Discover and read the best of Twitter Threads about #ngs

Most recents (24)

Let us take a look at $TWST and some #Synbio.

Twist is the #DNA company. They break themselves into 4 different segments with #Synbio, #NGS, #Biopharma, and #Storage.
The first segment is Synthetic Biology. This is what I call the Mail Order DNA business. Many companies need DNA for developing therapies like cell engineering or gene therapies. Many of these DNA strands can be synthesized for just a few cents per base.
This won't be a huge money maker as they can ship hundreds of thousands of DNA sequences a year for just a few dollars per. It is the back bone of their sales, and its still growing nicely. Its the cash cow that will fund the future developments which can be big winners.
Read 10 tweets
Reviewing the Oxford @nanopore presentation now available to replay. Two highlights/thoughts that I didn't tweet about before:
1) Spike-in for re-training
2) Strand-specific DNA modifications
1) Looking at the kind of stuff presented, where temperature settings, salt, etc. are being more available to end-users, there is an opportunity here to retrain models and improve basecalling for specific datasets.
On a much simpler level, Illumina sequencer did and still do some of that: one would need to spike-in a certain amount of PhiX for the machine to calibrate itself. For low-complexity applications, like 16S sequencing, this could be as high as 25-50% of the reads/throughput.
Read 12 tweets
Recap on #NGS after the @ElemBio #AVITI instrument release. Who are the main players in NGS?
Illumina remains the market leader with the short-read SBS technology. They segment their products into high-throughput (NovaSeq $1M), mid-throughput (NextSeq $220-350K) and low-throughput (MiSeq, MiniSeq, iSeq $40-150K).
Then there are to large players, but smaller to Illumina in comparison, in the long-reads field: Oxford Nanopore, with their MinION, PromethION and other modes of sequencing, and PacBio, with their Sequel2 instrument, but with a future play on short-reads with Omnione.
Read 18 tweets
One more from #JPM22, maybe the last one from me: PacBio's presentation which took place on the 13th January. Intro slide about the company. Image
There are now 374 Sequel II/IIe machines installed, the company's revenue is growing and is in the triple digit annually. Image
The number of SMRT Cells shipped has almost doubled since 2020, quadrupled since 2019. That's a good sign for PacBio. Image
Read 25 tweets
A recent publication by Dennis Lo et al applied long-read sequencing (LRS) in the prenatal screening (#NIPT) setting. It's a rather unorthodox technology/application pairing, and it's got me scratching my head a bit.

Open Acces Link:

pnas.org/content/118/50…
For context, earlier this year, Lo et al published a convolutional neural network ("the HK model") that enabled PacBio LRS devices to read methylation (5mC) across the entire genome with very high fidelity. This is important later.

What's methylation?
PDF of HK Model Paper:
pnas.org/content/pnas/1…

I'll summarize my main takeaways from the current paper and end with some of my open questions/concerns.
Read 30 tweets
MGI Tech has given a presentation on their updated DNBSeq CoolMPS (#NGS) technology. Some highlights below:
Their DNBSEQ-Tx sequencing factory, with dip-immersion reagent delivery and 4 high-throughput imagers, can produce >50K WGS annually. Technology being upgraded from PE100 to PE150 (2021Q3)
A presentation from a user shows how #singlecell 10X Genomics libraries can be inputted into the MGI machines. Small difference between FASTQ files, but tools available to transform.
Read 6 tweets
Catching up on 🧬 “Understanding #NGS and Interpreting Reports for Oncologic Pathology” with Dr. @sabahkadri and Dr. Cecilia Yeung at #CAP21 @AMPath 👩🏻‍💻

Super useful talk with excellent case studies! Here are just a few takeaways 🧵⬇️ #MolecularPath_CEJ #Informatics_CEJ
🤔 Considerations in developing an NGS assay

📌 @Pathologists has NGS assay development tools regarding test design, validation, quality, and bioinformatics: cap.org/member-resourc…
📌 How much do you want to know? ➡️ what test is needed? (WGS vs WES vs targeted sequencing)

1/
🧬 NGS in a nutshell with Dr. Yeung

1️⃣ Library preparation (hybrid capture vs amplicon-based)

2️⃣ Sequence the fragments of DNA (cyclic reversible termination vs detection of chemical byproducts ⚡️ as single nucleotide is added)

2/
Read 15 tweets
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
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
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
Good to see that #NextGenSequencing #NGS is become more and more available worldwide.
*becoming
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
Two large #antitrust probes in the same screenshot that relate to #Genomics and #Bioinformatics
(1) Possible buyout of #ARM by #NVIDIA does have an effect on the #Bioinformatics field: many applications now are deployable on CPU/GPUs with #ARM and/or #NVIDIA chips on them. Some recent examples are:
(a) the Oxford @nanopore MinION Mk1c device, which originally was specced at Jetson TX2 ARM+Pascal GPU accelerators (ARM processor 6 cores, 256 Core GPU), 8 GB RAM (may have changed since then.
Read 42 tweets
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.
Read 14 tweets
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
@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
DISCUSSION THREAD

Topic: $SRNGU/ $SRNG and potential Ginkgo Bioworks SPAC deal. Specifically, $20B valuation mentioned by Bloomberg

Will walk through some mkt data on chart below

Comments encouraged

#SynBio
$ZY
$AMRS $CDXS $ABCL $SYBX $PGEN
$BLI $TWST $TXG
$WUXAY $CRL $PPD
^Will preface this w list of most interesting things in $SRNGU/ $SRNG S-1

1). HUGE cash trust: $1.5B

2). Mostly entertainment experts (they SPAC'd DraftKings), but sector agnostic

3). Criteria: "High growth +FCF potential"

2). One bio link: $ALLO $KRON @Vida_Ventures @bt_prop
Let's also establish

i). Ginkgo is IP creation biz (a #synbio $TXN/ $INTC/ $AMD) housed in automated CRO (see $PPD $WUXAY $CRL) "on steroids." That gets paid in cash+ stock/royalties

ii). Biology inherently hard to scale, but part of revenue magic of Ginkgo is code reuseability
Read 23 tweets
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
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
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
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
Au 8 Fév, la France avait contribué un peu plus de 5.000 génomes de #SARSCoV2 sur la base de données internationale @GISAID

Énième illustration de l'abandon de la recherche et de la santé publiques, même depuis Déc 2020, nous sommes à 236 génomes partagés par semaine.

1/N
Depuis le 5 Fev, le séquençage est remboursé (avant, CHU et labos en étaient pour leur frais).

Mais le séquençage #Sanger (500 nucléotides donc 2% du génome du virus) est remboursé à 200 € comme le séquençage #NGS (>28.000 positions du génome).

legifrance.gouv.fr/jorf/id/JORFTE…
2/N
Pour info, le #Sanger coûte moins de 10 € alors que le #NGS oscille entre 50 et 200 € pour de tels échantillons selon les protocoles.

Mais en France on est surtout équipés pour le Sanger... Problème : ça n'apportera rien de plus que des PCR ciblées sur 3 ou 4 positions.

3/N
Read 4 tweets
We are not far away from routinely #genome sequencing every newborn suspected of having a rare/hereditary disorder.
In fact, there will be a point, especially in single-payer health care systems, where it'll be logistically preferable to routinely #genome sequence every newborn.
What will it take? Management, machines, and money (3M), in that order:
1/ A management system that handles sample collection, carries on the sequencing effectively, and makes the result available: we are not far away from this in, e.g. the UK's (@NHS+Wales/Scotland/NI).
We are much better at this now than, say, 1-2 years ago. See a successful system of coordinating this for lower throughput sequencing but high numbers of samples in #COVID19 cogconsortium.uk
Read 12 tweets
The is a tech bubble in the stock market, and it will burst soon. The question is, which of the #NGS companies below will come out stronger from the stock market tech bubble bursting? $ILMN $PACB @nanopore @MGI_BGI
Looking at the NASDAQ for the last 5 years, there was a big drop in March 2020, triggered by the first wave of worldwide #COVID19. The tech bubble was already inflated back then. But the market recovered with a matter of weeks, and kept climbing up.
By 9/8/2020 there was another attempt of a correction, mostly #COVID19 related, but again, with a highly inflated tech bubble, the market recovered and quickly jumped another 1,000 points (around 11,800):
Read 30 tweets
#JPM2021 @GenapSys My Highlights: I think it's fair to say I am more excited than most about this #NGS company, as I see them as an example of how to enter the market while keeping a small profile ($249M raised so far).
They now are aiming at 2021 to ship two new chips: 50MM read chip and 144MM sensor chip (not sure what the difference is between read/sensor).
They show a slide of price per Gb with #Illumina products as a reference, and their products now lined up, I think, for the first time with price per Gb info. Lowest will be the 144MM chip at ~$27/Gb.
Read 14 tweets

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