- and diversity-focused project underway involves 500 individuals: 50 from each of 10 different Australian Indigenous communities. Samples are taken with consent from and with involvement of these communities. From these individuals’ data, one genome that represents each Indigenous community will be assembled telomere to telomere. The scientists apply whole-genome sequencing with long reads from PacBio and ONT sequencers and Illumina short-read technology. “The jury is still out on what is the best technology for telomere-to-telomere sequencing,” says Hardip Patel from the National Centre for Indigenous Genomics at Australian National University, who co-coordinates the project with Ira Deveson at the Garvan Institute of Medical Research. Sequencing technology itself is rapidly changing. In 2023, the scientists will revisit their technology choices, says Patel. Technology choices have shaped long-read achievements to date and color the wish lists for the future of long-read sequencing...continues

Use link to read whole article.

[bamboo2] 06/1/2023 16:53

Scrutable, There is a substantial amount of other info out there.

I can recommend a regular twitter search on 'nanopore' as this will give you an overview of the situation with ONT as it changes on a daily basis. I normally will highlight anything useful and not too technical on this BB, although I have reduced the amount I post as I try to keep it relevant to the investing community. The jargon will sink in eventually, and much of the biological detail is not vital to know from an investing pov.

Simon Barnett [Ark] on twitter is worth following, and recently produced this article...



This provides additional info about the three main sequencers, and where ONT fits into the bigger picture.