An update on #NGS technologies:
NGS in the clinical setting: we've reached a point in the #NGS technology that the combination of low error rate but mainly high throughput has made the genome-wide or quasi genome-wise assays affordable enough to be applied routinely.
There are few barriers left for the wider use of genomics sequencing in clinical diagnostics: firstly, to be the first in class, there is still a large investment in sample size required to build a reference dataset. An example in point here is Grail Bio, and the rest of players.
Grail Bio managed to accumulate a large amount of investment and applied epigenomic profiling technologies that had been proven for 2-3 years then (maybe 5-6 years now) at a large scale to build their Galleri assay for multi-cancer screening.
Other competitors didn't have the money and/or motivation and are now playing catch-up, which is not an impossible task, but will take some clever decision making, and, no surprise here, also a lot of money. This is, most prominently, for liquid biopsy cancer screening.
Galleri and similar are at the moment based on short-read Illumina sequencing, although technically they could be swapped for MGI Tech DNBSEQ is needed. There are already entities in China and other parts of the World working on Galleri-equivalents backed by MGI Tech sequencing.
Oxford Nanopore has a technology that lends itself more readily for long-read sequencing, but in comparison to PacBio, does not need much sample prep adaptation to work on a wide range of DNA/RNA sizes to start with.
This is due to the fact that the pores accept many molecules per run, in comparison to PacBio, which has a determined number of wells in the chip, thus requires library prep modifications if the length of each of the starting DNA molecules is shorter than an ideal size.
An advantage to Oxford Nanopore is that the very small to null CAPEX investment gives great flexibility to set up a new sequencing capacity. This model of in-house NGS sequencing has turn-around time advantages over the centralized model for $1M+ instruments (Novaseq/DNBSEQ T7).
This doesn't mean Illumina could not remain competitive: they still have a lead in short-read technologies, and could lower prices to entice more customers into their platform. Yet Illumina as an organization is not good at selling small and cheap instruments.
Competitors to Illumina could disrupt their low-throughput market by bringing in instruments that produce data of equal quality to Illumina NGS, but with instrument/reagents that are more competitive low CAPEX alternatives in short-read NGS.
Thermo Fisher wanted to be one of such competitors, but it turns out that their NGS sequencing machine, the Ion Torrent technology, has grown larger and more expensive, rather than small and low CAPEX. They have good vertical integration and aggressive sales, but limited success.
Yet there can be a change in the market segmentation between short-reads and long-reads if costs equate: the neonate whole-genome sequencing could be done with high-quality long-read technologies, and provide a "once and done" electronic health record of the individual.
This can then be combined with other NGS technology combinations, such as short-read liquid biopsy or single-cell spatialomics of tissue biopsies, to zoom into a particular tissue or organ, during the life of the individual.
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More from @AlbertVilella

27 Jul
A post on the current #singlecell biology technology space.
Most of the information is my personal opinion after having followed the field first-hand or from comments I gathered from experts on either the wet-lab side or the data analysis side.
The largest player so far is 10X Genomics: in technological terms, they were the second to be able to apply the kind of high-throughput level to the problem of single-cell assays. Initially, they got into trouble with IP due to the fact that some of the founders were involved
in developing the technology in another company, which ended up being gobbled up by a larger player with big pockets and plenty of lawyers on retainer. Although never certain, it seems from the last 1-2 years of news that the IP issues have subsided, so now it's a play on tech.
Read 21 tweets
13 Apr
@ThinkingAboutV @nanopore The applied omics market based on #NGS technology is still an incipient market if we compare it to more established #diagnostics markets. But we are not far away from a point in time where every newborn's genome is ...
@ThinkingAboutV @nanopore ... sequenced at high quality (long reads, maybe with PCR-free including epigenome marks), and kept as an #EHR in the health system for future use. From then onwards, there will be recurrent #LiquidBiopsy assays, maybe once a year, to screen for a multitude of conditions.
@ThinkingAboutV @nanopore From 40-45 yo onwards, mainly cancer screening of healthy individuals, based on a #MachineLearning cancer classifier such as shown already by @GrailBio / $GH and others, but also other classifiers will come soon, such as #epigenomic profiling of #Neurodegenerative conditions, ...
Read 7 tweets
10 Mar
My highlights of the RNGS21 @MGI_BGI Satellite Workshop talks: vibconferences.be/events/revolut…
Talk on AMR genes by @johnpenders at Maastricht UMC+ (I hope it's the right one), and how these increase/decrease for example with intercontinental travel patterns. Travelers to South-Eastern Asia acquire the mcr-1 gene.
Mcr-1 gene is identified and well-known from 2015, but the patterns of AMR migration started earlier
Read 20 tweets
3 Mar
As we approach Q30+ on now 4 competing platforms, 2 short read and 2 long read platforms, it's a useful reminder that only PCR-free preps benefit from high quality base-calling, as any PCR-based method incorporates errors wrt the original material.
More importantly, any PCR-based method devised so far also erases #epigenetic marks, which can only be read in conjunction with the 4-base alphabet if it's from a PCR-free method.
So if your application where to benefit from, say, a Q33 better than a Q31 modal base-calling, first ask yourself: have I got enough DNA for a PCR-free prep?
Read 4 tweets
2 Mar
My highlights of the @10xGenomics #Xperience2021 event. The list of products keeps growing, I would highlight Chromium Connect as an underappreciated tool to bring the products up another level of throughput. Important as with #NGS, it won't take long to go from n=1 to n=96+. Image
#CellPlex species-agnostic multiplexing up to 12 samples: not dissimilar to products such as TotalSeq, but baked-in so that it's been tested to work with the rest of the workflow. Image
Going close to 1M cells, the #ChromiumX brings about 100x fold throughput increase, all marked with 'HT' in the Kits. I'd be interesting to know how the different #BodyAtlas projects embrace this and for what. ImageImage
Read 31 tweets
28 Feb
There are a bunch of Twitter accounts, real or fake to some extend, doing the rounds every time someone tweets about #NGS #genomics or #LiquidBiopsy. They seem clearly wanting to hype a certain listed company
in a pump-and-dump fashion, which is not new, and existed before the GameStop/Robin Hood saga. I chose to mute the accounts, so my threads are not polluted from these accounts. I may start blocking them if it gets worse.
I am not muting the ticker for the company itself, as I am genuinely interested in following their developments, and they are not responsible for the behaviour of the pump-and-dump accounts.
Read 5 tweets

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