Nanopore MinION – $1k solid-state DNA sequencers

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 capitalized).

The neat thing is that it’s very small. But that isn’t really compelling given the very low accuracy.

$1,000 for the starter pack - what kind of use can you get out of that, and how much are the ongoing costs for the flowcells and anything else that needs to be replenished?

Are you using it for fun? professionally? academically?

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 field. For production genome sequencing centers though, Illumina's still the dominant tech. Their HiSeq X platform can put out a human genome right about $1k.

Human dna is not particularly special except there's so much of it relative to bacteria and also the sequencing method is stochastic.

They are orders of magnitude more precise, and this is the important part. A human genome has 3 billion basepairs, even if you have 99,99% accuracy, this is not enough.

It far outstrips Moore's law :)

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

The forensic field moves very slowly in adopting new technology since they have to do a lot of re-validation every time anything changes.

This idea already here, but with technology based on older/simpler methods. One example is Intigenx: https://integenx.com/rapidhit-system/

The FBI has plans for implementing them: https://www.fbi.gov/news/testimony/fbis-plans-for-the-use-of.... The laws just need to catch up (or prevent it).

Too expensive with the current nanopore technology.

And with any other technology, including a miniaturized PCR implementation, it would be too slow.

That’s great, but for a company that has raised on a valuation of >2BUSD how are they going to compete with Illumina.

The read lengths might be long, but the error rate is a couple of orders of magnitude higher. I can’t see a market large enough for highly error’d log reads to support their valuation.

I'm somewhat confused by that article, one of its key pieces of data (saying that a full human genome sequence would cost $90,000 using this technology) comes from an expert comment made on Quora. The Quora post made the $90,000 estimate in early 2016, then updated it in July 2017 to $10,000. This article was written in December 2017, so why does it use the original figure and not the updated one?

The technology really works and is generating results at a rapid pace. This will absolutely not be the next Theranos, although you may be right that there are issues of burnrate and maybe even mismanagement.

To me the fact that they have a patent monopoly on "putting DNA through a protein pore with voltage sensing" is tragic. Who knows were we would be today if these patents had been granted to the public domain.

Maybe it's just the company's spin, but apparently they are not keeping up with the orders. Also, the technology is working, and it is working competetively well for certain applications.

There is a group in UK (Matt Loose's group) that I think is working a lot on read-until. I haven't really kept up with it. I think the key for read-until to work is ultimately probably going to be better hardware as you need to be able to analyze the trace signal and compare it against a database fast enough to tell the device to kick it out. There are plenty of software optimizations that can be done to compress the signal or extract relevant regions, but the comparison to a database will be difficult to do fast.

Read-until has had diminishing utility. Over the last year or so, the speed at which a read can pass through the pore has increased so that by the time you call the bases and determine what it is, the read is likely to have already passed through the pore.

Here's the Sequencing & Moore's Law plot that I'm tired of seeing in every genome sequencing presentation ever. https://wi-images.condecdn.net/image/W5YlBgPjX36/crop/1620

Since 2013, Illumina's brought the price of a genome to about $1k with the HiSeq X, which essentially scales up their existing tech. No idea what the next few years hold, but I'm excited to see insurance companies beginning to cover genome sequencing as an affordable diagnostic tool.

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.

I think we're already there. You can probably get around a $50 dollar bacterial genome by using robots and doing 384-well plates of samples at a time to get economies of scale.

A lot of the costs are outside of the sequencing itself. You have to extract the DNA from the sample and prepare that DNA for the sequencing platform you're using. These costs are both the reagents needed to do this, and also the associated labour costs, even when done at scale.

Perhaps you meant $100 human genome though? However I think roughly the same principles apply.

A $100 wildlife camera may solve that problem for you.

You're buying a service for the 500-800$. Here you're buying a flowcell for 1000$ (the "sequencer" is more or less free). The technology is pretty different and a lot more bleeding edge. If what you want is just a genome aligned to a known reference and you can wait a few days then this is not what you want.

We use ONT's minION for strange niche stuff, where either the DNA prep method matters or the latency (the time from loading to the first data out of the machine) matters. Read quality is typically not as good as illumina, so for applications where we need quality we stick with the NextSeq. There's no reason to think nanopore technology won't get better though, but for now, if you've got the money illumina is still the way to go most of the time.

There is a good reply to you that is currently dead for some reason, so I’m reposting it here for people who don’t have dead visible:

> You're buying a service for the 500-800$. Here you're buying a flowcell for 1000$ (the "sequencer" is more or less free). The technology is pretty different and a lot more bleeding edge. If what you want is just a genome aligned to a known reference and you can wait a few days then this is not what you want. We use ONT's minION for strange niche stuff, where either the DNA prep method matters or the latency (the time from loading to the first data out of the machine) matters. Read quality is typically not as good as illumina, so for applications where we need quality we stick with the NextSeq. There's no reason to think nanopore technology won't get better though, but for now, if you've got the money illumina is still the way to go most of the time. >

The minion is a device you own. You don't need to ship the samples (which can be a problem, imagine ebola samples). You wait a maximum of 2 days for most of the results.

That’s extremely interesting, thank you for posting the link.

Consumables consumables consumables.

It's remarkable the perverse economic rules that make disposables with vendor lockin a feature. Opex vs capex.

There's a Microsoft Research project that does something like this with mosquitoes for disease management: https://www.microsoft.com/en-us/research/project/project-pre...

(note: I work at MSR, but on other projects)

https://vimeo.com/125796581 is a grand vision ONT have in the works

All the technology required already exists. You'd just need a compelling enough application.

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.

It's really comparing apples and oranges. If you want a 30x whole genome for genotyping, you'll use short read technologies and it'll be way less expensive.

The enormous reads offer a different window into genomes, by spanning repetitive regions where short reads can't be accurately placed. For lots of applications, the sweet spot is to use long reads for "scaffolding", then build up coverage with short reads.

I looked in to it 4 months ago the cheepest service I could find was 2500 usd.

I believe Nanopore Technologies is about to announce that a $1000 Human genome is possible with the PromethION, a big brother of the MinION.

Software is only 1% of the story. We need reliable public data from many people linking genomes, diet, life history, and phenotype to do the other 49%.

Ah. ~$500 - $1000 each. That seems like an expensive consumable, but I have no basis for comparison. Is this a lot?

https://store.nanoporetech.com/flowcells.html