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Nanopore MinION – $1k solid-state DNA sequencers

nanoporetech.com

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Re: Nanopore MinION – $1k solid-state DNA sequencers

#71

Post by searine »

comstock wrote: post #35
daemonk wrote: post #8

I just ran a couple of flowcells last week. I've ran 8 total so far now. My impression is that it can be very inconsistent depending on the quality of the flowcell that they send you and your DNA prep. Great for smallish genomes (bacteria), not enough throughput/quality for large eukaryotic genomes (1gb+) unless you got money to burn.

It’s also comparatively expensive compared to other platforms (you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD). The error rate is stupidly high (somewhere between 10 and 20%) compared to Illumina or Ion Torrent who give error rates far less than 1%. It can give very long reads, which are useful in some niche applications. But it’s been massively over-hyped (and over capitaliz…

>The error rate is stupidly high (somewhere between 10 and 20%)

The Insertion/deletion error rate is 20-30%.

The point mutation error rate is something 0.1-1% (higher than HiSeq but not crazy high).

This means with a semi-decent reference genome you should be able to do re-sequencing fairly accurately. It also means, that in conjunction with HiSeq reads you can do cheap genome assembly, using the HiSeq reads for coverage, and the minion reads for scaffolding.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#72

Post by indescions_2018 »

A more interesting race for bio-entrepreneurs. Rather than $1K human sized whole exome. May be the race to develop a $1 plasmid, BAC or small microbial genome sequencer. At that cost, seed level investment in single purpose bio-factories becomes very attractive.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#73

Post by tjridesbikes »

GolDDranks wrote: post #21

How far away we are from a 100$ genome? I've heard that the cost/performance development rate is 'super-Moorean'.

I think I could help answer this. The cost of computation has gone down so much that its just a fraction of the price for your whole genome sequencing. The cost comes from preparation, reagents, and storage. Illumina sells their own reagents, so the cost is really dependent on them. We've worked really hard to get the computation cost of genome sequencing as low as possible, and we just passed a major milestone last year.

Source: Software Engineer for a well-known non-profit sequencing lab/center.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#74

Post by searine »

brohee wrote: post #70

Could it be used with e.g., a drop of blood, to see which bacteria strain is making you sick?

Yes, if you were willing to shell out 1000 bucks for the test, and if the bacteria was in your bloodstream (unlikely). If you swabbed, cultured, and sequenced, it'd be a better test.

I've personally used the oxford nanopore to diagnose malaria subtypes from ~1ml blood draws. Though it took awhile to do so, well beyond clinically relevant time periods. Our best turn around was about 2 days for sequence, but analysis takes much longer.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#75

Post by searine »

cup-of-tea wrote: post #47
atg_gcg_aca_aca wrote: post #16

Earlier quoted context omitted.

A few years ago, the sequencing field was really excited for this platform as an alternative/competitor to Illumina. Unfortunately, the MinION platform has never been able to generate enough high-quality data for most eukaryotic sequencing use cases. The MinION still has it's niche... long read sequencing can resolve problematic regions of the genome, and the minION is the only option for rapid sequencing in the fiel…

> Their HiSeq X platform can put out a human genome right about $1k. That's what Illumina will tell you. But that really depends what you mean by "a genome" and what you intend to use it for. Getting anywhere near the quality of the Human Genome Project is not possible.

> Getting anywhere near the quality of the Human Genome Project is not possible.

That is an unrealistic and inappropriate metric to use.

The HiSeq X isn't mean for making new human reference genomes. It's meant for re-sequencing at scale, and speaking from personal experience, it does an incredible job in quality, speed, and cost.

Even if we could reach reference assembly quality with a hiseq run, we wouldn't want to use it that way. Having reference genomes and annotations (hg19 and hg38) means we can compare and contrast individuals from a common foundation. It would increase the cost and time of genome analysis 100 fold if we had to do denovo assemble for each individual sequenced.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#76

Post by rotexo »

One thing I'm excited for here is targeted sequencing using read-until. In this method, you monitor the current trace coming off of individual pores, and if you determine that the DNA in that pore is not part of your sequence of interest, you can reverse the voltage to remove the DNA and start sequencing another molecule. I think this will open up a lot of applications for human genomics.

If you're interested in Oxford Nanopore, you might also keep an eye out for Roswell Biotechnologies (https://www.genomeweb.com/sequencing/roswell-biotechnologies...). TL;DR: their sequencer involves immobilizing polymerases in circuits so you can measure the current changes that occur as the polymerase adds bases to a strand. This might be a good approach, since it doesn't involve optics (like IonTorrent and minION, keeping costs down) and you get a current event per base (as opposed to per 5-6 bases as with minION), making basecalling easier and potentially more accurate. And it will be fast, since you're reading as fast as the polymerase can work. They want to get up to 10kb reads, and I imagine they could increase the consensus accuracy per read by looping around a single molecule of DNA several times, like with PacBio. Seems feasible too (after all, PacBio has successfully been able to integrate polymerases into very small features rather well, so I see no showstoppers there).

Re: Nanopore MinION – $1k solid-state DNA sequencers

#77

Post by chrisamiller »

comstock wrote: post #48
aFLH7U2daj wrote: post #23

Earlier quoted context omitted.

Flow cells are 1000$ each (unless you buy a lot of them), the sequencer is basically a USB dongle with a uC in it and all the important stuff is in the flow cell. Flow cells are basically disposable (but you mail them back). You get one-ish use out of a flow cell though they can be "washed" and realoaded. Reagent kits run a few hundred dollars depending on what your doing and you get several uses out of them. IIRC it…

NextSeq is expensive, but there are cheaper options (from 30k) and you can just send your samples to a sequencing service. I’ve seen costs for a whole human genome at high coverage of between 1 and 3000USD.

Be careful about defining "high coverage" as 30x. Many applications (especially cancer) really require 100x or more to overcome purity and ploidy, or to identify subclonal populations.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#78

Post by chrisamiller »

folli wrote: post #22
atg_gcg_aca_aca wrote: post #16

Earlier quoted context omitted.

A few years ago, the sequencing field was really excited for this platform as an alternative/competitor to Illumina. Unfortunately, the MinION platform has never been able to generate enough high-quality data for most eukaryotic sequencing use cases. The MinION still has it's niche... long read sequencing can resolve problematic regions of the genome, and the minION is the only option for rapid sequencing in the fiel…

Where do you see PacBio?

Niche uses where long-read sequencing is required (denovo assembly, reference improvement, bacterial genomes, whole-isoform transcriptomes. Nanopore is starting to eat into that market, though.

Re: Nanopore MinION – $1k solid-state DNA sequencers

#79

Post by chrisamiller »

userbinator wrote: post #7

For an interesting contrast, here's a look inside two DNA sequencers from the last decade, costing two orders of magnitude more (and also roughly two orders of magnitude larger in volume and weight): https://www.youtube.com/watch?v=XaumUp4GpCw https://www.youtube.com/watch?v=3K9whMm7vvc It's almost like Moore's law.

It far outstrips Moore's law :)

https://www.researchgate.net/profile/Orit_Shaer/publication/...

Re: Nanopore MinION – $1k solid-state DNA sequencers

#80

Post by chrisamiller »

searine wrote: post #74
brohee wrote: post #70

Could it be used with e.g., a drop of blood, to see which bacteria strain is making you sick?

Yes, if you were willing to shell out 1000 bucks for the test, and if the bacteria was in your bloodstream (unlikely). If you swabbed, cultured, and sequenced, it'd be a better test. I've personally used the oxford nanopore to diagnose malaria subtypes from ~1ml blood draws. Though it took awhile to do so, well beyond clinically relevant time periods. Our best turn around was about 2 days for sequence, but analysis t…

Culturing is the problem, though, right? Many types of bacteria (including some pathogens) really do not like to grow on most media. There's no doubt that sequencing is the future of infection diagnosis. It's just a matter of how long it takes to get there (cost and complexity both have to drop).
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