How far away we are from a 100$ genome? I've heard that the cost/performance development rate is 'super-Moorean'.
Nanopore MinION – $1k solid-state DNA sequencers
21–30 of 111 posts
Re: Nanopore MinION – $1k solid-state DNA sequencers
#22I 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…
Where do you see PacBio?
Re: Nanopore MinION – $1k solid-state DNA sequencers
#23I 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.
$1,000 for the starter pack - what kind of use can you get out of that, and how much are the ongoing costs for the flowcells and anything else that needs to be replenished? Are you using it for fun? professionally? academically?
Flow cells are 1000$ 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's not certified for use as a medical diagnostics device so it's "research only".
It's a nice system with great (none) upfront costs that has a lot of potential. But read quality and quanity per dollar aren't as good as what we get with our NextSeq (which by contrast costs something crazy like 300-400k)
Re: Nanopore MinION – $1k solid-state DNA sequencers
#24For 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.
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.
Re: Nanopore MinION – $1k solid-state DNA sequencers
#25Wow. Can I do whole-genome sequencing with this? Is this a similar product/result as buying whole genome sequencing from an established company for the $500 to $800 they charge these days?
You're buying a service for the 500-800$. 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…
If you want to do a human or a dozen related humans, and then discard the equipment, is there anything cheaper?
That is, without handing the DNA over to somebody else.
Re: Nanopore MinION – $1k solid-state DNA sequencers
#26How far away we are from a 100$ genome? I've heard that the cost/performance development rate is 'super-Moorean'.
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.
Re: Nanopore MinION – $1k solid-state DNA sequencers
#27So what’s a whole human genome sequence cost? That’s the usual metric machines are listed by.
I looked in to it 4 months ago the cheepest service I could find was 2500 usd.
Re: Nanopore MinION – $1k solid-state DNA sequencers
#28Earlier 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?
While I've been out of the area for almost 3 years now (I sysadmin-supported GS FLX from Roche/454, MiSeq and HiSeq from Illumina, and PGM from IonTorrent), the thing to remember is that each sequencer has it's strengths and weaknesses depending on what you want. Do you want to focus on read length, run time, reads per run, reagent cost, equipment cost, accuracy, etc.
As for pacbio, if I remeber correctly, their cost was low (high equipment cost though) and sequencing was relatively fast, but at a reduction of accuracy. Never dealt with them first hand though.
Re: Nanopore MinION – $1k solid-state DNA sequencers
#29How far away we are from a 100$ genome? I've heard that the cost/performance development rate is 'super-Moorean'.
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 sequencin…
Is there an updated plot going up to 2017?
Re: Nanopore MinION – $1k solid-state DNA sequencers
#30Earlier quoted context omitted.
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 sequencin…
Is there an updated plot going up to 2017?
https://www.nextbigfuture.com/2017/11/update-on-genome-seque...
Interestingly the cost had not dropped in the past two years.
Also the graph references genome.gov but that site appears to be unavailable at the moment.