Nanopore MinION – $1k solid-state DNA sequencers • Hacker News Board

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

#81

Post by inciampati » Tue, Jan 30, 2018, 3:18 PM UTC

atg_gcg_aca_aca wrote: post #16

dooglius wrote: post #9

I remember looking into this device before, but as I recall it was intended for small bacterial genomes. A quick Google turns up that a paper using the device to sequence a human genome has only just been published [0] hence the update to the website. I'm not at all familiar with the technology, but doesn't the fact that experts have only just now been able to sequence human DNA mean it would be pretty unlikely the d…

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…

I think we should be clear that for $1k you get something that is entirely different than a human genome. It's just a set of short reads that can be mapped onto a reference genome. You can't de novo assemble it, so you won't be able to see a lot of variation. In fact we can't even estimate how much large scale variation there is because all the studies are based on the short reads.

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

#82

Post by chrisamiller » Tue, Jan 30, 2018, 3:19 PM UTC

bmcusick wrote: post #3

So what’s a whole human genome sequence cost? That’s the usual metric machines are listed by.

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.

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

#83

Post by jrm5100 » Tue, Jan 30, 2018, 3:31 PM UTC

cstross wrote: post #50

I'm pretty sure we are now just a couple of marketing cycles away from a version of this being re-packaged and sold to police departments around the world as a tool for identifying suspects in a cloud database of DNA sequences belonging to People of Interest. (You don't need a complete sequence for that, just enough unique markers to ID somebody.) Goodbye "papers, please", hello "cheek swab, please".

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).

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

#84

Post by sdcuevas » Tue, Jan 30, 2018, 4:18 PM UTC

eggie wrote: post #63

sdcuevas wrote: post #54

Oxford Nanopore is burning through at least $1 million a week of their investors income with virtually no sales to support their market valuation. Will they be the next Theranos? https://www.jcapitalresearch.com/uploads/2/0/0/3/20032477/20...

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.

Let's assume the company statements are true, they are shipping on time; what is the break even point for shipping $1,000 starter kits, flow cells, and sample prep items? How many devices are they shipping? What's their revenue?

https://www.investopedia.com/terms/b/breakevenanalysis.asp

Are they anywhere near break even or are they going to require another large infusion of venture capital and can Nanopore find these new investors?

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

#85

Post by bayesian_horse » Tue, Jan 30, 2018, 4:41 PM UTC

comstock wrote: post #53

eggie wrote: post #51

Earlier quoted context omitted.

> you can get a full human genome sequenced at high coverage for between 1000 and 3000 USD This is not a "full" human genome, but a collection of 150bp fragments that can be realigned to an existing human genome. You cannot take this and infer the whole diploid genome of the individual. There is a huge amount that will be missed, and all of our current knowledge is based on this gappy picture of what's going on in si…

I’d agree with you, that long reads would be useful if the error rate wasn’t so shockingly bad. There is, likely value in long reads, but what non-niche research applications are there for highly error’d reads that justify a valuation of several billion dollars?

Virtually all applications can benefit from long reads. There are already hybrid assemblers out there which take Illumina, Pacbio and Nanopore reads. The long reads tie the short reads together, whereas the short reads improve the accuracy.

The area where DNA sequencing will first be revolutionizing clinical practice is in sequencing pathogens for sake of identification. In these instances nanopore sequencing rules, because it can give answers in minutes.

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

#86

Post by daemonk » Tue, Jan 30, 2018, 4:44 PM UTC

oh_sigh wrote: post #20

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.

$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?

I am using it professionally for a lab. The best bang for the buck right now is to buy their starter pack which includes library prep kit and 2 flow cells. This is limited to one per person. I got two members of the lab to buy two starter kits, effectively getting the flow cells for ~500 each. I am sure a lot of people are doing this too.

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

#87

Post by daemonk » Tue, Jan 30, 2018, 4:45 PM UTC

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…

It's fine for bacteria where even with 10-20% error, you can do consensus calling with very high (200-500X) coverage.

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

#88

Post by bayesian_horse » Tue, Jan 30, 2018, 4:46 PM UTC

aFLH7U2daj wrote: post #23

oh_sigh wrote: post #20

Earlier quoted context omitted.

$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?

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…

No sequencer on its own will ever be certified. You always need a pipeline from sample to a clinically useful answer to be certified.

The problem here is that everything in that pipeline keeps improving at a fast base. Also the reference databases are updated all the time. Whereas sequencing will probably always give the right answer to the precise question it was given, I don't see any luck in certifying these methods any time soon.

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

#89

Post by Brakenshire » Tue, Jan 30, 2018, 4:52 PM UTC

sdcuevas wrote: post #54

Oxford Nanopore is burning through at least $1 million a week of their investors income with virtually no sales to support their market valuation. Will they be the next Theranos? https://www.jcapitalresearch.com/uploads/2/0/0/3/20032477/20...

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?

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

#90

Post by daemonk » Tue, Jan 30, 2018, 4:53 PM UTC

rotexo wrote: post #76

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 Oxfo…

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.