To Respond To a Disease Outbreak, Bring In the Portable Genome Sequencers (ieee.org)

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.

Comments

This breaks my brain.

[Verdatum]

I'm an outsider, so I've just gotta be misunderstanding something. The oxford nanopore website seems to be claiming that you can sequence an analyte in real time, with a $1000 startup fee and $900 or less for a consumable...It uses a nanoscopic hole with an enzyme around it that ratchets a DNA strand through one nucleotide pair at a time, the whole time, spitting out the results to your computer....I can't process this. How can it be this portable, simple, and cheap? How did we get so good at this stuff?

Re:This breaks my brain.

[Rutulian]

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.

Re:nanopore tech still has accuracy problems

[Immerman]

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.