Discover and read the best of Twitter Threads about #ngs
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1) Welcome to a new #accredited #tweetorial, "Utilizing Immunohistochemistry Testing, Biomarkers, and Targeted Therapeutics to Optimize Outcomes in Patients with NSCLC," featuring the highlights of a symposium presented at the #ESMOIO22 congress.
@myESMO #LCSM #FOAMed
@myESMO #LCSM #FOAMed
2) The faculty for this outstanding program were @peters_solange (Chair) 🇨🇭, @HosseinBorghaei 🇺🇸, Natasha Leighl MD 🇨🇦, and @dplanchard 🇫🇷. A truly international roster of experts in #oncology!
Don't miss prior accredited courses in this space at oncologytweetorials-ce.com/category/lung-….
Don't miss prior accredited courses in this space at oncologytweetorials-ce.com/category/lung-….
3) This program is supported by an educational grant from Sanofi. Statement of accreditation and author disclosures are at oncologytweetorials-ce.com/disclosures/.
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
1/5 En el IPN contamos con servicios de secuenciación de genoma completo, análisis de metagenomas, descubrimiento de variaciones genómicas, análisis de expresión diferencial y genotipificación de SNPs, utilizando la tecnología de Illumina.
#ServicioDeSecuenciacionMasiva #NGS
#ServicioDeSecuenciacionMasiva #NGS
2/5 Un ejemplo de lo anterior, es la investigación del temperamento bovino dentro de la ganadería ya que, tiene influencia no sólo en el bienestar del animal, sino también en quien lo maneja. Es importante medirlo ya que, juega en la productividad de los hatos de ganado.
3/5 Encontrar genes que tienen efecto sobre la expresión del temperamento permitirá asistir la identificación de los animales más temperamentales del hato y tomar decisiones sobre su manejo.
#ServicioDeSecuenciacionMasiva #NGS
#ServicioDeSecuenciacionMasiva #NGS
#KRAS alert! Over the past 4 years, a multi-disciplinary team from @hopkinskimmel @VUMC_Cancer @DanaFarber @MSKCancerCenter & @Amgen has been studying the distribution and co-mutations of KRAS, NRAS and HRAS mutant #cancers under the auspices of @AACR project #GENIE. Read the 🧵
Our work is now published online at @CR_AACR and represents the largest study of RAS genomic architecture to date, leveraging #NGS data from >600,000 mutations and >66,000 tumors across 51 #cancer types.
Full text here
aacrjournals.org/cancerres/arti….
Full text here
aacrjournals.org/cancerres/arti….
Our findings provide insights in the genomic architecture of RAS mutant cancers and may serve as a blueprint for mapping therapeutic vulnerabilities for mut RAS. Given the vast array of findings we have put together a shiny app for interactive #dataviz:
ras-hallmarks.jhmi.edu
ras-hallmarks.jhmi.edu
Another twitter profile of one of the #biotech #stocks that I track, this time it's $TWST TwistBio. The company is a DNA Write company, currently applying their tech to #SynthBio, #NGS and #AntibodyDiscovery
The different segments are easy to explain, and in many cases we can draw analogies to $ILMN Illumina in #NGS: they provide products and services to different segments as a 'tools' provider. Now on to Twist Biopharma, here is were things get complicated.
Twist Biopharma is by all intends an purposes just another branch that concentrates on the antibody side of things. Part of what they offer is just more 'products and services', like they would do with NGS or SynthBio. The complicated part is their intention to also engage...
The field of #NGS is heating up and new contenders are now shipping their new instruments out there. MGI Tech is heading to both the US and the main European markets, whereas Element Bio, Singular and Ultima Genomics are starting in the US first, aiming at outside US the in 2023.
There are other companies with new tech out there that want to use to displace $ILMN Illumina's market share, including $PACB PacBio which is giving an update on their new tech in October, and $ONT.L Oxford @nanopore that has been shipping Kit14 for the last couple of months now.
$ILMN Illumina themselves are pencilled for their Chemistry X update, but for the noises they've made so far, it seems this will be a platform update, meaning the now 1000s of NovaSeqs and NextSeqs out there will need to be replaced. Think multi-year wave of stock update.
In #biotech #stocks news, $TXG @10xGenomics is opening upwards +4% in today's trading. The company is down more than 75% in the 52-wk window. They peaked in Q1 2021 and have since then declined at a similar pace as other $XBI stocks out there.
$TXG is in the #Singlecell and #Spatial biology field. They've recently made their pivot into Spatial Biology apparent, and have both an #NGS Next-Generation Sequencing and #InSitu imaging play on it, with their #Visium and #Xenium lines respectively.
The $TXG top institutional holders include Morgan Stanley with less than 10%, followed by 3 of the heavy hitters in #biotech: UK's Baillie Gifford, Vanguard Group, and Black Rock.
A LinkedIn post by Sarah Hartley-Kane on the UK becoming the 'Silicon Valley of Global Genomics' linkedin.com/posts/sarahhk_…
The cost of a whole genome is probably already in the $100 mark, but not widely available: the only companies that have shown realistic goals towards the $100 genome are: MGI Tech with their DNBSEQ-T7 and T10x4 large instruments, together with @UltimaGenomics with their U100 ...
which is expected to be commercially available in 2023 and produces $1/Gb reads (albeit short-reads with homopolymer noise), and $ONT.L Oxford @nanopore, which is currently closing into the $2/Gb mark of Q20+ single pass reads on the PromethION flowcells
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.
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.
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.
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.
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.
There are now 374 Sequel II/IIe machines installed, the company's revenue is growing and is in the triple digit annually.
The number of SMRT Cells shipped has almost doubled since 2020, quadrupled since 2019. That's a good sign for PacBio.
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…
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?
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.
pnas.org/content/pnas/1…
I'll summarize my main takeaways from the current paper and end with some of my open questions/concerns.
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.
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
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/
📌 @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/
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/
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.
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 ...
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.
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, ...
(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.
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.
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.
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.
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.
@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, ...
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
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
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
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
