Discover and read the best of Twitter Threads about #NGS

Most recents (21)

@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
#JPM2021 @TwistBioscience My Highlights: back to the #DNAWrite field. TwistBio chip: 1M oligos but only as centralised factory setting.
Expanding to a new factory in Portland (roadmap 2022) to reduce TAT. Also mentioned the "long tail" of Clonal Ready Gene Fragments.
They have a few slides on #DNAasStorage with a denser chip in prototype phase where they think they can archive 1Tb for $100 (pay once, archive forever*) which, if my calculations are correct, would allow for 10-12 years of @awscloud Deep Glacier or similar mth/GB=0.00099*12*1E3
Read 5 tweets
As a team of scientists from @scrippsresearch @karolinskainst @UniBonn @UniklinikBonn @IIIBonn @uni_tue @Illinois_Alma, we identified four potent neutralizing camelid nanobodies ...
Solved the #Xray structure of all four #nanobodies in complex with #SARSCoV2 spike #RBD @wchnihcholas and Ian Wilson ...
Used #CryoEM to determine that VHH E stabilizes the 3-up conformation of trimeric #SARSCoV2 spike @BMartinHallberg ...
Read 10 tweets
JPM Healthcare Daily Roundup #JPM2021

The first day of the conference hasn't disappointed, especially if you're a fan of talking cubes. What is this mysterious object and what sorcery is inside?

See disclosures at the end.
The Tempus One, meant to be carried in a doctor's coat or sat at the bedside, is a physical manifestation of @TempusLabs' genomic and phenotypic data-lake. Oncologists can ask One all sorts of questions regarding their patients, though I'm unsure if it'll (...)
(...) just reflex you to a computer after a sufficiently difficult question. I'm sure we'll learn more soon. Has this sort of form-factor been tried before?

I'm just hoping it has adjustable humor/honesty settings like TARS from Interstellar.

Moving right along.
Read 15 tweets
Long-read #NGS obeys Wright's Law.

For every cumulative doubling in sequence data generated across its install base, @PacBio has been able to lower (consumables) costs by roughly 30%, as shown below.

What could this imply about the future of long-read #sequencing?
First, let's acknowledge a Catch-22. Does PacBio need to (a) derive knowledge from platform utilization to lower sequencing costs or (b) lower costs first in order to unlock greater platform utilization?

At present, we believe it's more of the latter. Why?
PacBio's HiFi chemistry and Sequel II optics are relatively nascent (2019). This suggests a lot of near-term headroom left for optimization in these areas.

It's crucial that all long-read users, not just the top 1%, have access to this innovation.

pacb.com/smrt-science/s…
Read 15 tweets
We wrote a review on the potential of genome sequencing technologies in autism
@lornahoulihan @lgallagh_louise

authors.elsevier.com/a/1bnrL3A54zZV…

@AutismTCD @MaynoothBiology @scienceirel @MaynoothUni @tcddublin
#AutismGenomics #BelieveInScience

Let me tell you more (1/5)
WHY study the genetics of autism?

Studying genetics helps us to understand the biology of autism and brings us towards improved diagnosis and medical decision-making (2/5)

#ThinkGenetics #AutismGenomics Image
HOW can we identify genetic variants in ASD?

Sequencing of the whole genome and the whole exome is made possible by Next-Generation Sequencing technologies. These techniques allow us to look at many types of genetic variation across the genome. (3/5)

#NGS #Genomics Image
Read 5 tweets
Rapid whole genome (🧬) sequencing (rWGS) is one of the most exciting (and benevolent) collisions of #AI and #genomics I can think of.

rWGS can diagnose a critically ill child in minutes where previously it took years.

illumina.com/company/news-c…
A few years ago, Illumina ($ILMN) and Rady Children's Hospital (@RadyGenomics) collaborated to offer sequencing services for diagnosing critically-ill infants and toddlers.

Roughly 70% of rare diseases are genetic and they can take five years to diagnose.
As sequencing costs dropped and #AI got faster, this collaboration became Project Baby Bear: a pilot study for rWGS's diagnostic yield, clinical utility, and health economics in practice.

Several innovative companies joined Rady's in creating a rapid diagnostic pipeline.
Read 14 tweets
The more work we do, the less we think sequencing (#NGS) will be the best platform for non-invasive prenatal testing (#NIPT).

I'll explain using a dishwasher as my analogy.

If you don't already know how NIPT works, refer to the image below, if you do, read on! Image
Imagine that your sequencer is a dishwasher and your lab washes dishes instead of processing NIPT samples. You need each dish to be spotless when it comes out.

You cooked a hearty meal and you have 100 dishes to clean, some much dirtier than others.
You decide to set the washer to its highest setting so that even the grimiest plates come out shining. Though satisfied at the end of the cycle, you realize you over-washed the other 99 dishes. If you were a bigger washing operation, this could really hurt your margins!
Read 12 tweets
Digital spatial profiling (DSP) is a rapidly growing biological technique combining genomics, optics, and pathology. Previously, researchers manually examined stained tissue slides or used IHC, an approach lacking in scalability and uniformity.

(cont.)
DSP protocols allow researchers to barcode tissue regions of interest, analyze them quantitatively, and detect intercellular phenomena with stunning clarity. When combined with #NGS data, DSP should accelerate our understanding of immune-oncology.

(cont.) Image
Readcoor recently unveiled its RC2 platform at the Advances in Genome Biology and Technology (AGBT) conference. The RC2 workflow is vertically integrated, inclusive of consumables, hardware, and a cloud ecosystem that can flex data to other bioinformatic suites.
Read 5 tweets
Here's a short (?) thread on a recent #PCAWG paper focused on #cancer, long-reads, tumor mutational burden, and a very hard-to-pronounce word called chromothripsis.

'chromo-' = chromosome ; '-thripsis' = shattering into pieces

TL;DR at end (...)

nature.com/articles/s4158…
The researchers' used short-read (~40X) whole-genome #sequencing on ~2,700 tumors across 38 cancer types (most tumors were advanced).

The goal was to study the frequency of a mutational phenomenon (chromothripsis), which previously was though to exist in only 2-3% of tumors. Image
The prevailing view on tumor formation is that somatic mutations gradually accumulate over time, eventually overwhelming a cell's DNA repair machinery. Conversely, chromothripsis (above) is a single, catastrophic event defined by hundreds of structural rearrangements all at once.
Read 9 tweets
For some #NGS applications, it’s necessary to amplify (make copies of) DNA prior to sequencing. Sometimes this biases (creates errors) within the sample—and this is how I think about that:

(Tiny Thread)
Amplifying DNA is like the childhood game ‘Telephone’, where a message (a DNA template) goes around a circle (cycles of PCR) and usually ends up being distorted (having amplification artifacts).
Conceptually, this happens when you make a copy of a copy of a copy—errors can propagate forward, whether it’s a juicy bit of gossip in Telephone or a repetitive chunk of DNA, which are even more prone to bias! Why?
Read 5 tweets
#WCLC19 Registrational results for LOXO-292, now Selpercatinib, presented by @alexdrilon. This is a highly selective RET inhibitor with preclinical CNS activity. Enrolled remarkably quickly: 253 RET+ #NSCLC enrolled since May 2017! #OncoAlert #LCSM ImageImageImageImage
#WCLC19 Selpercatinib patient demographics. Incredible waterfall plot! In previously treated ORR 68% and nearly all patients with some reduction. CNS ORR 91%. Even better in 1L: 85%! mPFS 18.4 months. Impressive results for #RET #NSCLC #OncoAlert ImageImageImageImage
#WCLC19 Illustrative examples of the depth of response possible. Safety profile very reassuring. Impressive results from Selpercatinib - now awaiting update from BLU-667. A great time for #RET targeting! #OncoAlert #LCSM #PrecisionMedicine ImageImageImageImage
Read 8 tweets

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