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Biotech Hardware Science Technology

Commercial, USB-Powered DNA Sequencer Coming This Year 95

Posted by Soulskill
from the we've-come-a-long-way-from-the-human-genome-project dept.
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."
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Commercial, USB-Powered DNA Sequencer Coming This Year

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  • by Anonymous Coward
    By going through their trash.
    • by richardkelleher (1184251) on Monday February 20, 2012 @06:50PM (#39105167) Homepage
      Isn't this just another step closer to the world of Blade Runner? Soon Make! will have articles on home gene splicing and growing organs with your Arduino controlled Tissue Growth Chamber.
      • I was thinking more in terms of Gattaca.

        • by Anonymous Coward

          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)

    by NoNonAlphaCharsHere (2201864) on Monday February 20, 2012 @04:19PM (#39103505)
    So when can we expect to see one in every police cruiser, insurance office and personnel department?
    • Yes, goodie (Score:5, Insightful)

      by Theaetetus (590071) <theaetetus...slashdot@@@gmail...com> on Monday February 20, 2012 @04:20PM (#39103521) Homepage Journal

      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.

      • Re: (Score:2, Insightful)

        by Professr3 (670356)
        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.
        • Re:Yes, goodie (Score:5, Informative)

          by Theaetetus (590071) <theaetetus...slashdot@@@gmail...com> on Monday February 20, 2012 @04:30PM (#39103655) Homepage Journal

          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)

            by SomePgmr (2021234) on Monday February 20, 2012 @04:32PM (#39103681) Homepage
            And even with this device, the article says:

            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.

            • 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

              • by retchdog (1319261)

                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?

              • by Anonymous Coward

                ...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

              • 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. ;)

          • by Anonymous Coward

            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.

          • by Twisted64 (837490)

            Ah, that's just over 30:1, not 300:1.

            • by Anonymous Coward

              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)

            by Rutulian (171771) on Tuesday February 21, 2012 @12:56AM (#39107271)

            Errr...that's $30k per genome (human-sized), not per sequencing operation. The device advertised does not do genomes.

          • by AmiMoJo (196126)

            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.

        • Re: (Score:2, Funny)

          by Anonymous Coward

          Still cheaper than a Mac. (ducks)

          • Re: (Score:2, Funny)

            by Anonymous Coward

            And with a 4% error rate, it is still more accurate than the official calculator program that Apple ships with OS X.

        • 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?

        • by GNious (953874)

          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.

      • You're dreaming if you think medicine will ever be personal OR inexpensive. (At least in the U.S.)
      • Medicine never got cheaper just because the tools to practice it lowered in price. People in the supply chain and the doctors either made more profit, or used more and other expensive things added to the cheap technology, because there were now funds for it. Usually both, resulting in a higher bill for the person being treated, or their insurance company. By the way, there's nothing wrong with co-pay, if there is a chemically identical but cheaper medicine available from a competing manufacturer. If there'
    • 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?

    • I don't know, but the government is trying to get the power to spy on everything you do online or on phones RIGHT NOW. Lets worry about 1984 happening today, and deal with their attempts at GATTACA when it comes to it.
  • High error rate (Score:4, Interesting)

    by Guppy (12314) on Monday February 20, 2012 @04:30PM (#39103663)

    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.

    • 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%.

      • Re: (Score:2, Insightful)

        by Anonymous Coward

        I don't think you understand how DNA sequencing works.

    • Re:High error rate (Score:5, Insightful)

      by the gnat (153162) on Monday February 20, 2012 @05:02PM (#39104031)

      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?"

      • by ianbean (525407)
        They have a rack-mounted system that runs samples (or aliquots of the same sample) in parallel. They claim 20 of these could do a human genome in 15 minutes. So, big system for genomes, little USB system for fieldwork and smaller target sizes.
      • by timeOday (582209)
        Perhaps their initial market is limited to biologists working on smaller genomes. But it did leave me wondering, if I just sneezed onto the thing, what would it sequence? There are millions of different microbes on and in each of us. Is there a way to target human DNA specifically? (Or nonhuman, e.g. "what strain of cold do I have?) Then, is there a way to sequence specific portions of a genome? (E.g. the portion(s) pertinent to Alzheimer's)?
      • by Guppy (12314)

        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.

    • The technology has a 4% error rate, meaning that 4% of the bases are read incorrectly

      Brundlefly likes those odds!

    • 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.

    • by AK Marc (707885)
      With software mapping the human genome 100%, 4% error should be more than sufficient. Why? Because error correction would identify errors and correct them to expected results.
    • by bigdavex (155746)

      Needs to drop an order of magnitude to be competitive, unless it's much cheaper than expected.

      DNAcat is coming soon.

      • by Adriax (746043)

        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...

  • by jeffb (2.718) (1189693) on Monday February 20, 2012 @04:32PM (#39103683)

    <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>

    • <hidden>This result shared with: Friends of friends. Click here to change the privacy settings for this application.</hidden>

  • That's like the time I bought my first DVD-ROM drive. It was cool, but things got much better after buying my first DVD-RW drive. Muhehehe... :]
  • The press release says it's a DNA sequencer, not a protein sequencer. I'm sure they're working on a way to sequence proteins using a similar principle, but that's not what they're claiming to come out with in the next 6-9 months.
    • 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

  • Once it's in round three or four of evolution and the price drops through the floor for the entire process, expect an invitation to trot down to your friendly, neighborhood, federal building, county courthouse, city police precinct, etc. to give a blood sample for, um, voter registration purposes.

    "Trouble? I call it sport."
  • 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

    • by psydeshow (154300)

      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.

  • I am soooo coughing on one of these the next time I get the flu. This will make it so easy to identify which strains to mix for uber results.
  • by hercubus (755805)

    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

    • Don't forget the request to destroy all samples of the intellectual property in question. I guess cremation would be the most effective way...
  • You don't know something is disruptive before it comes out. It's disruptive when it comes out and actually disrupts.

  • Is it supported on linux ?!?
  • Joe Bloggs posts some of his DNA on his blog. Big pharmacy corp sues Joe Bloggs into oblivion because they have a patent on the gene he posted. Even though he pulled it out of his own DNA...
  • 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 '

  • I noticed the error in the original post and looked and saw that coldwetdog had mentioned it around 5 PM EST. I'm looking at 9:45 pm EST and see that it hasn't been fixed yet. DNA != protein. And vice versa.
  • That's neat and all, but can it read my midichlorian count?
  • 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

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