Discover and read the best of Twitter Threads about #sequencing

Most recents (24)

Guess who’s back? 👀 That’s right, it’s Keith Robison (@OmicsOmicsBlog)! He’s taking the mic once again to share some lessons from SARS-CoV-2 #sequencing data.
@OmicsOmicsBlog 1/ Hi again! Keith here, with a few plots and visualizations based on @GISAID data. Here’s a 🧵 on an intriguing set of SARS-CoV-2 mutations that is catching some attention online: deletions within NSP1. Let’s dive in.
2/ Many have paid attention to viral mutations on the Spike protein, b/c it’s an important target for the immune response, the antigen used in many vaccines & the target of therapeutic monoclonal antibodies. Spike has been the most active protein in terms of mutations arising.
Read 23 tweets
The top science themes in the $XBI and the companies to follow.

#AI/#ML based Drug Discovery
#ProteinDegraders
#iPSC
#SyntheticBiology
#PersonalizedMedicine
#Sequening
#CRISPR
Under #AI/#ML based Drug Discovery

$SDGR, $RXRX, $RLAY, $EXAI and $ABCL

All are using AI, ML, automation and/or deep learning to drive drug discovery to lower costs and improve success.
Under #ProteinDegraders

$ARVN, $KYMR, $CCCC and $GLUE

All are using targeted protein degradation to target old and new targets. Could be far safer then TKI and other approaches.
Read 9 tweets
Now that @Quantum_Si has given us a peek under the hood of its protein #sequencing platform (Platinum), we can begin comparing actual results to theory.

A few months ago, I shared this paper that gave a theoretical framework for protein sequencing:
pubs.acs.org/doi/10.1021/ac…
The author simulated how different factors, such as the # of readable amino acids (AAs) and the read length, would affect a protein sequencer's ability to unambiguously detect the 20,000 canonical human proteins in our bodies.

That chart is attached below.
I've marked in green where QSI currently stacks up. Based on its recent pre-print (linked below), Platinum can directly read seven (7) amino acids (F, Y, W, L, I, V, and R) with peptide reads that seem to max out around 20 AAs.

biorxiv.org/content/10.110…
Read 10 tweets
🔴Excellent 🧵 again from @trvrb👏

#OmicronVariant really seems weird, interesting and terrifying. #OpenData #OpenScience will save the world now. Global cooperation and openness. This is no time for ’normal’ greed (nationalism, 💉patents), as the globe and future are shared. 1/
What we can already say is that the world must be grateful to #SouthAfrica🇿🇦 #Botswana🇧🇼 @Tuliodna @ceri_news @nicd_sa, all experienced with #Sequencing (HIV, BetaVariant): THANK_YOU🌼.

Thank you for the quick #Omicron discovery and global alert. Thank you for your honesty.
2/ ImageImageImageImage
Like #China🇨🇳 in 2020, have 🇿🇦🇧🇼 been now extremely fast & open online, working by the principles of #OpenScience #OpenData. China solved in a week the #SARSCoV2 gen code publishing results online — allowing #US🇺🇸 to start vaccine development next week. 3/ mobile.reuters.com/article/amp/id… Image
Read 5 tweets
Happy & proud to share the results of our high level expert group our roadmap on towards stabilization of the #COVID19 #pandemic in the European Region #SARSCoV2 #Europe @WHO_Europe What are our 10 objectives (shortened, for full text see link): 1/
euro.who.int/__data/assets/…
1. Increasing as fast and massively as possible #vaccine coverage, close the vaccine gaps btw producing/high income countries & middle/low-income countries. No strong evidence for 3rd dose for all people but consider for vulnerable to keep them safe. 2/
Equity across countries should be seen as priority in Europe at this time. Before delivering 3rd doses, all at-risk populations in all countries of the region should be offered the first two doses of vaccine. 3/
Read 14 tweets
As short-read #sequencing (SRS) costs begin to drop again, undoubtedly fueled by a resurgence in competition, I suspect many liquid biopsy providers will add blood-based whole-genome sequencing (WGS) to supplement, or replace, the deep targeted sequencing paradigm.
With a few exceptions, most clinical-stage diagnostic companies build patient-specific panels by sequencing the solid tumor, then downselecting to a few dozen mutations to survey in the bloodstream.

I don't think this approach is going anywhere anytime soon.
However useful, this deep-sequencing approach suffers from several challenges:

1. It requires access to tissue.
2. It requires the construction of patient-specific PCR panels.
3. It requires significant over-sequencing ($$$).
4. It introduces a third layer of error (PCR).
Read 14 tweets
Here is a link to the @MMWR with the data from the #Provincetown outbreak which led @CDCgov to change their recommendation on #Masks due to the #DeltaVariant

Here is a🧵highlighting the important points
1/

cdc.gov/mmwr/volumes/7…
-There were 469 cases of #COVID19 in Barnstable, MA in July 2021
- 346 (74%) cases in fully #vaccinated
- #Sequencing in 119/133 (89%) specimens confirmed #DeltaVariant
-274 (79%) with breakthrough infection were symptomatic
-4/5 hospitalized were fully #vaccinated

2/
-Ct value similar in fully vax'd (127) vs. those not (84) (22.7 vs 21.5)
-Most cases in males (85%); median age 40
-Time from vax completion -> infection 86 d (6-178 d)
- Vax as cause for breakthrough
#PfizerBiontech (159,46%)
#Moderna (131,38%)
#Janssen (56,16%)

3/
Read 6 tweets
It's been a busy few days/weeks/months modelling steps 2, 3 and 4 of the #roadmap out of lockdown in England, with my #ateam @_nickdavies @markjit and John Edmunds. A 🧵 on our latest work looking at #step4 🪜👩‍💻 and a #photodump of some nice things I saw along the way A photograph of the West pier and Brighton beach with low ti
We project the dynamics of #SARSCoV2 transmission in England using an #agestructured #transmission #model which divides the population into vaccine states and disease states. The model has compartments for three #COVID19 variants (OG, #alpha and #delta) and 2 two-dose vaccines 💉 An illustration of the age-structured compartmental transmis
To capture changes in behaviour (➡️ the amount people mix in the model), we use historic #mobilitydata and make assumptions about what might happen to mobility when policies are implemented, e.g. #step4 🍀 We make low, medium and high assumptions to account for uncertainty... ⭐️ Figures showing google mobility data between January 2020 an
Read 11 tweets
We often discuss how more comprehensive and sensitive techniques improve the diagnostic yield for patients affected by rare genetic diseases. Indeed, yields have improved as we've gone from microarrays to whole genome #sequencing.

However, there's another critical component.
Case-Level Reanalysis (CLR)

By reanalyzing genomic data, as our global knowledge-base grows, we improve diagnostic yields.

We believe the broadest tests should be done first to avoid the need to re-contact and re-accession patient samples.

ncbi.nlm.nih.gov/pmc/articles/P…
The economics for both the lab (and patient) change dramatically as well in a 'generate-once-reassess-often' framework. As more is known, variant interpretation may shift from being more manual to more automated.

Still, this is a really hard technological problem.
Read 5 tweets
Have we reached to the peak of 2nd #Covid wave in India? May be, yes! Its already 2.5 months in to it. Most badly affected countries peaked within 1.5-3 months of onset of a new surge. Is it too early to comment? 1/
More interesting would be to see which way our curve goes: the UK/Israel or the US way! While both UK/Israel took 1.5-2 months to flatten their curves w/ strict lockdowns & aggressive vaccination, US had a long plateau (>3.5 months) 2/
However, there is heterogeneity in caseloads: While states like MH, UP, CG, PB, DL are showing ⬇️ in case load, some southern & eastern states (KA, KL, AP, TN, WB, ) still reporting cases in high numbers! What is driving Covid in these states? 3/ indiatoday.in/coronavirus-ou…
Read 9 tweets
1. A quarter of the world’s total #SARS-Cov2 virus genomes have been sequenced on @nanopore devices. First sketched out as an idea here by David Deamer in 1989 this series of tweets covers the long history of nanopore sequencing.
2. Taking 25 years to fully materialise the development of nanopore sequencing has involved close collaboration between academia and industry and many actors from different disciplines and backgrounds. Each has their own story to tell.
whatisbiotechnology.org/index.php/scie…
3. Another early pioneer of @nanopore sequencing was #HaganBayley, a British chemist who in the 1990s began working on stochastic sensing as tool to detect metal ions to track submarines as they move through water and for other applications.
Read 23 tweets
BCG analyzed 🔬 🇺🇸, 🇫🇷 , 🇩🇪 , 🇮🇹, 🇪🇸 Outlook

Testing's likely to follow similar trajectories

Peak COVID demand occurring in the seasonally affected first quarters of 2021 & 2022

#Novacyt #ALNOV #NCYT

bcg.com/en-in/publicat…
BCG anticipate continued need for testing in 2023 & 2024

Even if vaccines prove to be highly effective, the need to test people for COVID-19 will continue, for at least five reasons

#Novacyt #ALNOV #NCYT
TESTING DEMAND DRIVERS:

. Epidemiology of the COVID-19 🧬
. Impact of the vaccines 💉
. Impact of therapeutics 💊
. Government policy 📜

What makes a good test 🔍
#Novacyt #ALNOV #NCYT
Read 5 tweets
Two recent meta-analysis of the ex-post literature on #CarbonPricing (by @greenprofgreen & @JLilliestam etal) suggest carbon pricing is not effectively reducing emissions. This might be both a premature and misleading conclusion.

A thread.
When interpreting ex-post evaluations, we need to acknowledge that less than 10% of G20 emissions are priced at sufficient levels, more than 50% < USD 10/t

@mkalkuhl @Max_Franks_

2/N
In meta-analyses it’s also difficult to take updates in a dynamic literature into account. One example, literature on ex-post carbonpricing effects in the transport sector has seen some important methodological discussions.

See @julljus https://10.1257/pol.20170144 ...

3/N
Read 14 tweets
A Thread (🧵)

Let's discuss long-read #sequencing, optical mapping, and the implications of a recent study (linked below).

Please view my disclosures at the end. I've intentionally made this thread more technical as I think it's necessary.

biorxiv.org/content/10.110…
First, let's deconstruct the paper's title: "De Novo Assembly of 64 Haplotype-Resolved Human Genomes of Diverse Ancestry and Integrated Analysis of Structural Variation".

De novo (Latin: "Of New") assembly involves sequencing a genome without the help of a reference.
Assembling a #genome de novo is like solving a jigsaw puzzle without using the picture on the front of the box. You could start with the corners, assemble the edges, and try to fill in the rest using color- or shape-matching methods.

Let me use an analogy.
Read 31 tweets
Our nation-wide study on the #genomic #epidemiology of #SARS-CoV-2 #superspreader_events in #Austria is out in @ScienceTM !

doi.org/10.1126/scitra…

Please find the highlights in this thread. 1/8
Through #Phylogenetic #SARSCoV2 analyses and data integration with @GISAID @nextstrain , we unveiled the links between #Austrian clusters to the global #pandemic. Explore our data and data-driven narratives at #NextstrainAustria sarscov2-austria.org ! 2/8
#Epidemiological and #Phylogenetic data revealed the geographic origins and distributions of SARS-CoV-2 in Austria. Different viruses circulated in the ski-resort region of #Ischgl with the most dominant #Tyrol-1 linked to @nextstrain clade 20C. 3/8
Read 8 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
1/ Many discussions on #SARSCoV2 / #COVID19 are quite abstract and focus on infection routes and epidemiology. Further, we often get the question "Can you detect actual #Coronavirus at all, or only 'gene snippets' by this PCR?“ Here come some information, now in English!
2/ The novel #Coronavirus has been isolated countless times from patients, incl. "BavPat1/2020", from one of the first patients in Bavaria, by the team around @c_drosten. Several isolates can be ordered from bio material repositories, e.g. european-virus-archive.com/evag-portal/vi…
3/ The genomes of these isolated and laboratory grown viruses were sequenced, as were thousands of samples from patients around the globe: nextstrain.org/ncov/global. By #sequencing it is possible to clearly identify which exact virus is present. By the way...
Read 27 tweets
📢𝗦𝗲𝗿𝗶𝗲𝘀 𝗮𝗹𝗲𝗿𝘁!

We are thrilled to announce our new series #Tech4India as part of the #ETI in partnership with #NESTMEA @MEAIndia & @PrinSciAdvOff

Stay tuned for:

🔸Info on key #emerging technologies & sectors 📡🧬🚀⚛️ 🤖

🔸Details on participation in the #ETI Image
#Tech4India

Recent advances in 𝗤𝘂𝗮𝗻𝘁𝘂𝗺 𝘁𝗲𝗰𝗵 can bring paradigm shifts in #computing #communication & #cryptography affecting all sectors in the process

Participate in #ETI & help India prepare for the #QuantumRevolution 2.0⚛️

ℹ️thesciencepolicyforum.org/initiatives/et…

#NESTMEA
1/2 Image
#Tech4India

We encourage people from varied backgrounds to form multidisciplinary teams and send us EoI on innovations like #QuantumComputing #QuantumCommunication & #QuantumNetworks

Selected teams will be invited to prepare a consolidated tech dev & adoption roadmap 4 🇮🇳
2/2
Read 15 tweets
1/8

On this week's @ARKInvest newsletter (📰), I plan to discuss some exciting research on molecular (prog)nostics. I'm also going to touch on why long-read #sequencing is so important within oncology.

Here's some context:
2/8

We believe multi-cancer liquid biopsy screening will allow dozens of cancers to be detected earlier. However, not all tumors are lethal. Some may never cause symptoms.

By reflexing to surgery, we risk overtreating patients whose tumors may never need it.
3/8

Companies like Veracyte (VCYT) and Castle (CSTL) offer prognostic tests, using a combination of machine learning and gene expression, to risk-stratify suspicious nodules beyond standard cytopathology.

biospace.com/article/releas…

Read 8 tweets
Anyone who has followed me since QT began in late ‘17...know these charts are a Summation of my work for the last 2+ years... from the Peak of the Credit Cycle in January 2018.
#BankReserves
As they say Tops are a Process (u can make a lot of 💰waiting in ).. & Bottoms are Events.
Tsy Strips have done absolutely nothing but lose money -3% since its March 9, 2020 Peak.

Total Returns: (Since March 23)

: +118%
: +55%
: +49%
: +48%
: +46%
: +37%

#Reflation
Read 10 tweets
📢🎉The work of #Bat1K is featured on the cover in the latest issue of @nature: “Six reference-quality #genomes reveal evolution of #bat adaptations” 🦇🧬 #bats Our thread 👇 on the paper:nature.com/articles/s4158… 📸: Olivier Farcy(1/n) Image
📢Have you ever wondered how 🦇 manage to do what they do? #bats have extraordinary adaptations, including powered #flight, laryngeal #echolocation, #vocal #learning and an exceptional #longevity with unique #immunity and resistance to #cancer! 📸: @DanielWhitby5 (2/n) Image
A #Bat1K team led by @Sonja_Vernes @EmmaTeeling1 @hillermich @TheGeneMyers has just published the raw genetic material that codes for these unique 🦇 adaptations and #superpowers in @nature! #bats #genomics #cool! (3/n) Image
Read 32 tweets
Our collaborative study unravels #SARSCoV2 #SuperSpreader events in #Austria and the inter- and intra-host mutational dynamics.

Preprint at @biorxivpreprint available now: biorxiv.org/content/10.110… !

1/7 Graphic design @alex_lercher
Through #Phylogenetic #SARSCoV2 analyses and data integration with @GISAID @nextstrain , we unveiled the links between #Austrian clusters to the global #pandemic.

Explore our data and data-driven narratives at #NextstrainAustria cemm.at/research/sars-… !

2/7
With #Epidemiological and #Phylogenetic data we investigated the geographic origins and distributions of SARS-CoV-2 in Austria. Different viruses circulated in the ski-resort region of #Ischgl with the most dominant #Tyrol-1 linked to @nextstrain clade 20C.

3/7
Read 7 tweets
Precision therapies for #cancer are underutilized for a variety of reasons: lack of sensitive diagnostic tools, lack of clinician awareness, et cetera.

This is changing one step at a time.

(A Thread)
Conceptually, precision drugs exploit genetic defects in a patient's tumor. Using comprehensive next-gen #sequencing (NGS), clinicians can surface mutations that indicate the use of a precision drug.

If we don't catch mutations, we underutilize therapies.
One notoriously difficult variant class is an #NTRK Fusion, which is common in certain pediatric cancers and sometimes present in common adult cancers.

While precision therapies targeting NTRK-fusions exist, only recently have we improved our ability to detect them in tumors.
Read 11 tweets

Related hashtags

Did Thread Reader help you today?

Support us! We are indie developers!


This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3.00/month or $30.00/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal Become our Patreon

Thank you for your support!