Discover and read the best of Twitter Threads about #sequencing
Most recents (24)
1/50 #Science is an ongoing process that serves to investigate phenomena, gain new insights or "correct prior knowledge" and this only works in #discourse. This includes diversity of #Opinion, #tolerance and a broad debate space. This is a large thread.
2/50 "#trust the science" is in my view the most #antiscience statement ever. #Questioning science is how you do #Science. This thread gives some examples and further questions.
scientificamerican.com/article/why-do…
scientificamerican.com/article/why-do…
3/50 What about good ##scientific #Practice? I found a glaring example here (of all things, in what I consider to be a rush to #vaccine #approval). #blotgate
trialsitenews.com/a/startling-ev…
trialsitenews.com/a/startling-ev…
🚨🚨🚨 NEW EVIDENCE #zoonosis
Chinese researchers (who have had troubles getting data out) finally managed to sneak upload full #sequencing data from environmental swaps at Huanan market.
Show: Co-occurance of #animal sequences with SARS-CoV-2 RNA
Added to the evidence map 🔽
Chinese researchers (who have had troubles getting data out) finally managed to sneak upload full #sequencing data from environmental swaps at Huanan market.
Show: Co-occurance of #animal sequences with SARS-CoV-2 RNA
Added to the evidence map 🔽
@KatherineJWu 's atlantic article first reported on this new development.
(independent reseachers have been waiting on these data to come out for over a year)
I will give some context in the next few tweets:
theatlantic.com/science/archiv…
(independent reseachers have been waiting on these data to come out for over a year)
I will give some context in the next few tweets:
theatlantic.com/science/archiv…
1⃣ Does this prove that SARS-CoV-2 came from racoon dogs?
Not definitively. Co-occurance of sequences could be from chance contamination in theory. Also, even if racoon dogs were indeed infected, they might just have been amplifiers at market, not the original source.
BUT...
Not definitively. Co-occurance of sequences could be from chance contamination in theory. Also, even if racoon dogs were indeed infected, they might just have been amplifiers at market, not the original source.
BUT...
🧵You can own the Future of Tomorrow Today.
I have heard many people try to call this crash in biotech the end of the #Biotechnology sector. A sector that has been around for decades. One of the most necessary sectors in the entire market.
I have heard many people try to call this crash in biotech the end of the #Biotechnology sector. A sector that has been around for decades. One of the most necessary sectors in the entire market.
1/ Here I am going to lay out for you the opposite case. I have been investing in tech and biotech for 27 years. I have seen so much technology that excites me about the future, and I see it today.
2/ The biggest question I always get in biotech investing is when will we run out of things to discover or great new technologies to invent. I my response is we will never run out until we cure every disease.
2022 was another challenging year for the @ecb. My personal review of the year collects some of my speeches and a few striking charts. All speeches and accompanying slides can be found on the @ecb’s website. A special thanks goes to #ECBstaff for their continuous support! 1/19
The speech “Looking through higher energy prices? Monetary policy and the green transition” (8 Jan 2022) argued that monetary policy cannot afford to look through higher energy prices if they pose a risk to medium-term price stability. #ClimateChange 2/19 ecb.europa.eu/press/key/date…
#Chart US shale oil production has been responding more slowly to rising oil prices, as fossil investments may no longer prove profitable to investors over the medium term. 3/19
1/@GraphiteBio presented preclinical results supporting the use of a single-#cell #RNA #sequencing method to assess #gene correction outcomes in #patients treated with nulabeglogene autogedtemcel (nula-cel) - GPH-101. #BioTech #CRISPR #GeneEditing #Genomics $GRPH #ASH22
2/GPH101 (nula-cel) is a #CRISPR #Cas9 #GeneEditing autologous #stem #cell-based #therapy in clinical development aimed to treat #SickleCellDisease. GPH101 is designed to directly correct the underlying mutation, thereby decreasing HbS production & restoring HbA expression #ASH22
3 $GRPH gene correction platform involves editing hematopoietic #stem cells found in the #bonemarrow that develop into various types of #blood #cells. Since red blood cells lose their genomic DNA during maturation-tracking #GeneEditing in mature cells via sequencing is impossible
Are you interested in learning about #bioinformatics and working with #genomic data? Here's a detailed #learning path to get you started:
To build a strong foundation in biology, you'll need to learn about:
The #structure and #function of #cells, including the various #organelles and their roles in the cell. This will help you understand how cells work and how they carry out essential functions such as #metabolism and #energy production.
The #SynBio Report
I am going to build this thread as I go. There are not a lot of companies in the Synthetic Biology space yet. It is good to get up to date with them before new ones come into the space.
I am going to build this thread as I go. There are not a lot of companies in the Synthetic Biology space yet. It is good to get up to date with them before new ones come into the space.
1/ Gingko Bioworks $DNA
I think this is the top Synthetic Biology company working on 2 platforms. The first is #Biosercurity. This was born form the Covid pandemic and is one of the most important issues of our time.
I think this is the top Synthetic Biology company working on 2 platforms. The first is #Biosercurity. This was born form the Covid pandemic and is one of the most important issues of our time.
2/ The Covid pandemic has shown us how woefully unprepared we are for the next pandemic. We live in the age where anyone can create a bioweapon that could wipe out half the world. Biosecurity is the biggest new area of national defense.
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.
The top science themes in the $XBI and the companies to follow.
#AI/#ML based Drug Discovery
#ProteinDegraders
#iPSC
#SyntheticBiology
#PersonalizedMedicine
#Sequening
#CRISPR
#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.
$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.
$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.
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…
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.
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…
biorxiv.org/content/10.110…
🔴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/
#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/
Thank you for the quick #Omicron discovery and global alert. Thank you for your honesty.
2/
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…
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.
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 ($$$).
4. It introduces a third layer of error (PCR).
1. It requires access to tissue.
2. It requires the construction of patient-specific PCR panels.
3. It requires significant over-sequencing ($$$).
4. It introduces a third layer of error (PCR).
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…
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/
- 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/
-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/
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.
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
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 💉
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... ⭐️
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.
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…
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.
Still, this is a really hard technological problem.
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…
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…
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.
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…
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…
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.
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
@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
See @julljus https://10.1257/pol.20170144 ...
3/N
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…
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.
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.
Let me use an analogy.
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
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
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?
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?
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…
It's crucial that all long-read users, not just the top 1%, have access to this innovation.
pacb.com/smrt-science/s…
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...
