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Biotech Medicine Technology

Device Can Extract DNA With Full Genetic Data In Minutes 95

Posted by samzenpus
from the looking-at-your-code dept.
vinces99 writes "Imagine taking a swab of saliva from your mouth and, within minutes, having your DNA ready for genome sequencing. A new device from University of Washington engineers and a company called NanoFacture can extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way than conventional methods. It will give hospitals and labs a much easier way to separate DNA from human fluid samples, which will help with genome sequencing, disease diagnosis and forensic investigations."
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Device Can Extract DNA With Full Genetic Data In Minutes

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  • by denis-The-menace (471988) on Monday May 06, 2013 @04:56PM (#43647121)

    GATTACA here we come!

    • This is only half of the GATTACA scanner. The other half is instantaneous DNA sequencing.

      • by EmagGeek (574360)

        You know it's coming.

      • This is only half of the GATTACA scanner. The other half is instantaneous DNA sequencing.

        You mean, you need to feed the output of your GATTACA extractor into a plug-compatible CTAATGT sequencer?

      • by pjt33 (739471)

        Or in other words: in an example of /. editing at its finest, it's not even necessary to read the article to see that the headline is plain wrong.

      • The created a new class of genetically gifted in society. This caused class tension with the ordinaries and defectives.

        Unlike GATTACA, rapid testing would mean everyone is analyzed and databsed at birth or before. Then just rapid sub-testing of a few markers culd match the database instead full resequencing every identity check.
      • by Pseudonym (62607)

        ...and the third half is instantaneous DNA assembly.

    • Re:I can't wait (Score:5, Insightful)

      by interkin3tic (1469267) on Monday May 06, 2013 @05:12PM (#43647307)
      It always annoys me how here, on slashdot, for nerds, we love technology and advances EXCEPT WHEN IT COMES TO BIOLOGY. Then it's nothing but "whatcouldpossiblygowrong" or GATTACA, or I am legend or zombies.

      Yes, technology has downsides and dangers. All technology does. Always. Yes, you need to be aware of it. No, it is not going to cause a dystopian future or apocalypse just because that was the premise of a movie. A lot of other things would have to fail for us to reach gattaca. For example, we'd have to be dumb enough to allow discrimination based on genetics, and we'd have to for some reason decide that nature was all that matters when it comes to nature vs nurture. But given the patriot act and other current events, I'd say we can create a dystopian future for ourselves even if we stopped all scientific progress.

      Instantaneous sequencing would be extremely useful in medicine. There's no way to quantify it, but I'm going to say this technology is approximately a billion times more likely to save your life than it is to cause you to be a discriminated underclass of people who are outcasts due to genetics. Anyway its a billion times a billion times more likely this will amount to nothing more than marketing hype. I'm still waiting on this to show up in my lab. [nanoporetech.com]

      But bigger point: either don't fear biotech advances, or at least be equal: every article about faster or better computer components, how about we fret about the Matrix or Skynet or a million other scifi dystopian works of fiction that involve computers rather than biotech.

      Hypocritical Luddites...
      • Re:I can't wait (Score:4, Interesting)

        by Jah-Wren Ryel (80510) on Monday May 06, 2013 @05:36PM (#43647547)

        It always annoys me how here, on slashdot, for nerds, we love technology and advances EXCEPT WHEN IT COMES TO BIOLOGY. Then it's nothing but "whatcouldpossiblygowrong" or GATTACA, or I am legend or zombies.

        Hhhm, looks like most of these are not biological:
        http://slashdot.org/tag/whatcouldpossiblygowrong [slashdot.org]

        • It always annoys me how here, on slashdot, for nerds, we love technology and advances EXCEPT WHEN IT COMES TO BIOLOGY. Then it's nothing but "whatcouldpossiblygowrong" or GATTACA, or I am legend or zombies.

          Hhhm, looks like most of these are not biological: http://slashdot.org/tag/whatcouldpossiblygowrong [slashdot.org]

          Why do you have to go ruin his misguided rant like that? A rant that was entirely entertaining to read. A rant that is already a part of his government documentation... [slashdot.org] Of course, despite the fact that all other information which can be gathered about a person already is; the incredibly intriguing tidbit discussed in this article probably won't be.

        • by danudwary (201586)

          With that tag, that is the single most hilarious list I think I've ever read.

      • by Beorytis (1014777)

        There's no way to quantify it, but I'm going to say this technology is approximately a billion times more likely to save your life than it is to cause you to be a discriminated underclass of people who are outcasts due to genetics

        What then is the relative likelihood that we will receive targeted advertising based on our genetic profile?

      • But bigger point: either don't fear biotech advances, or at least be equal

        But they're not equal. Dystopian futures involving computers promise a future where we're ruled over by machines - which, might be more capable than we are. There is an element of coolness to robotic/computer overlords.

        Biotech dystopian futures, on the other hand, promise a future where we're ruled over by humans who think they're more capable than we are (but probably aren't)....just like now. And there's nothing cool about being ruled over by a human...just like now.

        • I always thought a biotech disaster would most likely just kill all or most of us. Technological disasters are more likely to bring about some new form of Fascism, witch is easily remedied via the 2nd amendment or hacking, or some other cool thing that the average slashdotter would love to be involved in even if in reality they'd probably end up just as dead either way.

        • by dan828 (753380)

          But bigger point: either don't fear biotech advances, or at least be equal

          But they're not equal. Dystopian futures involving computers promise a future where we're ruled over by machines - which, might be more capable than we are. There is an element of coolness to robotic/computer overlords.

          Biotech dystopian futures, on the other hand, promise a future where we're ruled over by humans who think they're more capable than we are (but probably aren't)....just like now. And there's nothing cool about being ruled over by a human...just like now.

          Or perhaps, a utopian future where the amoral sociopaths aren't allowed to hold public office?

          • by Tanktalus (794810)

            Or perhaps, a utopian future where the amoral sociopaths aren't allowed to hold public office?

            You win the patented Slashdot Delusional Optimist of the Hour award. Your prize is 2 Internets.

          • Any technology that would prevent amoral sociopaths from public office in the future would be made illegal by amoral sociopaths holding public office in the present.

      • by Sarten-X (1102295)

        I blame your confirmation bias. Really, Slashdot is also heavily biased against certain advances in:

        • Agriculture: Every new technique or discovery by Monsanto or another research company
        • Computer science: All algorithms that end up in software patents, regardless of any merit
        • Law: Any legislation favoring public welfare over personal freedom
        • Political science: Anything supporting confidential diplomacy
        • Cryptoanalysis: Anything compromising confidential discussions
        • Military science: Everything that goes boom
        • Chem
        • Agriculture: Every new technique or discovery by Monsanto or another research company

          GMO yes, but that's biotech, which is my point.

          Computer science: All algorithms that end up in software patents, regardless of any merit. Law: Any legislation favoring public welfare over personal freedom Political science: Anything supporting confidential diplomacy Cryptoanalysis: Anything compromising confidential discussions

          The opposition to those is not based fear of a sci-fi nightmare. Though I would watch the hell out of a dystopian future where there is nothing but lawyers suing each other, with the winners eating the losers. Kind of like highlander, only with briefcases instead of swords.

          I digress. What I object to is not people having knee-jerk reactions in general, since everyone has some of those. I'm objecting to the fear slashdot has for biotech.

          Military science: Everything that goes boom

          I disagree with yo

        • Everyone bashes conservatives on science ignorance or bias. As you pointed out the libertarian slashdoters have their version of junk science. Whenever I post a list of leftist junk science I get bashed too. All parties need to be more open minded and enlightened.
      • by foobsr (693224)
        we'd have to be dumb enough to allow discrimination based on genetics

        Indeed, now that we have overcome discrimination based on skin colour or nationality for centuries.
        nature vs nurture
        On a side note, history shows that fascists lean to the "nature" side. Given the lack of states that develop fascist attitudes, we are definitely on the safe side here.
        But given the patriot act and other current events, I'd say we can create a dystopian future for ourselves even if we stopped all scientific progress.
        T

      • Deep down inside, we all know the robots would be stopped by the first flight of stairs they run into (or whatever the technological limit of the day is). A general purpose robot that can compete on the battlefield better than a human infantryman is still a long ways off (thought always getting closer). The same goes for most other sci-fi dystopias, we're just not there yet with the possible exception of nuclear weapons (which gets used in dystopic sci-fy constantly, especially the more mass market ones).

      • by Ellie K (1804464)

        ... [on Slashdot] we love technology and advances EXCEPT WHEN IT COMES TO BIOLOGY. Then it's nothing but "whatcouldpossiblygowrong" ... Yes, technology has downsides and dangers. All technology does. Always. Yes, you need to be aware of it...

        It annoys me too, the fear reaction to some technology but not others. I don't know anything about biotechnology, but I worked as a statistician for a public health department, focusing on infectious AND non-infectious diseases. Yes, I realize that there are risks if one is sloppy. I also know that in biotech there are decent controls in place, which are observed by researchers to protect themselves as much as others.

        Only a guess: More Slashdot readers are familiar with computing and engineering (of the n

      • by Cyberax (705495)
        Hey, you can always buy some of our stuff: http://www.illumina.com/technology/moleculo-technology.ilmn [illumina.com] - 10kb fragments with Q50 accuracy should be enough for everyone!
        • Isn't that a lot more expensive than the evidently vaporware USB sequencing was supposed to be?
          • by Cyberax (705495)
            Definitely. We're using Illumina sequencing with our preparation on top of it. The upside is that our technology really works right now :)
      • I am currently forced into the position of doing my own genetics study on my own family. I would give good money to have me and three family members' genomes sequenced quickly and accurately. I am tracking the much hyped progress of nano-pore technology, which may eventually make such sequencing possible, but for now, it's a freaking miracle that I can get an exome sequenced for $650 (at Axeq). If you had much of a clue, you'd realize that this article is simply about extracting a DNA sample from blood o

      • by Anonymous Coward

        For example, we'd have to be dumb enough...

        DONE

      • by AmiMoJo (196126) *

        The problem is that once DNA sequencing becomes extremely cheap and quick there is little you can do to regulate it. It might be illegal to discriminate against people because of genetic predisposition to certain diseases, but when you go for a job interview how would you ever know they didn't pick up a strand of hair and test it afterwards?

        Celebrities will have no privacy what so ever and won't be able to hide anything that their DNA can reveal about them. Paternity, diseases, interesting genes that gossip

      • The main problem with your argument is - the only technology that can replicate itself these days is biotech. This and the incredibly low (and exponentially dropping) prices of this technology are the real reasons we must be far more cautious with biotechnology than other technologies. Sooner will a nutjob create a superbug in a garage lab than he would create skynet.
      • Is GATTACA the new Hitler? (corollary to Godwin's law [wikipedia.org])
  • ...you gotta sequence a lot of DNA RIGHT NOW! In all seriousness though, this is pretty neat. Not every step in technology has to be earth shattering.
    • by Hatta (162192)

      You'd be surprised how big a deal quick whole genome sequencing is. Instead of asking "is this gene dysregulated in this syndrome" and iterating hundreds or thousands of times, we can directly ask "which genes are dysregulated in this syndrome".

    • Guy comes into an ER unconscious. Has a high fever, complained of general aches and pains beforehand. No idea what's going on. I'm sure there's an SOP doctors follow to determine what could be wrong with the guy, I'm not a doctor so I don't know what that is, but I'd wager that whatever it is, this could be really useful for that.

      You take a blood sample, you feed it through this machine or something like it. You would be able to identify some problems that may arise from his genome. You could identi
      • Guy comes into an ER unconscious...

        Darn. I was waiting for a good joke.

        • Guy comes into an ER unconscious, the doctors get a towel.

          I... uh... I tried. I'm sorry I disappointed you.
          • by OhSoLaMeow (2536022) on Monday May 06, 2013 @07:51PM (#43648987)
            Guy comes into an ER unconscious. When he finally wakes up they ask him what happened.

            "I was having a quiet round of golf with my wife," he tells the doctor, "when she sliced her ball into a pasture of cows. We went to look for it, and I noticed one of the cows had something white in its rear end. I walked over and lifted up the tail, and sure enough, there was my wife's golf ball stuck right in the cow's butt. That's when I made my mistake."

            "What did you do?" asks the doctor.

            "Well, as I was standing there holding up the tail, I yelled to my wife, 'Hey, this looks like yours!'"
      • by kaliann (1316559)

        This doesn't sequence the genome or expand it. It just collects the DNA from the sample.
        Real-time sequencing is what you are talking about, and that's still a long way off.

        The gizmo is very cool, it takes a step that is the better part of an hour in the lab (depending on how many samples at a time you are running, and what the samples are) to something that is minutes, but it doesn't make the sequencing faster.

        The most useful thing about it is that it is automated and potentially point-of-care. This means

      • by ewieling (90662)
        Many diseases such as Parkinsons, breast cancer, cystic fibrosis are caused by one of several mutations, some of which already have medication available to treat. Some people have mutations which make some medications cause major side effects. Fast sequencing would eliminate much trial and error in treatment of many conditions.
  • I can see this drastically reducing the cost of getting your DNA sequenced, and at the same time I can see police starting to take it anytime they would take fingerprints.
  • This would be the ultimate goal in Identity Verification... And then we find ourselves being cloned...

    • Hey, I just bought this new Canon A4 scanner, let's print something!

    • by subanark (937286)

      So? Finger printing does a pretty good job as it is. And why anyone would want to clone me is beyond my understanding. Not that I would care much; who I am is far more dependent on environment than my genetic makeup.

  • by Anonymous Coward

    Some people are missing the point here, so for emphasis: this product only prepares DNA for sequencing, it doesn't do the sequencing itself. Half an hour of preparation is reduced to minutes, but the actual work still takes days.

    • Some people are missing the point here, so for emphasis: this product only prepares DNA for sequencing, it doesn't do the sequencing itself. Half an hour of preparation is reduced to minutes, but the actual work still takes days.

      It used to take days, and still does if funding is short but an Illumina HiSeq 2500 can produce 150-180 Gbases in 40 hours in rapid run mode [1]. Most labs still run it in high output mode because of the reagent cost but the option is there. This means that if I was prepared to pay the extra and I sent a sample into "core sequencing" where I work, they could potentially return mapped DNA in a week. After that there's still some improvement tools we'd need to run to clean up artefacts, followed by calling

  • extract human DNA from fluid samples in a simpler, more efficient and environmentally friendly way

    This will be serious competition for these guys [fleshlight...ational.eu]

  • You can also do it in minutes with common household items: http://learn.genetics.utah.edu/content/labs/extraction/howto/ [utah.edu]

    Extraction's not the problem. Sequencing is not actually a problem, either (~$150k gets you an ION Torrent Proton that will come close to sequencing a person in a few hours). Data analysis is currently the hardest and costliest part of sequencing. Of course, that's getting better, too.

    Don't get me wrong, incremental process improvements such as this are important, they're just not grou

    • by Nrrqshrr (1879148)
      This.
      As much as I love the idea of having DNA samples to play around with on the fly, I actually thought it was more in the lines of a device capable of sequencing the DNA quickly.
      Imagine the potential of a handheld sequencing device... can't wait to clutter the databases with more sequences.
    • I see more and more of that. Right now fairly simple things are done. But with cheap sequencing and all the genetic unknowns out there I would not be surprised by some significant science fair discoveries.
    • by jfengel (409917)

      Yeah, that's always the peril of science reporting. Everyone wants The Big One (flying cars, fusion, cheap fast sequencing) but all we get is the dull daily grind of scientific and technological process.

      So each incremental bit is magnified, first by the university's PR department and then again by the popular press, trying to attract attention (and with it, more funding). I empathize with the desire to feed the gaping maw of people craving the future (the same maw that began caring more about the 2016 Presi

  • by Guppy (12314) on Monday May 06, 2013 @06:08PM (#43647995)

    W engineers designed microscopic probes that dip into a fluid sample – saliva, sputum or blood – and apply an electric field within the liquid. That draws particles to concentrate around the surface of the tiny probe. Larger particles hit the tip and swerve away, but DNA-sized molecules stick to the probe and are trapped on the surface.

    I read through the entire article link, and didn't learn a whole lot about how it actually performs. The above paragraph was the only technical information included. From what I can see, neither really tests performance against really challenging samples with a lot of crud or difficult-to-extract material. We only have the PR blurb's claim that it's better than a typical Miniprep column.

    Found a couple of papers that might be more relevant:
    Size-Specific Concentration of DNA to a Nanostructured Tip Using Dielectrophoresis and Capillary Action [acs.org] (Has downloadable PDF)
    Nanotips for single-step preparation of DNA for qPCR analysis [rsc.org] (Paywall)

    Ok, from the first paper, we find out what this is really for:

    Extracellular DNA is of great interest in the fields of disease diagnostics and environmental molecular biology. Unlike the genomic DNA in normal cells, extracellular DNA is the free DNA released from dead cells. Thus, extracellular DNA circulating in body fluids can be used as an early indicator for various acute diseases such as cancer. For example, the concentration of extracellular DNA for a normal person is 30ng/mL, but the concentration is increased to 300 ng/mL for a cancer patient. When the issue comes to environmental monitoring, extracellular DNA dissolved in lakes and soil is an indicator for environmental quality because the dissolved DNA is generated from cell lysis and excretion. In spite of such a great potential, the study of extracellular DNA is limited by the standard sample preparation methods.

    The conventional methods begin with filtering, centrifuging, and collecting DNA from a raw sample. In aggressive experimental protocols, genomic DNA from normal cells is released and mixed with extracellular DNA. In addition, a few hours is required for the sample preparation process, which can degrade and mutate extracellular DNA.6 As a result, the original information of extracellular DNA is partially or completely lost. Therefore, a rapid process that can concentrate extracellular DNA is very important for identifying pathogenic information. This paper presents a size-specific concentration mechanism directly extracting extracellular DNA from a sample mixture using a nanostructured tip. The concentration process is performed with two sequences: (1) an alternating current (AC) electric field is applied to attract DNA and other bioparticles in the vicinity of a nanotip; (2) only the DNA is size-selectively captured onto the nanotip by the combination of dielectrophoresis and capillary action. In the analytical section, the forces involved in the concentration are estimated to investigate the capturing process. An analytical model is presented for capillary induced size-selectivity that is described as the function of the ratio of a particle to a tip diameter.

    Basically, this is a special purpose method for concentrating extra-cellular DNA while leaving whole cell material intact. It's not meant to compete against a Miniprep, but analyze a whole different type of sample material; you are trying to fish out what genetic material is already floating around outside of your cells. Really a niche kind of research thing, I don't know if this will make a whole lot of impact, either practically, academically, or economically.

    • by kaliann (1316559)

      Thank you for clarifying, it's even less generally useful than I'd thought. Niche research indeed!

      • by Guppy (12314)

        it's even less generally useful than I'd thought.

        Same goes for the Slashdot story posting. The Slashdot summary and only linked article is useless to anyone who actually works with genetics and sequencing. As for the linked article, the more you know about the words being smashed together, the less sense it makes (the very definition of technobabble). It's a content-free wad of marketing promises.

        There were some 80+ replies to this story by last night, and NOT ONE of them discussed anything specific to the actual device or technology featured in the st

  • I though it was already possible - dont u guys see CSI?
  • "Imagine..."

    having no privacy.

    and no health insurance.
  • I give it 6 years. Then we will have a complete scanner. Another year or two after that and it will be included in the handheld-bio-metric-scanner-device-thingy.

What ever you want is going to cost a little more than it is worth. -- The Second Law Of Thermodynamics

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