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IBM Researchers Working Toward Cheap, Fast DNA Reader 90

Posted by timothy
from the reminds-me-of-creepy-ibm-ads dept.
nk497 writes "IBM scientists are working on ambitious research where nano-sized holes will be drilled into computer chips and DNA passed through to create a 'genetic code reader.' A DNA molecule would be passed through a hole just three nanometers wide, while an electrical sensor 'reads' the DNA. The challenge of the silicon-based 'DNA Transistor' would be to slow and control the motion of the DNA through the hole so the reader could decode what is inside it. IBM claimed that if the project was successful it could make personalised genome analysis as cheap as $100 to $1,000, and compared it to the first-ever sequencing done for the Human Genome Project, which cost $3 billion."
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IBM Researchers Working Toward Cheap, Fast DNA Reader

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  • Amazing! (Score:2, Interesting)

    by newcastlejon (1483695)
    All that remains now, I guess, is a device that can write arbitrary stands of DNA.
    • by Shakrai (717556)

      Just watch a few episodes of Judge Judy or Cops. You'll see all sorts of characters that "write" with arbitrary strands of DNA ;)

    • Re:Amazing! (Score:5, Informative)

      by toppavak (943659) on Tuesday October 06, 2009 @11:12AM (#29658273)
      Oh its been done. [google.com] In fact, ordering custom DNA sequences is pretty cheap [idtdna.com].
      • Thanks for that. I was more amazed at the similarity to rapid prototyping machines to be honest. I mean, ordering a custom strand is undoubtedly a Good Thing, but being able to make it on your desk is much better.
      • by casi0qv (1184909)
        Current existing Illumina IIG sequencing technology, which is widely used can re-sequence the human genome cheaply and easily with short read fragments (36-76 base pairs long). These short reads are more than sufficient to resequence a human genome. As I see it, the major advantage of this nanopore sequencing isn't cheaper resequencing- but longer reads, which will make it easier to assemble the genomes of new organisms that haven't already been sequenced.
        • by dAzED1 (33635)

          ...and to verify that we aligned the initial sequences (that we use as guides) correctly in the first place ;)

        • Re: (Score:1, Informative)

          by Anonymous Coward

          If by longer reads you mean read the whole thing at once, then yes. The removal of shotgun sequencing techniques would remove much of the cost I would think.

          • by dAzED1 (33635)

            they aren't reading the whole thing at once - mostly because it isn't practical. Think about the shapes involved, and then try to imagine fitting the whole thing through a hole that is purposefully barely large enough for the dna to squeeze through. They are however reading much much larger fragments. How large? no idea, haven't found anything that quantifies it. Wouldn't be surprised if it was in the 10s of thousands of base pairs, though.

      • Not to my exact needs though:

        What I want is a DNA writer that will write realtime. It will look a lot like an old typewriter, but will have only 5 keys, ATCG and U. You push the buttons in the sequence that you want (the keys will actually clack), and then hit the return bar, but instead of the roller sliding over, it will instantly shoot out an eppendorf tube full of that sequence on the side with a nice "ding."

        I've asked Santa for one every year, but the one at the mall just said what my parents have be

    • Re: (Score:3, Funny)

      by SEWilco (27983)
      Actually, first we need a device to thread DNA through a tiny hole.
    • by Ihmhi (1206036)

      All you'll have to do is unpop the write protect tab on the side of the reader. Simple.

  • by Anonymous Coward

    If you can read DNA through a fabricated chip, possible next step is fabricating microcircuits from transistors scaffolded on DNA.

    Yours In Belarus,
    Kilgore Trout

  • Other uses (Score:2, Insightful)

    by NoYob (1630681)

    âoeUltimately it could improve the quality of medical care by identifying patients who will gain the greatest benefit from a particular medicine and those who are at most at risk of adverse reaction,â he added.

    Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".

    Travelers to the US will have to stick their fingers and give a DNA sample along with their finger prints and photo.

    Government will use for the "war on [insert buzzword here]"

    Genetic propensity for mental illness, well, we'll have to keep an eye on you! Especially, if there is some sort of genetic predisposition towards pedophilia - think of the children!

    Have to take thi

    • Re: (Score:3, Informative)

      by Taibhsear (1286214)

      Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".

      There is already a law banning them from doing this.

      • Re: (Score:1, Insightful)

        by NoYob (1630681)

        Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".

        There is already a law banning them from doing this.

        Yeah, so? If they do it, exactly how do you prove it? And even then if you do prove it by some miracle , all the insurance has to do is say, "Oops, it was an error. We are investigating and we'll correct the problem." They pay a small fine and on they go.

        • Re:Other uses (Score:4, Insightful)

          by Taibhsear (1286214) on Tuesday October 06, 2009 @11:21AM (#29658413)

          You prove it by the piece of paper that tells you your health benefits was denied because of a pre-existing condition. Your records will show if you've had treatment for it or not. It's not a conspiracy/finger pointing kind of thing. Proof is easily come by.

          • Insurance companies have been known to reject claims as pre-existing conditions, even when it is obvious that this is false, in hopes that the patient will give up and pay for the treatment themselves. CNN had a recent news item about an insurance company initially refusing to pay for a broken wrist, claiming that the injury was a pre-existing condition.
    • Re:Other uses (Score:4, Interesting)

      by Shakrai (717556) on Tuesday October 06, 2009 @11:28AM (#29658509) Journal

      Well, since you are being a complete nay-sayer to further your own agenda, allow me to respond with some other potential uses of this technology:

      Law enforcement will use it to help solve crime.

      The innocence project will use it to get wrongfully convicted people out of prison/off death row.

      Businesses and private individuals will be able to use it to enhance the security of their homes/offices/factories/etc.

      Adopted children will be able to use it to figure out who their biological parents are.

      The child support system will be able to use it to weed out those who aren't parents and confirm those who are.

      The point I'm trying to make is that technology isn't inherently good or evil. It's what we do with it that matters. I find it disturbing that you couldn't name a single positive use for this technology.

    • by izomiac (815208)
      This does not make DNA for identification any easier. DNA sequencing would be faster, but nowhere near GATTACA speeds. There are probably limitations in that regard, not even cells can do it that quickly. Perhaps a DNA hashing function would work, but that's pretty much completely unrelated to this. To use this in an airport the TSA would need one machine per passenger and delay each passenger for a while for it to process. There also isn't a gene for "predisposition for alcohol", it's the summative ef
    • Re: (Score:1, Insightful)

      by gad_zuki! (70830)

      >Insurance companies will use it to deny health insurance outright or label any diseases that this thing finds as "pre-existing conditions".

      Sounds like all the more reason to support healthcare reform and to shut people up who equate it with Nazi Germany, or whatever the right complains about in public.

    • Re: (Score:3, Interesting)

      by interkin3tic (1469267)

      Have to take this DNA test as part of our drug screening. Predisposition towards alcoholism or any other disease or disorder that will send our health care costs through the roof? Well, you don't have the necessary "skills" for this job. Sorry, best of luck finding another job. (Yeah, good luck in proving that we violated the ADA or EEOC!)

      nothing but good (TM) can come of this!

      Incredibly short sighted. I sequence DNA all the time, it's a valuable tool for biomedical research. If sequencing my samples took a matter of hours instead of days, that would really speed thing up. My research is on neural stem cells. I may be an idiot, but I think my research could eventually lead to some findings that would be useful to many people. Shortening the amount of time it will take me to find stuff is, in my opinion, a good thing, and not just for me. The same is true for most biologists

  • Say hello to DNA code readers.

    "Please insert your DNA in the hole for authentication"

    • Re: (Score:2, Insightful)

      by newcastlejon (1483695)
      Sounds even easier to bypass than cutting off a finger. Perhaps this will usher in a golden age of sperm-jacking and blood-letting?
      • Re: (Score:2, Funny)

        by travisb828 (1002754)

        Perhaps this will usher in a golden age of sperm-jacking and blood-letting?

        Hasn't the Internet already brought a golden age of sperm-jacking?

  • Challenge (Score:3, Interesting)

    by Taibhsear (1286214) on Tuesday October 06, 2009 @11:11AM (#29658265)

    Well I would imagine that slowing and controlling the motion of the DNA wouldn't be all that difficult. DNA has a net negative charge due to the backbone. However, how the EM fields they'd use to manipulate it would interact with the circuitry of the reader I do not know. That might be the real challenge.

  • I Smell Synergy! (Score:4, Insightful)

    by fuzzyfuzzyfungus (1223518) on Tuesday October 06, 2009 @11:14AM (#29658321) Journal
    High speed, computer-assisted, genetic analysis technology should go beautifully with IBM's existing expertise in Data-driven eugenics solutions... [wikipedia.org]
    • by iammani (1392285)
      I dont understand why guys keep picking on IBM. They made things more efficient for nazis and probably knew the holocaust was happening, much in advance of the rest of the world. I dont think they could have some how magically stopped the holocaust from happening.

      I really dont understand the fuss, given that even some Nazi SS officers/scientist were honored by the US later on.

      Wernher von Braun and his team of rocket scientist were among them. He was an SS officer and used slave labor in manufacturing
  • by Michael G. Kaplan (1517611) on Tuesday October 06, 2009 @11:17AM (#29658363)

    The New York Times published an article in August about a technology that decoded a human genome for less than $50,000 [nytimes.com]. The inventor speculates that the technology will be able to decode a genome for just $1,000 in 2-3 years.

    That being said it will be amazing to see the IBM project succeed. Either way the cost of decoding a genome is dropping so quickly it puts Moore's Law to shame.

    • Re: (Score:3, Informative)

      by dAzED1 (33635)

      From the article: Dr. Quake's DNA sequencing machine, about the size of a refrigerator, works by splitting the double helix of DNA into single strands and breaking the strands into small fragments that on average are 32 DNA units in length.

      That's not terribly different than what happens now; we cut things into chunks of X units (say, 400 base pairs), and then use all sorts of tools to guess how to put it all back together. The major problem being something elsewhere mentioned in that article: A computer

    • Either way the cost of decoding a genome is dropping so quickly it puts Moore's Law to shame.

      I don't see what Moore's Law has to do with this. Moore's Law is about the number of transistors doubling every 18 months. It has nothing to do with costs.

  • GATTACA! GATTACA! GATTACA!

  • by thewils (463314) on Tuesday October 06, 2009 @12:24PM (#29659459) Journal

    the first-ever sequencing done for the Human Genome Project, which cost $3 billion.

    It cost a lot more than that. I mean first we had to evolve from amoeba and create a civilization.

    • by trb (8509) on Tuesday October 06, 2009 @01:15PM (#29660371)
      the first-ever sequencing done for the Human Genome Project, which cost $3 billion.

      And it cost $15 billion for the first person to drive into Boston after the Big Dig. [wikipedia.org] That's creative accounting. [wikipedia.org]

      • by trb (8509)
        the first-ever sequencing done for the Human Genome Project, which cost $3 billion.

        The biggest problem with this sentence is its misplaced prepositional phrase. The Human Genome Project probably cost $3B up to some point, but the sentence may imply that the first sequencing cost $3B. There was a recent article [nytimes.com] in the NY Times discussing this problem.

  • A reader for all sorts of diseases, especially communicable ones. It'd cut costs in countries with relatively modern health systems by wasting less of medical professionals' time, and since it'd likely be small (and hopefully very cheap) it'd help countries with very poor or non-existent health care systems. Would also be very helpful during/before epidemics break out. I know some of these exist for specific diseases, but we need ones that can test for thousands at once.

    A reader specifically for STDs. Would

  • It's about time. (Score:3, Insightful)

    by Animats (122034) on Tuesday October 06, 2009 @12:46PM (#29659865) Homepage

    It's about time someone did this. People have been talking about real nanotechnology for about two decades. Most of what's now called "nanotechnology" is surface chemistry of finely divided powders, or simple self-assembling structures like carbon nanotubes. Real nanotechnology, useful mechanisms made of deliberately placed individual atoms, hasn't been happening much. A DNA reader is one of the few applications where building a very small number of devices at the atomic scale is useful. You don't need self-replicating assemblers turning out vast numbers of nanomachines. Small numbers of devices can be created, slowly, with STM-type devices.

    At least readers are safe. DNA writers are going to be an issue.

  • Am I the only one here thinking of the slight parallel with the coulter counter and the way it made such a huge difference to blood counts once a tech no longer had to sit behind a microscope staring at a haemocytometer? Only real diff is that one does whole cells and the other is planned to read sections of individual macromolecules. Only a matter of scale really. Definitely a "darn, why didnt anyone think of that before?" moment. Hope they make it work.
  • For example, Pacific Biosciences:
    http://www.nytimes.com/2008/02/09/business/09genome.html [nytimes.com]
    ``There, Pacific Biosciences has been developing a DNA sequencing machine that within a few years might be able to unravel an individual's entire genome in minutes, for less than $1,000."
  • There is a private company called Pacific Biosciences that is doing something very similar, single DNA molecule sequencing. They managed to get reads from a single DNA molecule, and this was sort of the hot topic at a few computational biolgoy conferences I went to last year. It's not clear who is going to win this race, but I think a lot of people think this is the future of DNA sequencing.

  • It sounds like the major problem with this technology is controlling the rate of passage of a single DNA strand through the detection pore. Instead of trying to solve that "hard" problem, why not design the system so that you don't need such tight control over the speed of the DNA strand?

    In the current system, if the strand moves to slowly between reads, a base will be scanned twice. If the strand moves too quickly, some bases may be skipped altogether. You could slow down the rate of strand passage rela

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