Commercial, USB-Powered DNA Sequencer Coming This Year 95
Zothecula writes "Oxford Nanopore has been developing a disruptive nanopore-based technology for sequencing DNA, RNA, proteins, and other long-chain molecules since its birth in 2005. The company has just announced that within the next 6-9 months it will bring to market a fast, portable, and disposable protein sequencer that will democratize sequencing by eliminating large capital costs associated with equipment required to enter the field."
I'm going to sequence all my neighbors! (Score:1)
Re:I'm going to sequence all my neighbors! (Score:5, Interesting)
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I was thinking more in terms of Gattaca.
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I re-watched Gattaca again a couple of weeks ago. I remember not thinking much of it when it first came out, but I was much younger then. Highly recommended to those that haven't seen it. Although I want to believe it's a work of science fiction, as time goes on, it seem more likely that everything in the movie will eventually come true (with the exception that NASA gets enough funding to do manned space exploration).
Oh goodie!! (Score:5, Funny)
Yes, goodie (Score:5, Insightful)
So when can we expect to see one in every police cruiser, insurance office and personnel department?
More importantly, we can expect to see one in every doctor's office and hospital, allowing inexpensive personalized medicine.
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Re:Yes, goodie (Score:5, Informative)
It wouldn't be just one. They aren't reusable, so it's going to cost $900 per sequencing operation - apparently, you have to throw away the whole device afterwards.
It currently costs around $30,000 per sequencing operation [singularityhub.com]. So I'm okay with this first-generation model only reducing the price by more than 300:1.
Re:Yes, goodie (Score:5, Interesting)
During interviews just proceeding the product announcement at AGBT 2012, Clive Brown, the Chief Technology Officer of Oxford Nanopores, revealed that the expected $900 price tag for the MinION has a good bit of margin built in. We can thus expect prices to fall quickly as production becomes routine in its challenges.
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It would be nice if they figured out what they planned on sequencing. TFS thinks protein, TFA says DNA. I'm inclined to go with the atter since sequencing protiens isnt all that entertaining.
But this doesn't really change things. You can't just drop some blood into this device and get a useable result - you have to purify the sample and know what you purified. It's not set up to do SNP (single nucleotide polymorphism analysis - which is what current forensic 'DNA sequencing really is). They don't talk much
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if it really does deliver a bunch of base pairs in a row, can't you just match on the flanking sequences on dbSNP or whatever?
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...sequencing protiens isnt all that entertaining.
It's not that protein sequences aren't useful/entertaining, it's just that sequencing proteins directly is vastly more difficult than sequencing "DNA" (and typically sequencing the DNA gives you the protein sequence anyway).
...you have to purify the sample and know what you purified....A couple hundred thousand base pairs in a row is awfully hard to interpret.
You definitely need good software. And if you're assembling a genome from scratch then having a pure sample is very important. But there are plenty of applications where you're just matching your sequence fragments to reference genomes so sample purity isn't a huge issue.
And the future h
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I'm inclined to go with the atter since sequencing protiens isnt all that entertaining.
Protein sequencing is just as important as DNA sequencing. You can learn things from each technique that you can't learn from the other. Sequencing is rarely entertaining in either case. ;)
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Actually, it looks like this would be about the same price, since each device only sequences 100 million base pairs before you dispose of it. Normal human DNA consists of ~3.2 billion base pairs.
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Ah, that's just over 30:1, not 300:1.
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Nope, about 1:1. You need 32 devices, at least, to sequence a whole human genome. Each device can sequence 100 million base pairs (out of 3.2 billion base pairs in a normal human genome).
Re:Yes, goodie (Score:4, Informative)
Errr...that's $30k per genome (human-sized), not per sequencing operation. The device advertised does not do genomes.
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We are going to need some new laws. There is little anyone can do to prevent their DNA getting left all over the place anywhere they go, and in the future grabbing and sequencing it is going to be so cheap any interested party will be able to.
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Still cheaper than a Mac. (ducks)
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And with a 4% error rate, it is still more accurate than the official calculator program that Apple ships with OS X.
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It wouldn't be just one. They aren't reusable, so it's going to cost $900 per sequencing operation - apparently, you have to throw away the whole device afterwards.
Isn't $900 close to the amount of money a GP charges the insurance company for an hour anyway?
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If it was 900 EUR for the device, and it was very reusable, I'd almost offer to buy my doctor one.
Is still a very good price, though.
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I think he means personalized medicine that is inexpensive compared to the current cost of personalized medicine (i.e. totally infeasible).
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Me thinks you misapprehend the meaning of personalized... The "personalized" part comes from having unique prescriptions tuned to your specific genetic make-up. The entire process would be automated, and the only personalized part would be a doctor to provide the needed oversight to ensure there were no clerical errors in submitting your DNA to the prescription process.
This would save Doctors unprecedented amounts of time and effort in generating tremendously better diagnoses.This would prevent untold amoun
the genome belongs to the species, not you (Score:2)
Of course, there are plenty of distopian possibilities as well... seen GATACA? We just need to make certain that we invent a whole new raft of privacy laws that protect free speech, the freedom of genetic diversity, and right to one's own genome not being used to segregate, subjugate or in any way marginalize a person.
Welcome to the brave new world, if your butt isn't just a little puckered, you're just not paying attention.
Whaaat? Your genome doesn't belong to you, dude. You are, at best, a transitory tenant in a house whose foundations were laid three and a half billion years ago. The genome, if it can be said to belong to anyone, belongs to the species, not to any particular instantiation of the phenotype. GATTACA was indeed a pretty bleak glimpse of the future, but only from the perspective of the poor sod who had the bad luck to be born before all the inferior DNA was screened away. Certainly, the film focused on tha
Inexpensive? (Score:2)
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Darth Vader: Obi-wan never told you what happened to your father.
Luke: He told me enough. He told me you betrayed and called him!
Darth Vader: No Luke. I AM YOUR FATHER!!!
Luke: Yeah, um, okay. Just hold on, I'm gonna get my notebook here and DNA sequencer. Crap! Forgot the cable. Listen, you're a cyborg, you wouldn't happen to have a USB-A cable on you, would you? Oh yeah, and I think you've got one actual arm left, so could you take the glove off and give me a blood sample?
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High error rate (Score:4, Interesting)
The technology has a 4% error rate, meaning that 4% of the bases are read incorrectly
Needs to drop an order of magnitude to be competitive, unless it's much cheaper than expected.
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Well, as others have pointed out, they're already reducing the cost of DNA squencing by 300:1 at their starting price (which is expected to fall). If accuracy is important for your use case (it doesn't necessarily need to be for every single one you know) just run samples 3x and you'd still be cutting costs by 100:1 and your error rate would be .001%.
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I don't think you understand how DNA sequencing works.
Re:High error rate (Score:5, Insightful)
All of the "next-generation" sequencing technology has a relatively high error rate compared to traditional Sanger sequencing (used on the original human genome sequences, and still the gold standard for truly novel genomes). The massive redundancy typically compensates for this, although some technology is clearly pretty marginal no matter how much data you have. If my memory is accurate, the Human Genome Project was collecting somewhere between 6x and 10x redundant data; projects using the newer tech shoot for more like 30x.
What I don't get is what this device is intended to be useful for if it's only able to sequence 150 million b.p. before wearing out. The article mentions that this is smaller than some human chromosomes, but unless they factored the necessary redundancy into that figure, it's not going to go very far. It'll be enough to sequence most bacterial genomes, and probably enough to sequence human cellular RNA transcripts, or something else targeted, but I just can't see it being useful for whole-genome analysis of the sort that tries to answer deep questions like "am I likely to get Alzheimers in twenty years?"
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What I don't get is what this device is intended to be useful for if it's only able to sequence 150 million b.p. before wearing out. The article mentions that this is smaller than some human chromosomes, but unless they factored the necessary redundancy into that figure, it's not going to go very far.
Seeing as how this device uses a protein-based pore complex, I'm not surprised by the limited lifespan. Apparently, they offer a large array of pores to get the ensemble of fragments needed to assemble a complete sequence.
It's a IRIX system! I know this! (Score:2)
The technology has a 4% error rate, meaning that 4% of the bases are read incorrectly
Brundlefly likes those odds!
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That depends on your sequencing depth. Do i really care if you get each individual position wrong 4% of the time when you give me 5000 base calls for that position? There might be 200 A+T+Gs, but the 4800 Cs are going to make it pretty obvious what's really going on there.
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Needs to drop an order of magnitude to be competitive, unless it's much cheaper than expected.
DNAcat is coming soon.
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Well, a DNA scanner you just swipe over someone's arm will be nice, but requiring a PS/2 connector will kill it for laptops and the bandwidth of it emulating a keyboard typing out the GATC sequence will be atrocious...
Get one for just $100! * (Score:5, Funny)
<reallysmallprint> * special discount rate available when results are analyzed and stored by AllYourGenome.com. Terms and conditions apply. Please read our privacy and data-marketing agreement before clicking "Submit".</reallysmallprint>
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<hidden>This result shared with: Friends of friends. Click here to change the privacy settings for this application.</hidden>
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Booring... (Score:2)
Brr. (Score:3)
DNA is not a protein (Score:2)
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The article and slashdot story claim that the chip can sequence proteins. The video I linked to below shows that their chip 'analyzes' proteins by reading specialized aptamers for recognition (aptamers are a bit like a small nucleotide based antibody; they can bind to target molecules with high specificity).
While this is potentially very useful in many fields, not the least of which is medical, it is not the claimed disruptive sequencing technology. The method proposed by ON requires a great deal of foretho
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Perhaps you didn't read my post.
Also, to the best of my knowledge, a target protein would not need to be crystallized in order for an aptamer to be developed. I'm pretty sure they just screen the proteins against a large aptamer library and then sequence the bound aptamers to see what worked. I'm a little fuzzy on this, so somebody correct me if I got that last part wrong.
Moore's Law and Corollaries...Coming to an FBI Off (Score:1)
"Trouble? I call it sport."
Hooray for field biologists! (and DNA paparazzi?) (Score:2)
You know, I would imagine every field biologist (and people like me who wish they were one ;) would love these things once they get just a bit cheaper.
How cool would it be to find some plant or little creature and say, what is that? (Big animals it might not be safe to get a sample from!). Maybe if the results went to some central repository like 'The Encyclopedia of Life", it could really help biological studies (not necessarily by finding undiscovered species but helping to determine the range of existi
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How cool would it be to find some plant or little creature and say, what is that?
Or to buy a hamburger at McDonald's and be able to say, "Hey, this doesn't have any cow in it at all! It's all soy protein!"
Seriously, every year one of the expensive private schools in NYC sends a class out into high-end restaurants and grocery stores to buy samples, which are then tested to see if they are really made from what they claim to be made from. Not surprisingly, much of the sushi they bought one year was not the fish it claimed to be.
Flu (Score:1)
GIAA (Score:2)
Dear Doctor Amy Farrah Fowler,
The Genetics Industry Association of America (GIAA) understands you have been using a "genetic sequencer" device to decode genetic sequences that members of our association own as their intellectual property.
We are reminding you that your activities are strictly prohibited as you do not have a license for the sequences in question. We therefore require you to CEASE AND DESIST all such activities and destroy all devices you have been using to illegally decode other's intell
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"disruptive" (Score:2)
You don't know something is disruptive before it comes out. It's disruptive when it comes out and actually disrupts.
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USB device ?!? (Score:2)
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I see this going badly (Score:2)
'Oxford Nanopore megaton announcement' (Score:2)
For some commentary with a bit more substance than 'gizmag', see:
http://pathogenomics.bham.ac.uk/blog/2012/02/oxford-nanopore-megaton-announcement-why-do-you-need-a-machine-exclusive-interview-for-this-blog/ [bham.ac.uk]
e.g:
'Why a USB stick? "The form factor is determined by the requirements" - as there are no fluidics you don't need a big machine. There are no fluidics. "Your fluidics is a Gilson [pipette]", said [Oxford Nanopore CTO] Brown. The prototype version has an ugly battery pack attached to it but it will eventually use USB power. The USB stick is disposable. "Why do you need an instrument?" he says. We wander into the realms of sci-fi at this point. DNA molecules pass through the nanopore and nucleotide sequence is detected by the electronics. Bases are streamed - live - to your laptop as FASTQ (bases with qualities). This is where the "run until" makes sense, if you are interested in a particular gene just wait until the sequence comes out and shut it down to preserve the circuitry."
tl;dr?:
- This technology has enormous potential and looks like it could fundamentally change the way sequencing is used. Features like the long read length and lack of infrastructure required are hugely attractive.
- It isn't going to make genomes dramatically cheaper initially, promising only to be '
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...and for balance, here's a slightly more sceptical take on the announcement:
http://www.omespeak.com/blog/?p=507 [omespeak.com]
'Until ONT demonstrates actual sequencing of a more complicated genome (a microbial one at minimum), there will be a healthy degree of skepticism,'
See also:
http://omicsomics.blogspot.com/2012/02/oxford-nanopore-doesnt-disappoint.html [blogspot.com]
'So, Oxford has unveiled an amazing pair of sequencers. Not one which completely clears the field of everyone else, but one which will offer a host of new opportunities for genomics. Now it is up to Oxford to deliver the instruments to the field, and for Oxford and its early access sites to start pumping out data for all to evaluate. '
and:
http://www.bio-itworld.com/news/02/17/12/Oxford-strikes-first-in-DNA-sequencing-nanopore-wars.html [bio-itworld.com]
'...he nanopore war is about to start.'
DNA not protein, please (Score:2)
Oblig (Score:2)
Pirate Gene Testing (Score:2)
Another step closer to being able to do pirate gene testing. Right now if you, say, wanted to have your DNA checked for a predisposition to breast cancer (oh and you have boobies in this hypothetical situation, follow along - j/k, men can get it too), the testing lab would have to pay exorbitant licensing fees to the company that has the patent on the fact that those genes are linked to breast cancer (I shit you not) or if caught running these tests, they would have their asses sued off.
But with this device