Oxford @nanopore vs #Illumina #NovaSeq: how far away are they from each other?
I followed with attention the recent PromethION updates, both in terms of new flowcells, with denser pore surfaces, and software and reagents, with the Q20+ basecalling.
It is reasonable to assume that the rollout of the Q20+ updates will be commonplace in the next few months, which means that there is only another decimal in base calling accuracy to put the ONT technology on par with Illumina short-reads. Oxford Nanopore has already announced...
... their work and preliminary results for their updated dual strand base calling, and the modal shows a peak near Q30, which means there wouldn't be much to debate anymore when it comes to per-base accuracy between the two technologies.
In terms of throughput, the two instruments, i.e. the Oxford Nanopore PromethION 48 and the NovaSeq 6000 are already fairly matched against each other. The max theoretical throughput per day of both is similar, and the flexibility of flowcell number/size also makes them on par.
Beyond the original PromethION 24 and 48 models, Oxford Nanopore also announced new versions of the same platform in the PromethION P2 and P2 Solo, which mean they will be encroaching into Illumina's midsize market where the NextSeqs are dominant.
So what's there left to achieve for the PromethION and GridION systems so that they can be used in research projects and clinical applications instead of Illumina systems?
As these are nanopores that can produce long reads, they compete against Illumina and PacBio in markets where fully phased assembled genomes are an advantage over short-read mapping. Most prominently this is the case in neonate genome sequencing.
There are other markets that have been established with short-reads, or are being established as a short-reads NGS market, such as NIPT or Liquid Biopsy Cancer Screening, where the starting DNA material is short and doesn't immediately benefit from long read technology.
In these cases, Q-scores but mainly throughput are king, so methods to pre-treat the short DNA fragments into tagged concatenated dsDNA may mean the ONT technology has an advantage.
If this concatenation is achieved in a PCR-free manner, then the fact that ONT can natively read 5mC methylation (and other modified bases) means there is a path forward to turn the current Liquid Biopsy Cancer Screening assays based on epigenomic profiling into ONT-based assays.
What is needed for these improvements? A lot of these are related to sample prep, high plexing of samples, and the robustness of the ONT instruments to perform within a window of operation every time they are used.

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More from @AlbertVilella

16 Sep
Another twitter thread on (#NGS) technologies, this time focussing on Oxford @nanopore. The company sells their larger instrument, the PromethION, which has some advantages/limitations over other competing technologies:
The advantages of the PromethION are mainly (1) the read length of Oxford Nanopore's technology, which depending on the sample prep method, can go over several megabases, and (2) it's a high-throughput instrument that can run up to 48 individual flowcells, at the lowest cost.
Another major advantage of the technology is that it's not limited to a 4-letter alphabet of unmodified A,C,G,T, but can also natively basecall commonly epigenetic modifications, such as 5mC (methylation) and others, making the use for epigenomic profiling very straightforward.
Read 15 tweets
15 Sep
In #biotech #stocks today, I highlight $BLI Berkeley Lights which is currently down -11%. The trend is still looking downwards since Dec 2020 when it had a remarkable burst of what I would call "frothiness" and since then it's been on a gentle downwards trajectory. Image
Sometimes these big short hikes are not entirely rational, and as of late, with the emergence of the meme stock phenomenon, normal decent-looking #biotech companies can be hijacked by pump-and-dumpers that don't even care at all about what they invest in.
This is nowadays magnified by the Robin Hood's of the world of investing, which act as an amplifier of the crowd behaviour that is decoupled from any logical thinking.
Read 6 tweets
2 Sep
In #biotech #stocks news, one of the #LiquidBiopsy #CancerDx stocks in my list is $BNR Burning Rock, a company with presence mainly in Asia that started trading in the NASDAQ a while ago. It is now at lowest levels having recently gone below the $20 mark Image
At around $2B valuation, they are still in the top 10 of companies in the #LiquidBiopsy #CancerDx field: bit.ly/liqbiopsy Image
Notice that #GrailBio is still marked at $2B valuation in my table: this is not the $8B figure that #Illumina is intending to buy it at, but I'll wait until the acquisition is completed (and not legally challenged by the US/EU authorities) before updating the value in the table.
Read 10 tweets
31 Aug
Industry Overview on Biotechnology and Genomics Space (thread):
The era of genomics has now decisively entered the applied sectors of the market, after many years, decades, where the RUO segment was the largest piece of the pie. The lines between genomics and Medtech industries are now blurred and there is lots of crosstalk between both.
Who are the main players in the space: Illumina should be first of the list by market share, with Thermo Fisher Scientific second by overall company size. BGI Genomics dominates in China (NIPT, Cancer Dx). Smaller but distinct in some offerings is Qiagen, who at a point was ...
Read 8 tweets
24 Aug
In the #biotech #stocks #NGS field, there is a company that's recently IPOed and has now presented an update of their plans: $OMIC Singular Genomics @SingularGenomi1 investor.singulargenomics.com/static-files/0…
Their two planned instruments, the G4 and the PX, look physically a lot like competitors to the #Illumina NextSeq and NovaSeq, or the #MGI #DNBSEQ G400 and T7 instruments. But the PX is more of a multi-omics play rather than a higher throughput #NGS machine.
It seems we are about 1 year or 1.5 years away from Early Access / Commercial Launch for the PX, maybe around 6 months earlier for the G4 instrument.
Read 9 tweets
24 Aug
Good to see that #NextGenSequencing #NGS is become more and more available worldwide.
There is an argument that in markets where #Illumina has lesser IP coverage to block #MGI #DNBSEQ instruments, the fight for the #shortreads market will become more akin to the 2024 IP cliff for #Illumina. An example here, but also China, certain Eastern Europe countries, ...
Read 4 tweets

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