Discover and read the best of Twitter Threads about #nanoporeconf
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Here is the slightly cheesy montage for the great #nanoporeconf for 2023 - and, with a reminder of my conflict of interest - I am a longestablished paid consultant for Oxford Nanopore and a shareholder - here are my thoughts on the conference.
For long time nanopore scientists -and I am definitely one of those- one can definitely both plot progress London Calling conference (on the Thames in London) both in terms of what the company presents as near and long horizon+how the plenary speakers use and talk about nanopore
From the company side, much of this was giving a roadmap of key software and flow cells; the R10 flow cells (which is a distinct step up in quality) are now routine; what is not yet is high yield duplex which has being moving from Oxford to Alpha to broader Beta testers.
Duplex: 1.5% of the time, the complement strand follows the first strand naturally.
Initially, modified the adapters and reached 30% duplex rate.
Initially, modified the adapters and reached 30% duplex rate.
Stereo base caller uses similar ML approaches as ChatGPT,
On library prep at #Nanoporeconf, a description for PCR-free methods showing the difference between ligation (max output) and rapid mode (10minutes, minimal lab equipment needed). Ultralong reads (ULR) also enabled, all Kit14.
Rapid ULR. Current record is about 4 megabases.
PCR expansion kits enable the use of samples with low input amount.
As 2022 draws to a close, we’ve been reflecting on some of the highlights (in no particular order) — you can read the full article here: bit.ly/3IfaKYc, or digest the thread below. Wishing you a happy new year and all the best for 2023! 1/23
The #cancer research community has made huge strides leveraging the unique attributes of #nanopore sequencing to characterise cancer at unprecedented resolution, unlocking previously hidden variation and accelerating research to support human health. nanoporetech.com/cancer-research 2/23
In May, @mdelledon took a group of scientists into the Gobi Desert to capture small mammals, including bats, to study their microbiome and they set up a genomics lab in a tent. They demonstrated the utility of the MinION in the harsh, off grid and sandy desert environment! 3/23
Updates on plans for outy sequencing #nanoporeconf
Outy sequencing accuracy #nanoporeconf
Detection of very low frequency variants with outy sequencing #nanoporeconf
Time for the latest @nanopore technology updates. Up next in the auditorium: an Update from the Oxford Nanopore team. #nanoporeconf
Please note, we invite you to read the disclaimer in the slides
CB: More information on Clive’s previous technology updates:
10 minute reminder: @VanessaPorter will be on stage in the auditorium shortly with her talk: 'Identification of novel #genomic structures and regulation patterns at #HPV integration events in cervical #cancer'. #nanoporeconf
VP: HPV is a necessary driver of cervical cancer. HPV integration is present 70% of cervical cancers. Often disrupts E2 gene & causes structural rearrangements. #nanoporeconf
VP: HPV integration often upregulated neighbouring genes. #nanoporeconf
@euanashley's plenary talk: 'The potential of ultra-rapid #nanopore genome sequencing for critical care medicine', will begin in 5 minutes — check out the agenda to find out what else is in store: bit.ly/3M3WlwM #nanoporeconf
@euanashley EA: seeing a $398k car, I recently thought that if luxury cars had dropped in cost as much as sequencing, I could have bought the car for 1c #nanoporeconf
EA: its not enough to have confidence in the genomic data, sometimes we need speed too. #nanoporeconf
GS: Lord Kelvin believed in meaningful measurement to see the whole picture. With nanopore sequencing you gain more comprehensive insights than ever before. #nanoporeconf
GS: In the 3 years since the last time we were at Old Billingsgate, @nanopore has released 200+ products, increased our single-molecule raw read accuracy from 95% to 99.6% & hugely improved our scalability & output. #nanoporeconf
So, as promised, here are the observations of @beggs_lab at @unibirmingham about the new LSK114 kit on the R10.4.1 "Marathon" flow cells - we're happy enough that we have put 4 samples on this afternoon on our @nanopore P24 - ready for London Calling 22 - wet lab by @JoStockton1
Firstly - output - this is just a representative example but on our tumour samples we are seeing between 80-120gbases of data generated per sample. This is with LSK114 prep, Covaris sheared to ~10kb. Run for 72hrs. Note the data output - much higher thanks to Marathon flow cells
As you can see we have got roughly the read length we want, and we have found as you increase the read length, data output drops (obvs). Longest read in this run was 668kb.
We've put out a short preprint today showing some updates in Readfish for @nanopore adaptive sampling. biorxiv.org/content/10.110… @alexomics is giving a talk shortly at the #nanoporeconf about this - but a short thread here.
Readfish now exploits the barcoding features ready baked in to @nanopore guppy to allow a few new features. You can switch off barcodes as you wish but more interestingly, you can assign different targets to different barcoded samples.
This is interesting in lots of places, but we show the use of three different human gene panels on three different samples on a single GridION flow cell.
Opening the Nanopore Community Meeting Tech Update is James Clarke, valiantly speaking through a bad, bad cold. We'll be live tweeting in this thread, with Stu Reid and Rosemary Dokos up next #nanoporeconf
JC: @nanopore accuracy has come a long way. Right now, in just 3-4 seconds, I can pass 1,000 bases of a **single molecule** of DNA through a hole, and know its sequence with over 99% accuracy. That’s better than Q20, by looking at a single molecule - once #nanoporeconf
JC: Beyond single molecule, you can of course use multiple strands in a pile-up. We’ve achieved Q50 consensus accuracy on bacterial genomes, from 20X coverage. #nanoporeconf
Up in a few minutes, Clive G Brown @the_taybor with a plenary talk on @nanopore sequencing. We'll live tweet in this thread 1/n #nanoporeconf
@The_Taybor CB: our goal is to enable the analysis of anything, by anyone, anywhere #nanoporeconf
CB: A reminder of how nanopore works #nanoporeconf
Coming up in a few minutes, Clive Brown @the_taybor, with an update entitled “Nobody Expects the Strandish Exposition”. Follow the talk live in this thread #nanoporeconf
CB: Our goal is to enable the analysis of anything by anyone, anywhere. Here are some examples of global use: nanoporetech.com/portable-seque…
CB: As a reminder, this is how nanopore sequencing works. #nanoporeconf
Super excited to finally share this pre-print of our work demonstrating <30 minute sequencing-based somatic variant calls using @nanopore sequencers!
We had a need for speed. A (long) thread... 1/
We had a need for speed. A (long) thread... 1/
Why focus on speed? Intraoperative sequencing. Being able to quickly (<1hr) identify actionable mutations *during surgery* has a host of amazing potential use-cases. Imagine generating a personalized molecular diagnostic during biopsy… 2/
...combining biopsy/resection surgeries in real-time, confirming indeterminate frozen section results, intra-operative clinical trial enrollment to test targeted therapies, molecularly targeted chemo delivery directly into resection cavities. The list goes on… 3/
Opening the tech update at the Nanopore Community Meeting, from Oxford @Nanopore, James Clark, VP platform technology #nanoporeconf
JC: a reminder that our goal is to enable the analysis of anything, by anyone, anywhere #nanoporeconf
JC: Looking at about the key qualities of nanopore sequencing: high accuracy data, with high yields, information-rich data, a versatile platform that scales from portable to ultra-high throughput #nanoporeconf
Tuning back into #NanoporeConf to hear the great @BenedictPaten talking about their human genome work on nanopore - 11 Genomes in 9 days, assembled by SHASTA - very good results (whole MHC in one contig) and with HiC gets you to almost chromosome assemblies. Whoop!
That was then read data a 89% accuracy back last year - now, just software updates (in Guppy) 93% accuracy and pulls in the left hand tail. This gets even better with R10 chemistry - homopolymers well called to 8 or 9 length.
SHASTA has improved a lot, taking NG50 from 19.2MB to recalled nanopore and better shasta to 32.2MB NG50 - with ultra-long and R10 this can go to 58.5 MB (this is bonkers!)
Finally George Githinji from Kenya's NIH/Wellcome supported centre on infectious disease #NanoporeConf - build capacity in rapid outbreak monitoring - portable sequencing very useful in Africa! Brings together groups in Kenya, Tanzania and Uganda.
Built amplicon based sequencing for Measles and rubella - and sequenced SARS-CoV-2 as April- have sequenced over 100 SARS-CoV-2 already (this is pretty impressive - better than a number of developed countries)
They can see a transition from introduced SARS-CoV-2 via travel to local transmission.
Next up in the SARS-CoV-2 #NanoporeConf Session - Estée Török - looking at healthcare workers in Cambridge - part of @CovidGenomicsUK - 18 different hospitals, takes us through the technical details from samples RT-PCR positive.
Sequenced 747 genomes analysed. Most community transmitted (70%), but hospital aquired infections in the other set, with 0 to 1 SNP difference in the sample location and similar location - implying linked infection.
Estée takes us through an example of the dialysis data where the low SNP differences shows there was a dialysis cluster (linked transmission) - shared patient transportation as a risk factor to dialysis units. (nice example in narrowing down infection control)
Joseph Fauver (Yale School of Public Health) on the Coast-to-coast spread of #SARSCoV2 10 samples on ARTIC protocols. #NanoporeConf 24 hours from recieving RNA to complete SARSCov2 genomes. Put them into the big SARS-Cov-2 tree. 7 of the 9 genomes are in the big US clade
(editorial note: genomic epidemiology analysis has the endless headache of uneven sample ascertainment)
Now up to 121 genomes, using only 4 flow cells with use of nuclease washes between flow cell runs, continuing to track the epidemic.
Plenary speaker Nancy Murphy from Princess Marget in Ontario #NanoporeConf. Tells a story around a specific patient with leukemia where she got the result within 48 hours (I think - could not quite follow the timeline, but it was fast) and changed the path for this patient.
Takes us throw the leukemia pathway - complexity of bringing patients in and treatment, and in particular residual disease; some patients are not chemo-responsive. Mixed Linneage Leukemia is complex due to the translocation which is key to track.
Nanopore allows tracking patients throughout the treatment course. Diagnositic samples + Remission + Relapse. 40 samples; Sequence on PromethION to get both methylation and structural biology
Tuning back into #NanoporeConf online and hearing thumping 70's, 80's and 90's tune in the warm up. London Calling is such a great track and now will forever be linked to hitech DNA sequencing :)
Gordon (@GSanghea) opens saying that this a sombre time with a global pandemic - but the innovation does not stop, in particular LamPORE as Nanopore's first diagnostic offering focused first on SARS-CoV-2 but in the future broader infectious agents.
Q-line is the new product line focused on diagnostics (editorial - diagnostic stuff rightly has far more regulation which makes a different beast). Q-line GridIONs are available from nanopore store today.
And now at #nanoporeconf, an update from the team @RosemaryDokos, James Clarke and Stu Reid. A thread
First up, James Clarke with an introduction to @nanopore sequencing. More than 1,000 publications use nanopore sequencing nanoporetech.com/resource-centre, and we estimate that ~1.7 petabases of nanopore sequence has been generated to date #nanoporeconf
JC: Here’s how nanopore sequencing works. Library prep straightforward: add an adapter to each end of the sample DNA molecule, containing leader, motor protein, motor stall, tether #nanoporeconf youtube.com/watch?v=RcP85J…
Getting to watch Dan Turner on LamPORE for #nanoporeconf explain how LamPORE works. Reminds us about how LAMP works - isothermal (just heat, dont heat cycle) and make insane amounts of DNA (micrograms) ("explosive amplification")
LAMP traditionally coupled to a colour change (of flourescent primers nearby) but these have false positives (weird dimers) and dodgy "mid colour" changes. Rather than using fluorophore, ligate nanopore primers, and then put on a nanopore
LAMP gives multiple copies of the target into a long read, and it can have a 10nt bar code. Easy dual bar code, but also the first "LAMP" barcode is *in the LAMP tube*. By having a beta-actin internal control to distinguish "negatives" from "failed reaction" / "failed swab"
