Discover and read the best of Twitter Threads about #liquidbiopsy

Most recents (24)

The London stock market is now closed and $ONT.L Oxford @nanopore is presenting technology updates. I'll live tweet my highlights, but won't be thoroughly complete with screenshots (thread)
First talk is James Clark for Platform updates.
Read 57 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
Clive (probably sipping a piña colada by the beach) is updating on tech at @NanoporeConf @nanopore
Three steps: (1) Sample Preparation, (2) Data Acquisition and (3) Sequence Data (basecalling)
"[...] everything apart from the computer is designed by Nanopore, but [the computer side] may change in the future, by the way". Unreasonable to think they will build their own silicon specialized for base-calling?
Read 42 tweets
Inspired by the beautiful #urinemicroscopy pictures posted by @dani_nephron and recent posts by @DShadowgazer + @CatchTheBaby ...
I present to you Taylor Swift as #urinarysediment 🔬findings ...
1/ Bilirubin pigmented RTEC (renal epithelial cell cast)
🧵
2/ Dense Pigmented “Muddy Brown” Casts
@Neph_SIM
3/ Long Convoluted Waxy Cast
#SpinUrine
Read 16 tweets
A few notes (in no particular order) on the Oxford @nanopore 30-Sep-2021 document timed for their IPO (data.fca.org.uk/artefacts/NSM/…)
(1) The importance of GPUs and SSDs as part of the computational equipment perceived to be needed now and in the near/mid term future Image
They only mention competitors by name in stating the difference between synthesis-based sequencing and the nanopore approach. They mention Illumina and PacBio later on in patent litigation risks but not too interesting. Image
Their TAM and potential TAM slide is probably the most insightful: reiterating what the company always said about long-reads, ubiquitous and fast TAT products and the markets they can disrupt with these Image
Read 5 tweets
In #biotech #stocks, more market jitters at NASDAQ opening, all biotech stocks down except for $ONT.L Oxford @nanopore and $NEO NeoGenomics Image
$ONT.L Oxford @nanopore floated on Wednesday, today still on a steady uphill. Trades in London stock exchange, so off by 4-5 hours US East time. Image
$NEO NeoGenomics has been on a tear in the last few days. A company growing both organically and by acquisition, aggressively positioning itself in the #LiquidBiopsy #CancerScreening segment. Image
Read 4 tweets
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
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
1/ 🚨#Tweetorial alert. Let’s discuss a couple cases of #Hypercalcemia 🦴🥛
@NSMCInternship #NSMC2021 #TeamTwobules #NephTwitter #MedTwitter #MedEd 🧵
2/ A patient admitted with c/o decreased appetite, abdominal pain, & constipation. Found to have severe #AKI (with hyperkalemia + acidosis) & hypercalcemia.
3/ What’s your differential for #hypercalcemia?
C - Calcium supplements
H - Hydrochlorothiazide
I - Immobilization
M - Multiple Myeloma, Milk-alkali
P - Parathyroidism
A - Alcohol
N - Neoplasm
Z - Zollinger-Ellison
E - Excessive Vit D
E - Excessive Vit A
S - Sarcoidosis
Read 24 tweets
Delighted to share our new study nature.com/articles/s4158… introducing PhasED-Seq out today @NatureBiotech.
A fantastic collaboration from @StanfordMedicine led by Dave_Kurtz & Joanne Soo with @max_diehn to help transform #cancer interception & monitoring by improving #LiquidBiopsy #ctDNA detection of #MRD.
For many cancers & nearly all currently available techniques, the impressive KM plots of #ctDNA #MRD immediately after definitive Rx w/ curative-intent unfortunately still miss ~50% of all events which occur in the MRD-negative subset, thus having modest NPV.
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
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
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
@sbarnettARK Epigenomic biomarkers are becoming more established for #LiquidBiopsy and #CancerScreening, and we have seen the big players positioning themselves in this #epigenomics race recently.
@sbarnettARK 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?
@sbarnettARK The first generation of high-throughput technologies was predicated on finding mutated (tumor) DNA in the individual's body (somatic), different from their (normal) DNA. Tumor/Normal (T/N) comparisons of the individual's samples, biopsies or ctDNA will indicate if there
Read 38 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 #BiologicalDynamics @BiodynSD My Highlights: I'll cover this from the point of view of #LiquidBiopsy and #Epigenomics profiling, which is where my interest lies: their next-gen multiomics intro is about exosomes (and EVs, exosomal vesicles?)
The slide about Verita Biomarker Isolation Platform seems to be about isolating cells, with the right-most image showing "Visualized EV", which I presume is exosome vesicles
Later on, they do mention methylation markers, above the exosomes image, so I wonder if it's only DNA inside or bound to the exosomes?
Read 7 tweets
#JPM2021 #ExactSciences #LiquidBiopsy My highlights: I will focus on the liquid biopsy / #epigenomics profiling side of the presentation, which is where my interest lies: Exact described the data from Thrive multi-cancer screening, based on 'mutation+protein'
The details they gave on their other recent acquisition, #BaseGenomics are illuminating: they will use their bisulfite-free methylation profiling method for their Cologuard 2.0 test for CRC, but also for the multi-cancer test, and possibly the MRD test as well.
So this means that #ExactSciences intend to upgrade their tech in two steps: from current Cologuard 1.0 to a new test that includes Thrive's tech, and then a second upgrade using the #BaseGenomics #Epigenomics profiling tech.
Read 5 tweets
#JPM2021 #LiquidBiopsy notable by their absence, which is more than excusable in these pandemic times: @freenome, Biocartis, Biodesix, Epic Sciences, ArcherDx (not by this name anyway). Worth following developments for them. In my book, worth following #Freenome of the ones here.
Smaller #LiquidBiopsy #Oncology #Diagnostics players also not at #JPM2021 but important in the field: Personalis, Inivata, Exosome Diagnostics, Epigenomics Ag, Personal Genome Diagnostics, Foundation Medicine, Singlera, Cambridge Epigenetix, and Bluestar Genomics.
Now added #BiologicalDynamics to my #LiquidBiopsy list crunchbase.com/organization/b… which displace #Biocept in the #Top30 bit.ly/liqbiop (thanks Kevin Han for the follow).
Read 5 tweets
#JPM2021 #AdaptiveBiotech My Highlights: my interest lies in their angle on #LiquidBiopsy for #EarlyCancerDiagnostics, but they also deal with Life Science Research and Drug Discovery.
Their T-Detect method is aiming at #MRD monitoring, here shown in a slide that relates it to their ImmunoSEQ T-MAP Cancer mapping tool, and their Identification of clinical TCR candidates.
They stress the T-cell Diagnostics angle in different slides. I recall only @freenome explicitly mentioning immune-profiling from the group of companies in early cancer diagnostics and #epigenomics profiling (Grail/GH/Thrive/Freenome/BioStar/CEGX/etc.)
Read 5 tweets
#JPM2021 @carisls My Highlights: in the #CancerDiagnostics area, they position themselves favorably wrt Foundation medicine, Tempus, and Personalis (haven't heard of NEO before).
They put #LiquidBiopsy at the end of this trajectory slide: (couldn't see any years in milestones for this)
No indication that #Caris are pursuing #Epigenomics profiling of #LiquidBiopsy: they mention exome and transcriptome in their slides.
Read 4 tweets
#JPM2021 $GH #GuardantHealth my highlights: jpmorgan.metameetings.net/events/healthc… #LiquidBiopsy they are at the forefront of #Epigenomic profiling (Methylation+Fragmentomics) Image
#LUNAR1 #CRC bringing #Epigenomic profiling to recurrence testing with #Methylation profiling (no fragmentomics?) Image
Read 5 tweets
$ARKG Tweet series
This series of tweets is my opinion only. Cathie Wood has created a group of ETFs that target the disruptive innovation that is both happening and accelerating. These funds have had stellar performance based upon innovation trends and economic theory.
1/ Image
The $ARKG fund description is a good place to start. This has changed recently to a #CRISPR theme but started more with the sequencing cost declines which would drive diagnostics adoption and precision medicine
2/ Image
The economic driver of the Genomic Revolution is a multiplier. Not only sequencing cost declines but the impact of moving from #ZFN to #TALENs to #CRISPR is key. As the editing cost has dropped CRISPR is seeing a dominant increase in publications.
3/ Image
Read 23 tweets
Here it is: #LateBreakingAbstract at #ASTRO20 SS19 available to view now! Early analysis of trial (NCT03340974) using high-dose SBRT with avasopasem (GC4419) in #PancreaticCancer #PancSM #ASTRO20 Thread👇
This trial tried to address an unmet need for a specific group of #PancreaticCancer #PancSM patients whose disease had not progressed but remained unresectable after chemotherapy. #ASTRO20 @ACKoongMDPhD
Patients would be enrolled on the trial after finishing a minimum of 3 months of standard-of-care chemotherapy. They would receive SBRT with Avasopasem or a placebo control just prior to each SBRT treatment. #ASTRO20
Read 14 tweets

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