@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, ...
@ThinkingAboutV @nanopore @GrailBio classifiers based on #epigenomic profiling of cardiovascular conditions, respiratory, and importantly also infective diseases. Easy to bridge the last one with another big use of applied omics, which will be genomic surveillance for vectors/agents of disease such as #SARSCoV2.
@ThinkingAboutV @nanopore @GrailBio So there is a lot of the applied omics market that is untapped, and the technology is either already there or quickly making its way. Screening based on these technologies is hugely beneficial to the health system, directly and quantifiably in single payor systems, e.g. NHS, ...
@ThinkingAboutV @nanopore @GrailBio but also overall in other less optimal models of health care. George Church @geochurch has calculated the x-fold value of a genome to the health care system, i.e. for every $ spent on a genome sequenced and available as an #EHR, how many $$ are saved in outcomes to health system.

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More from @AlbertVilella

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
28 Feb
Is @NebulaGenomics using @MGI_BGI for their 30x 2x150bp #WGS genome sequencing? Image
I received an email from @NebulaGenomics today, with a discount code for a $299 genome sequencing offer. Which made me wonder: are they using the already cheaper @MGI_BGI #DNBSEQTx sequencing for this? It would mean they can run it at cost or make a small profit from it.
Then you realise there is "analysis" charge on top of the $299 which you can't untick, so the $299 #WGS 30x genome goes up to $499. Still, at $499, you would find it difficult to make money if you were @NebulaGenomics and you were using something like an @illumina #NovaSeq
Read 9 tweets
18 Feb
A more polished thread on #epigenomic #biomarkers for #LiquidBiopsy and #CancerScreening:
Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
Catching signs of #cancer early is crucially important to the disease management and survival rates, so the question is: how can we find out if there is something wrong going on early enough, ideally in a low-cost assay that can be performed regularly on healthy individuals?
Read 39 tweets

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