To Respond To a Disease Outbreak, Bring In the Portable Genome Sequencers (ieee.org) 33
the_newsbeagle writes: Epidemiologists working on Zika virus could benefit from portable genome sequencers, like these used during the Ebola outbreak. In spring 2015, researchers conducted the first experiment in real-time genetic surveillance during an infectious disease epidemic. The researchers packed all their equipment in a couple of suitcases and set up a mobile lab in Guinea, where they used palm-sized sequencing devices to analyze viral RNA from 142 patients. Genomic data can illuminate the chains of transmission in an outbreak, and can help scientists develop diagnostics and vaccines.
Is this an advert? (Score:2)
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This breaks my brain. (Score:4, Informative)
Future implications (Score:2)
Yep, pretty impressive.
I wonder how long it will be be until technology evolves to the point that it will be standard practice at the doctor's office for them to draw a little blood or biopsy as you walk in and have your entire micro-biome gene-sequenced to identify every pathogen you're currently carrying before you've even gotten out of the waiting room. There will no doubt still be room for human judgment, but no more trying to guess at the problem based on symptoms and likelihoods and trying different t
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There's a 5-million-fold difference between sequencing the genes of one cell, and sequencing the genes from every cell in a drop of blood. There are techniques to identify all the pathogens in a sample, but sequencing is not one of them.
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True. But bulk genome sequencing is already being explored. Heck, we've got a ship sailing around the planet doing just that to seawater by the hundreds of gallons, which has discovered that something like 20% of all DNA in the ocean belongs to unknown organisms unlike anything we've ever seen.
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That depends on how you define sequencing. PCR amplification of specific DNA sequences,
PCR is definitely not sequencing. I wasn't aware of anyone doing PCR then sequencing - when is that done?
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Though it hasn't yet lived up to its potential (Nanopore sequencing has been Next Year's Big Thing for several years now) it is rather incredible what can be done with such a small and cheap piece of kit. It still has major problems with accuracy, but is starting to find a niche in applications where speed, portability and long sequence reads are required. Here's a nice piece from a fan of the technology that has a bit of history and an appraisal of where it stands in 2016: http://omicsomics.blogspot.co.... [blogspot.co.uk]
Very cool but has competition (Score:2)
It's very cool in it's portability and in real time. a traditional illumina has higher throughput. they processed 1450 samples in 6 months (their peak rate was much higher). An illumina can do many more samples in a single run, in batch. But you might not want to take it into the field and your latency would be higher since you would accumulate samples until you had enough to justify one run. The cost of that run per sample would be less but the cost of the batch run more which is why you wait. Anoth
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An illumina can do many more samples in a single run, in batch. But you might not want to take it into the field and your latency would be higher since you would accumulate samples until you had enough to justify one run.
But they are still (probably) burning one nanopore per sample, so that's $900 per run (yeah, I'm sure ONP gave them a hefty discount). So the overall cost is much higher than with Illumina, but you are right about the latency. In cases where that matters, I would go with PacBio (cheaper and faster).
Another way this thing is superior is in read-length (50kbases)
Well, let's say "up to 50 kb". The average is a different story, especially if you need to get the higher-quality 2D reads for your downstream analysis. ONP has been promising >100 kb reads for a long time but
Re:This breaks my brain. (Score:4, Informative)
I'm an outsider, so I've just gotta be misunderstanding something.
Well, like pretty much all press coverage of the Oxford Nanopore sequencer, there is a ton of hype but questionable value. I'll give the nanopore portability. It is an incredible feat compared to the large sequencers (even the benchtop MiSeq). But here's the thing:
1) The accuracy is terrible. This is especially important when you are looking at SNP variants. You need accuracy.
2) The sequencer may be portable, but data analysis in this version currently uses a cloud service that (obviously) requires an Internet connection, so I'm not sure the hype about service in rural areas is really that great.
3) The throughput is ok, but not great. For virus genomes this might be fine, but for bacterial and larger genomes, it's a no go.
4) The speed isn't all that great. It's around 24 hrs. to complete a 2D run. That is right in line with what is offered by other sequencers.
5) Yes, you DO need a library prep, contrary to what the proponents claim. It might be a little bit simpler than some conventional protocols, but you cannot just drop DNA into the pore.
All of this, in my mind, comes down to two features that matter most for any sequencer: cost and speed.
Cost:
The best cost/bp currently, by far, comes from Illumina technologies. This will never compete with that. That said, Oxford Nanopore has an advantage in read length that Illumina will never have. However, PacBio has been competing in the read length niche for a while now and is well-established. So is the cost of Oxford Nanopore better than PacBio? Cost is mostly a function of yield x read length. For PacBio, the cost of a sequencing unit (a SMRT cell) is ~$600 (the library prep cost is ~$400, but is a one-time cost for each sample). One SMRT cell yields ~0.5 - 1 Gb per run, so $0.0000006/bp (Note: this is with the older RS II system. With the newer Sequel system the throughput is better). The Oxford Nanopore site claims up to 1 Gb per chip, at $900/chip, but the reality is a bit less. Based on a recent paper where they assembled the E. coli genome with nanopore data, the proportion of actual usable data is closer to 150 Mb. So that's about 10 times the cost of PacBio sequencing.
Speed:
The Oxford Nanopore site claims they are fast, but to get the higher quality 2D reads that you need for assembly, the run times are typically about 18-24 hrs. For a MiSeq, the run time can be as low as 12 hrs, and for PacBio it is 3 hrs. So the nanopore is not really winning with speed either.
It seems to me that portability is the biggest strength of the nanopore, but the majority of groups are still going to get their sequencing done at core facilities, so I have doubts about how that will play out in the market. What they really need to focus on is cost. But everyone is doing that at the same time, so it is a hard race to keep up with.
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It's really a very simple device. Make a nanopore (very small hole) and run the DNA/RNA through it (all this takes is a few simple chemical steps to get the DNA/RNA to unfold). Measure the change in electrical potential as the DNA/RNA goes through the hole one base at a time (kind of like reading a string of different colored beads).
The expensive part is the proprietary software to analyze the data... but that should get cheaper over time.
Re:nanopore tech still has accuracy problems (Score:4)
So? It's not like you're having to work with only a single strand of DNA. Unless the error is systematic you can sequence several dozen strands and use standard error-correcting algorithms to recreate the original sequence with fairly high confidence.
Or maybe they're already doing that and accuracy plateaus at 96%. Still, does it really matter? They're not trying to do genome-research class sequencing, they just need to identify the DNA strands of interest (which are probably way more than 4% different than any other ambient virii) and identify the presence of mutations to trace the source of an infection, which probably have a 96% chance of being in the accurately-sequenced sections.
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Or maybe they're already doing that and accuracy plateaus at 96%
Yes, this is correct.
They're not trying to do genome-research class sequencing, they just need to identify the DNA strands of interest
Well, it does depend on what kind of downstream analysis they plan to do, but 96% is not great. That is 1 error per 25 bases. Good enough for alignment procedures to work, but definitely bad if you are looking for SNPs.
As one commenter on ONP has been stating for a while: what's the point of a portable sequencer if you have to haul around a full-size Illumina sequencer along with it to get the accuracy you need?
The nanopore's advantage in this example is the virus genome, which is a rel
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Good to know, thank you. I can see how a 4% error rate would leave much to be desired when building a reference sequence, though if necessary you could presumably do many additional passes to bring the error rate down further. I assume that 96% is just the point where they decided that diminishing returns weren't worth the incremental cost, and that will presumably improve with time.
I agree that 96% is not great, but it's more than sufficient to recognize a virus. And once you have a database of related
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though if necessary you could presumably do many additional passes to bring the error rate down further.
In its present state, not really. The biggest problem with nanopore data right now is systematic errors in homopolymer regions. These can't be easily corrected out with higher coverage. Incidentally, some of the most significant mutation events are in homopolymer regions, so this is bad.
but it's more than sufficient to recognize a virus.
Correct. But you need to know more. In particular, which strain of virus? Strain variations can easily be much less than 4%.
but so long as you're taking many samples from a community you can probably make a pretty high-confidence conclusion about even SNPs
If the errors were mostly random, you are correct. That is the problem here, the errors are systemat
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Seems to me the big practical advantage is actually having a sequencer available in relative backwaters. Satellite internet is available everywhere, while physically shipping non-degraded samples to labs that may be many days away seems like it could be a challenge.
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Yes, absolutely. However, the nanopore sequencer has to have more than one limited-applicability advantage for it to be commercially successful against competitors. Just consider seriously for a minute what has actually been described (not hyped about) in this paper.
1) A mobile lab in a suitcase including sequencer - yes, that's awesome
2) Deployed to a region experiencing an outbreak
- ok, can be useful, but how many outbreaks occur every year that a
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All right, I think I understand your objection. The details are always far more significant from "in the trenches". On the other hand this is my first exposure to the technology outside of I think hearing of it as proof of concept years ago, and it seems like it has great potential. Watching from a distance the speed of evolution of gene-sequencing technology in general is quite breathtaking. The mere existence of these tools today leads me to expect much more sophisticated implementations to be commonplac
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Only if the error is random, which it is not in this case.
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> Base calling accuracy: up to 96%
Um, bullshit. See, this has been the problem with Oxford Nanopore since the beginning. They distract and confuse through a lot of misleading statements and media hype, which is why I can't trust any of their claims. The typical accuracy of single-pass 1D reads on real data is about 70%, about 80% on 2D reads. The 96% accuracy they are quoting on their site is after they error-correct the reads.
Hope they're more careful this time around (Score:2)
http://www.theecologist.org/News/news_analysis/2987024/pandoras_box_how_gm_mosquitos_could_have_caused_brazils_microcephaly_disaster.html [theecologist.org]
I was on the design team for a rapid DNA sequencer (Score:2)
I was on the design team for the MiSeq DNA sequencer at Illumina that can sequence 1 billion bases in one day, doing embedded systems/FPGA/control loop work. I no longer work there, but think they've managed to increase throughput. This particular unit fits on a tabletop, and costs about $100K.
A story was related to me while working there about an outbreak in the intensive care unit in Cambridge England where 7 preemie infants got sick. With this instrument, they could see how the virus mutated on a
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Very informative answer @volvox_voxel!
IMHO, one of the big issues with Illumina sequencing is that (apparently by design), it does not facilitate "real time" sequencing (streaming) as the MinIONs/Promethion does, i.e:
https://www.biostars.org/p/156... [biostars.org]
If those .bcl files being generated could be fed ASAP into a socket or similar, that would bring Illumina closer to the new generation (4th now?) of sequencing.
Can you please contact me (OP of BioStars post above)? I'm really interested in discussing this to