Discover and read the best of Twitter Threads about #liquidbiopsy
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PŁYNNA BIOPSJA 🩸
Część 1⃣
Czasem pewne nowe metody mogą być na tyle rewolucyjne, że określa się je mianem "Świętego Graala" jakiejś dziedziny
Ja tak widzę potencjał płynnej biopsji w obszarze #ONKOLOGIA. Czas pokaże. Ale co to dokładnie jest i czemu jest to bardzo istotne? 🧵
Część 1⃣
Czasem pewne nowe metody mogą być na tyle rewolucyjne, że określa się je mianem "Świętego Graala" jakiejś dziedziny
Ja tak widzę potencjał płynnej biopsji w obszarze #ONKOLOGIA. Czas pokaże. Ale co to dokładnie jest i czemu jest to bardzo istotne? 🧵
Temat inny niż zwykle, ale od dawna chciałem o tym napisać, ponieważ:
🔹 moim zdaniem jest to ciekawe zagadnienie
🔹 i BARDZO WAŻNE, indywidualnie i społecznie. Mowa przecież o nowotworach, przyczynie 1/4 zgonów w Polsce i OECD.
Korzystam więc z urlopu, by narobić zaległości ;)
🔹 moim zdaniem jest to ciekawe zagadnienie
🔹 i BARDZO WAŻNE, indywidualnie i społecznie. Mowa przecież o nowotworach, przyczynie 1/4 zgonów w Polsce i OECD.
Korzystam więc z urlopu, by narobić zaległości ;)
Na początek kilka statystyk, by przypomnieć, jak ważny to temat (co każdy i tak chyba dobrze wie):
🔹 w 🇵🇱 #nowotwory to przyczyna ~26% zgonów
🔹 w trakcie życia u ok. 40% Amerykanów pojawi się #nowotwór złośliwy i u co trzeciego Polaka
🔹 ponad połowa rodzin z tym się spotka. 3/
🔹 w 🇵🇱 #nowotwory to przyczyna ~26% zgonów
🔹 w trakcie życia u ok. 40% Amerykanów pojawi się #nowotwór złośliwy i u co trzeciego Polaka
🔹 ponad połowa rodzin z tym się spotka. 3/
Standard cancer detection tests are done with #tissuebiopsies.🧫
These are invasive, risky, and expensive as they require an endoscope and open surgery.
An alternative approach to this is Liquid Biopsy which is performed by drawing blood.🩸
2/n
These are invasive, risky, and expensive as they require an endoscope and open surgery.
An alternative approach to this is Liquid Biopsy which is performed by drawing blood.🩸
2/n
Liquid biopsy is an innovative solution to #cancerdetection.
▪️They use a much smaller sample and have a quicker turnaround for results compared to tissue biopsies.
▪️They are more advantageous in detecting a metastasized tumor - when cancer has spread to multiple sites.
3/n
▪️They use a much smaller sample and have a quicker turnaround for results compared to tissue biopsies.
▪️They are more advantageous in detecting a metastasized tumor - when cancer has spread to multiple sites.
3/n
An article describing the "45 is the new 50" change in guidelines in the US for #ColorectalCancer #Screening. Slightly biased towards $EXAS Exact Sciences Cologuard. ache.org/blog/2022/upda…
$EXAS Exact Sciences is one of the companies I track, in many ways a pioneer in the #LiquidBiopsy #CancerScreening field although with a low-tech method compared to other players in this field such as $ILMN Illumina (via @GrailBio), and what other companies are planning ...
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)
My COIs bit.ly/avilcoi
First talk is James Clark for Platform updates.
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) 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.
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?
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)
🧵
I present to you Taylor Swift as #urinarysediment 🔬findings ...
1/ Bilirubin pigmented RTEC (renal epithelial cell cast)
🧵
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
(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
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.
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
In #biotech #stocks, more market jitters at NASDAQ opening, all biotech stocks down except for $ONT.L Oxford @nanopore and $NEO NeoGenomics
$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.
$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.
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
At around $2B valuation, they are still in the top 10 of companies in the #LiquidBiopsy #CancerDx field: bit.ly/liqbiopsy
(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.
1/ 🚨#Tweetorial alert. Let’s discuss a couple cases of #Hypercalcemia 🦴🥛
@NSMCInternship #NSMC2021 #TeamTwobules #NephTwitter #MedTwitter #MedEd 🧵
@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
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
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.
@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, ...
1/ I often get asked about the presence of granular casts on the automated UA reported by the lab whether it is equivalent to seeing muddy brown casts.
❓Do you think granular casts can be used to diagnose ATN?
More to see in #NephMadness on #liquidbiopsy
@NSMCInternship
❓Do you think granular casts can be used to diagnose ATN?
More to see in #NephMadness on #liquidbiopsy
@NSMCInternship
2/ Spin the urine! This is one of the maneuvers that I enjoy doing with residents the most as there is a lot to uncover.
I totally underestimated the power of this test. How many times have you spun the urine yourself before nephrology training?
I totally underestimated the power of this test. How many times have you spun the urine yourself before nephrology training?
3/ The clinical properties of urine have long been described by the medical community.
‘Diabetic’ (polyuric) disorders were classified as ‘mellitus’ (honey-sweet) or ‘insipidus (flavorless) based on the urine’s taste!
#NephMadness #liquidbiopsy
‘Diabetic’ (polyuric) disorders were classified as ‘mellitus’ (honey-sweet) or ‘insipidus (flavorless) based on the urine’s taste!
#NephMadness #liquidbiopsy
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.
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?
@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
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.
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).
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
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):
#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?
#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.
#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).
#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.)
