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IBM Researchers Working Toward Cheap, Fast DNA Reader

Posted by timothy on 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."

90 comments

  1. GET SOME PRIORITIES! by Anonymous Coward · · Score: -1, Troll

    David Letterman just admitted to raping teenage girls and all you people can talk about is a DNA reader? GET SOME PRIORITIES!

    1. Re:GET SOME PRIORITIES! by Jeremiah+Cornelius · · Score: -1, Offtopic

      Did you get sweetly fucked in his bunker?

      --
      "Flyin' in just a sweet place,
      Never been known to fail..."
    2. Re:GET SOME PRIORITIES! by Anonymous Coward · · Score: 0

      Kiss and tell!

    3. Re:GET SOME PRIORITIES! by HisOmniscience · · Score: 0

      I know I'm feeding the troll, but, we have our priorities in order because this is more important than one horny old comedian. One person's actions/crimes are way less important than accurate, cheap DNA sequencing.

  2. Amazing! by newcastlejon · · Score: 2, Interesting

    All that remains now, I guess, is a device that can write arbitrary stands of DNA.

    --
    If God forks the Universe every time you roll a die, he'd better have a damned good memory.
    1. Re:Amazing! by Shakrai · · Score: 0

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

      --
      I want peace on earth and goodwill toward man.
      We are the United States Government! We don't do that sort of thing.
    2. Re:Amazing! by toppavak · · Score: 5, Informative

      Oh its been done. In fact, ordering custom DNA sequences is pretty cheap.

    3. Re:Amazing! by CodingHero · · Score: 0

      All that remains now, I guess, is a device that can write arbitrary stands of DNA.

      Not if I chmod 744!

    4. Re:Amazing! by newcastlejon · · Score: 1

      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.

      --
      If God forks the Universe every time you roll a die, he'd better have a damned good memory.
    5. Re:Amazing! by casi0qv · · Score: 1

      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.

    6. Re:Amazing! by dAzED1 · · Score: 1

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

    7. Re:Amazing! by Anonymous Coward · · Score: 1, Informative

      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.

    8. Re:Amazing! by SEWilco · · Score: 2, Funny

      Actually, first we need a device to thread DNA through a tiny hole.

    9. Re:Amazing! by spazdor · · Score: 1

      Nanosprockets! DNA is just tiny, tiny tractor-paper.

      --
      DRM: Terminator crops for your mind!
    10. Re:Amazing! by Ihmhi · · Score: 1

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

      --
      Random Thoughts From A Diseased Mind (Not For Dummies)
    11. Re:Amazing! by dAzED1 · · Score: 1

      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.

    12. Re:Amazing! by interkin3tic · · Score: 1

      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 been saying "You'll give yourself ebola!"

    13. Re:Amazing! by sayno2quat · · Score: 1

      Or if there isn't a write protect tab, just put tape over the hole.

      --
      Sure I sold you robot insurance. But you were attacked by a cyborg. Not covered.
  3. The implications are huge by rcolbert · · Score: 0

    Now, if we added the storage and compute power necessary to complete the picture, imagine the ability to store massive populations of DNA information and then apply BI-like analytics. Genetic research could be greatly accelerated. The implications and applications of this technology at first glance seem broad and promising.

    1. Re:The implications are huge by Anonymous Coward · · Score: 0

      It sounds like a good idea, but building DNA is a bit more complicated than reading it.

    2. Re:The implications are huge by fuzzyfuzzyfungus · · Score: 3, Funny

      dd if=~/OMG_hax/smallpox.img of=/dev/dna0

    3. Re:The implications are huge by rcolbert · · Score: 0

      It sounds like a good idea, but building DNA is a bit more complicated than reading it.

      Absolutely. But in order to know what to build, we certainly must understand it better. Right now, DNA research is tedious work to say the least, and relatively few samples are taken, with relatively few theories tested. What if we had the ability to cost-effectively take thousands of samples from populations that exhibited traits we want or need to know more about, and then cross-reference all that data?

  4. Cynicism by dyingtolive · · Score: -1, Troll

    Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous? Just once, I want to see IBM or somebody backing Tor or Freenet or something similar.

    --
    Support the EFF and Creative Commons. The war is coming, and they're supporting you...
    1. Re:Cynicism by Lloyd_Bryant · · Score: 3, Insightful

      Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous? Just once, I want to see IBM or somebody backing Tor or Freenet or something similar.

      Please remember that IBM is, like most corporations, a for-profit entity. Which means that the vast majority of their research is going to be aimed at projects that will allow them to make a buck.

      In short - Tor and Freenet don't spend gazillions of dollars on technologies, while governments do.

      --
      Don't tell me to get a life. I had one once. It sucked.
    2. Re:Cynicism by MozeeToby · · Score: 1

      You look at this as a potential privacy invasion, which I supose that it is technically, although it is way overkill for mere identification purposes. I look at this and see the possibilities for huge medical breakthroughs. Having one human DNA sequenced is neat, but it isn't really enough to tell us much about what our DNA does. To really discover or rule out genetic causes of disease, we'll need tens of thousands of sequenced genomes that we can cross reference and compare; something that is within the realm of posibility if the cost can be pushed down to $1000 a sequencing.

    3. Re:Cynicism by Rhacman · · Score: 1

      Before we continue this conversation I'm going to need access to your source code to verify that you are not trying to corrupt me with your ideals. I promise that if I make any modifications I will distribute them with any clones that I produce of you.

      --
      Account -> Discussions -> Disable Sigs
    4. Re:Cynicism by Laxitive · · Score: 5, Insightful

      If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.

      There are enormous resources in scientific research that goes toward generating datasets. Sequencing of humans is a significant part of it, but most of that applies to medicinal uses, such as cancer genotyping (which uses sequencing to identify specifically the genotypic characteristics of a particular tumor colony so it can be treated much more effectively than just trying to guess by looking at it "from the outside"). Also, a huge new area in medicine is going to be "personalized" medicine. Medicine that's actually tailored to the specific genetic traits that YOU have, so that the chances of side-effects are reduced and effectiveness is increased.

      Then there are the thousands of researchers that need to collect sequence datasets on organisms that have NOTHING to do with humans. A big chunk of this is plant genetics: crop stress tolerance (e.g. make wheat grow more reliably in colder or dryer climates, or resist disease better), natural product optimization (e.g. make canola plants produce 10% more of the kinds of oils you care about, and less of the crap you don't). Another big chunk of this research is basic science: figuring out the specific details of how evolution has progressed, or to identify the core biological processes that make organisms tick. That's core evolutionary biology and biomechanics research.

      Then there's the people trying to do constructive genomics: actually build organisms that do specific things. Like modifying yeast to produce some complex bioproduct that requires a network of potentially hundreds of genes. Or creating organisms that filter waste from water. Or building algae variants that run on sunlight and produce oil.

      All of these things could desperately use robust, cheap, accessible sequencing platforms. Genetic sequencing is not all about your privacy. It's a platform which has the scope to save scientists and researchers millions, and put that towards more research and better results than towards trying to scrape out a few bases from a tissue sample.

      IBM is trying big time to get into the life sciences (that's wrong actually, they actually already HAVE products they market to the life sciences, like systems for large-scale data processing). It is worth billions to them, and they want to tap it.

      -Laxitive

    5. Re:Cynicism by Anonymous Coward · · Score: 1, Insightful

      At $100 for a reader, who is to say they cant screen job applicants to see if they will have future medical issues and deny them a job (and health insurance).

      Who is to say medical insurance wouldnt require such a test, to flag any possible "pre-existing conditions"

      Gattaca, here we come

    6. Re:Cynicism by dyingtolive · · Score: 2, Insightful

      I completely agree that the technology can be used for awesome and amazing things. I just have a feeling that most of the things it's going to be used for are things that aren't going to benefit humanity in such lofty ways.

      --
      Support the EFF and Creative Commons. The war is coming, and they're supporting you...
    7. Re:Cynicism by Xtifr · · Score: 1

      Wait. A modified "clone"? With--say--only 50% of my DNA included? Isn't that what they call a "normal child"!

      So just what is it that you're volunteering for here, and are you sure it's legal in this state? Tell you what. Bend over, pick up that pencil I just dropped, and let me see if I might be willing to let you "access" my "source code". :)

    8. Re:Cynicism by Anonymous Coward · · Score: 0

      Well, yes. But it does mean that we need to work out reliable, mathematically provable to be correct, robust, and so on and so forth, methods to give close control to you over data pertaining to you. Laws alone are not enough, technology alone is not enough, most of all we need to understand why it is important and how to go about it. We need to make sure everyone knows that, from average joe to managers to congress critters and worse. We have to make it a basic human right. And we do need to do this stat.

    9. Re:Cynicism by interkin3tic · · Score: 1

      Why is it that multibillion dollar companies are constantly researching exciting new tech that makes it more and more impossible for us to remain annonymous?

      Look at it this way, with so many more people's genomes sequenced, there will be that much more data to sort through to find yours. Security through obscurity!

      Anyway, DNA is useful, they're developing it for other uses, it's not IBM's fault your ancestors foolishly chose to make everyone have unique DNA that can be used to identify you.

      (Yes, this was a joke, but I prefer to believe dyingtolive was also joking.)

    10. Re:Cynicism by interkin3tic · · Score: 3, Insightful

      I completely agree that the technology can be used for awesome and amazing things. I just have a feeling that most of the things it's going to be used for are things that aren't going to benefit humanity in such lofty ways.

      That second part is true of every single technology ever invented. The first sharpened stick man ever made may have been used to kill food, but the second one was probably used to kill another dude and steal his woman.

      Tor isn't a holy technology that can only be used in good ways either. I'm guessing 5 seconds after it was finished, someone said something like "Think of the children! This will be used to transmit child porn." You probably scoff at that objection and, and rightfully so, but that's exactly our reaction to your objection to the DNA reader.

    11. Re:Cynicism by RDW · · Score: 1

      'If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.'

      Indeed. For a great summary of what some of the people who really do grasp it think, check out the answers to Nature Genetics' question of the year in 2007 - 'What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000?':

      http://www.nature.com/ng/qoty/index.html

      Right now, commercial genome sequencing is about $50,000 USD with the Solexa/Illumina system. Several teams are currently competing for a $10 million USD Genomics X-Prize, which will bring it down to the $10,000 USD level:

      http://genomics.xprize.org/

      You can't accuse them of being under-ambitious (e.g., from Reveo: "The ultimate mission of this proposed program is to commercialize an instrument in 5-10 years that will cost less than a $1000 and sequence the whole genome and simultaneously the epigenome (methylation code) nearly error free in a minute for pennies per genome.").

    12. Re:Cynicism by BungaDunga · · Score: 1

      And if they DID back Tor, would you trust it?

    13. Re:Cynicism by Anonymous Coward · · Score: 0

      Agreed, I don't think a cheaper / more rapid DNA sequencer is really going to provide the health benefits that most seem to think it will. Much of ones genetic code is controlled by epigenetic markers such as methylation and acetylation of DNA and various transcription factor levels. These markers seem to be even more pertinent to whether or not we get a particular disease than our actual code sequence. So unless this sequencer can read methylation and actylation states, it won't provide more info than current genotyping microarrays that are already exist below the $1000 cost point. So in all actuality, an insurer wouldn't pay to get your "full genome"

      The real world uses will likely be as you suggested, to sequence unknown and engineered genomes; Monsanto is no doubt rooting for IBM

    14. Re:Cynicism by Pseudonym · · Score: 1

      If you think that fast and cheap DNA reading applies only (or even mostly) to monitoring of individuals, you do not have a real grasp of the scope and applicability of DNA sequencing.

      For most extant species on the planet, we don't even know how many chromosomes they have, let alone having sequenced them. This will speed things up enormously.

      --
      sub f{($f)=@_;print"$f(q{$f});";}f(q{sub f{($f)=@_;print"$f(q{$f});";}f});
  5. I for one... by ground.zero.612 · · Score: 0

    will introduce myself as your newly appointed, genetically self-modified, cybernetic overlord once I get my hands (manipulators?) on one of these bad boys.

    --
    "Be prepared, son. That's my motto. Be prepared." --Joe Hallenbeck
  6. From The YouTube Title by Anonymous Coward · · Score: 1, Interesting

    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

  7. Other uses by NoYob · · Score: 2, Insightful

    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 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!

    It's interesting. While editing this post, my cursor stays as a pointer on the right side of the entry field. To edit, I had to click to the left and then use the arrow keys to get to the right. Any spelling errors left are Slashdot's fault so flame them.

    --
    It's NOT me! It's the meds! I'm on 1000mg of Fukitol.
    1. Re:Other uses by Taibhsear · · Score: 2, Informative

      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.

    2. Re:Other uses by NoYob · · Score: 1, Insightful

      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.

      --
      It's NOT me! It's the meds! I'm on 1000mg of Fukitol.
    3. Re:Other uses by Taibhsear · · Score: 3, Insightful

      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.

    4. Re:Other uses by Shakrai · · Score: 3, Interesting

      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.

      --
      I want peace on earth and goodwill toward man.
      We are the United States Government! We don't do that sort of thing.
    5. Re:Other uses by BrokenHalo · · Score: 0

      But I challenge you to find a law banning government agencies from doing it.

    6. Re:Other uses by Anonymous Coward · · Score: 0

      I find it disturbing that you couldn't name a single positive use for this technology.

      Especially considering that he's the chairman of his local Optimists Club!

    7. Re:Other uses by Anonymous Coward · · Score: 0

      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.

      DNA systems don't kill people, people kill people!

    8. Re:Other uses by izomiac · · Score: 1

      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 effect of countless genes. One day we might understand how that works, but not anytime soon.

      Beyond that, all better knowledge of one's DNA would allow would be a narrowing of probabilities. If a woman has a family history of breast cancer, then knowing it's BRCA2 and being genetically tested and found negative would allow her insurance company to lower her rates. Being found positive allows her to be more proactive in preventing breast cancer, so there's a very good chance she still won't get it. Either way she pays less (a. she doesn't have the defect, b. she manages it). OTOH, I think insurance companies using genetic information to determine rates is illegal anyway, as is genetic discrimination. Not to mention it'd be prohibitively expensive, ethically reprehensible, and scientifically unsound for employers to discriminate in this way.

      Plus, there's a lot more to DNA than the base pair sequence. Certain parts of your DNA are inactivated for example (in part by cells that don't need to express those genes, in part due to what you inherit from your parents).

    9. Re:Other uses by Taibhsear · · Score: 1, Informative

      Challenge accepted.

    10. Re:Other uses by gad_zuki! · · Score: 1, Insightful

      >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.

    11. Re:Other uses by interkin3tic · · Score: 2, Interesting

      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.

      So this could speed up a lot of biomedical research. It will also bring new research projects into the realm of feasibility, some of those could be extremely valuable too.

      Sarcastically saying nothing but good can come of this technology? That's more ridiculous applied here than it would be about a faster computer processor.

    12. Re:Other uses by jfeldredge · · Score: 1

      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.

  8. Say goodbye to fingerprint scanners on laptops by davegravy · · Score: 1

    Say hello to DNA code readers.

    "Please insert your DNA in the hole for authentication"

    1. Re:Say goodbye to fingerprint scanners on laptops by newcastlejon · · Score: 2, Insightful

      Sounds even easier to bypass than cutting off a finger. Perhaps this will usher in a golden age of sperm-jacking and blood-letting?

      --
      If God forks the Universe every time you roll a die, he'd better have a damned good memory.
    2. Re:Say goodbye to fingerprint scanners on laptops by Anonymous Coward · · Score: 0

      Just think of the applications of this technology for realdoll manufacturers.

    3. Re:Say goodbye to fingerprint scanners on laptops by travisb828 · · Score: 2, Funny

      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?

    4. Re:Say goodbye to fingerprint scanners on laptops by newcastlejon · · Score: 1

      Not unless you can fit your fireman into one of the tubes...

      --
      If God forks the Universe every time you roll a die, he'd better have a damned good memory.
    5. Re:Say goodbye to fingerprint scanners on laptops by Anonymous Coward · · Score: 0

      Must resist urge to make a "Thats what she said" joke. /Failed

    6. Re:Say goodbye to fingerprint scanners on laptops by Anonymous Coward · · Score: 0

      That's what she said?

  9. Challenge by Taibhsear · · Score: 2, Interesting

    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.

  10. Project Extension from WWII by Anonymous Coward · · Score: -1, Flamebait

    Is this an extension of the cataloging/tattoo system they used on the Jews in WWII... or is this an entirely new project?

    -Godwin

  11. I Smell Synergy! by fuzzyfuzzyfungus · · Score: 3, Insightful

    High speed, computer-assisted, genetic analysis technology should go beautifully with IBM's existing expertise in Data-driven eugenics solutions...

    1. Re:I Smell Synergy! by iammani · · Score: 1

      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 V1, V2 missiles (V2 being the worlds first ballistic missile). He was responsible for the death of thousand of slaves who were hardly fed and also death of allied soldiers (because of his missiles). He was later praised by Apollo space program director Sam Phillips, who was quoted as saying that he did not think that America would have reached the moon as quickly as it did without von Braun's help. Later, after discussing it with colleagues, Sam even amended this to say that he did not believe America would have reached the moon at all.

      I surprised people dont pick on Nazi turned Americans, while they do want to pick on American companies that made the Nazi process efficient.

      PS: the above is a frank opinion, I welcome any comments pointing flaws in my opinion/argument.

  12. Viruses? by Anonymous Coward · · Score: 0

    Will this be able to identify viruses? Mass availability of this capability could help significantly if a significant pandemic actually hits.

    1. Re:Viruses? by BrokenHalo · · Score: 1

      Will this be able to identify viruses?

      No reason why not, since the genetic payload of most viruses is quite small, even allowing for the open reading frame. But I suspect the technology will be used primarily for less benign purposes.

    2. Re:Viruses? by SnarfQuest · · Score: 1

      Think along the lines of going to a doctors office, and getting a shot specifically designed on the spot to wipe out all of your specific diseases.

      --
      Who would win this election: Andrew Weiner vs Andrew Weiner's weiner.
  13. First Godwin! by Anonymous Coward · · Score: -1

    Just as the Nazi's were supported by IBM, now the rest of the world's totalitarian governments will be able to bag and tag Their Hated Race (TM)

  14. Another technology is ahead so far by Michael+G.+Kaplan · · Score: 5, Informative

    The New York Times published an article in August about a technology that decoded a human genome for less than $50,000. 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.

    1. Re:Another technology is ahead so far by dAzED1 · · Score: 2, Informative

      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 program then matches the billions of 32-unit fragments to the completed human genomes already on file...

      There are many situations where this is simply not ideal. Not the least of which is when someone wants to sequence a species that has yet to be sequenced. Additionally, you're basing your alignment upon the alignment of the previous set, without actually knowing whether the previous set is properly aligned. More to point, it is well accepted that it is not properly aligned, so you're testing against a known bad. This is (imo) the biggest problem in bioinformatics right now.

      IBM's machine doesn't seem to be taking that same approach, and instead appears to be cutting the DNA in to exponentially larger chunks (from what I've read about it). This isn't something where Moore's Law applies; it's a paradigm shift, not a technology improvement.

    2. Re:Another technology is ahead so far by harmonise · · Score: 1

      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.

      --
      Cory Doctorow talking about cloud computing makes as much sense as George W Bush talking about electrical engineering.
  15. Simple equation by Anonymous Coward · · Score: 0

    Perfect DNA = read DNA - unwanted DNA + wanted DNA
    Soon everyone will have to jump through this thing and we'll all be the same.

  16. How does the current tech work again? by Anonymous Coward · · Score: 0

    The way this works is quite easy to understand, however the method used for the first few decades was rather different but no less ingenious. I remember they used enzymes to first replicate the DNA a few thousand or more times, then other enzymes to cut these in random places and then some other trick and then you can, after re-reading a certain spot 20-30 times, say whether an A, T, G or C was there. Right-ish?

    Could someone provide a better description of this process?

    1. Re:How does the current tech work again? by reverseengineer · · Score: 2, Informative

      There are a few different ways of doing DNA sequencing now, but most automated sequencing uses what's called the dye termination method, which is an advancement on the Sanger (aka dideoxy) method. If the sample needs to be amplified, you can use the polymerase chain reaction, which uses heat to separate strands of DNA, then uses a heat stable DNA polymerase to make copies- a process that can be cycled to exponentially increase the sample. Once again, PCR is only necessary if you need more material to work with.

      The sequencing itself starts by unzipping your DNA sample to a single strand, and then making copies of this strand in an environment where a small fraction of the available deoxynucleotides used for building the copied strands are replaced with labeled dideoxynucleotides, which are added to the growing strand but then terminate further growth. This produces a series of DNA fragments of differing lengths, each with a tag on the last base added. You can use electrophoresis to separate the fragments by size, which creates a map of where your tagged dideoxy bases are located. If you have managed to tag each location at least once, then you know the entire sequence.

      The original Sanger method used radioactive tags, and you had to run the reaction 4 times- with labeled A, T, C, and G separately. Modern automated sequencers usually use four fluorescent tags at different wavelengths, so all four can be run in the same pot.

      --
      "FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
    2. Re:How does the current tech work again? by Anonymous Coward · · Score: 0

      Informative indeed, thank you for explaining!

  17. To echo "Dog Day Afternoon" by sehlat · · Score: 1

    GATTACA! GATTACA! GATTACA!

  18. And The First DNA sequence to be read... by cutecub · · Score: 1

    G A T T A C A

    -S

  19. Summary is wrong by thewils · · Score: 2, Funny

    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.

    --
    Once I was a four stone apology. Now I am two separate gorillas.
    1. Re:Summary is wrong by trb · · Score: 3, Insightful
      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. That's creative accounting.

    2. Re:Summary is wrong by trb · · Score: 1
      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 in the NY Times discussing this problem.

  20. Other "fast readers" we need by darCness · · Score: 1

    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 revolutionize casual sex and libertine lifestyles. Meet, test, have sex without worry. Very liberating.

    A nutrient reader. No more relying on labels for store-bought food. Would also allow you to test food from eating establishments that do not supply nutritional information. Stick your reader in your food, find out the exact calorie, fat, etc. content instantly. Would also help with obesity/portion control.

  21. It's about time. by Animats · · Score: 2, Insightful

    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.

  22. The world is about information. by maillemaker · · Score: 1, Interesting

    You could argue that the entire purpose of mankind is to acquire, and then use to his benefit, information. This has been the ongoing work of mankind since the dawn of mankind. Our appetite for information is insatiable, as the ways to benefit from information seem endless.

    Consequently, privacy is doomed.

    --
    A work that expires before its copyright never enters the public domain and thus enjoys eternal copyright protection.
    1. Re:The world is about information. by RDW · · Score: 1

      'You could argue that the entire purpose of mankind is to acquire, and then use to his benefit, information. This has been the ongoing work of mankind since the dawn of mankind.'

      Better hope we don't finish it any time soon, then:

      http://lucis.net/stuff/clarke/9billion_clarke.html

  23. fp@ Gnaa! by Anonymous Coward · · Score: -1, Troll

    troubles of Walnut people's faces is bloodfarts. FreeBSD ooficial GNAA irc fate. Let's not be their hand...she OF AMERICA irc conductedD at MIT All our times have about outside fucking surprise, Reciprocating bad from within. bunch of retarded

  24. Hmmm... by davebooth · · Score: 1

    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.

    --
    I had a .sig once. It got boring.
  25. This is also being done other ways using proteins by Anonymous Coward · · Score: 0

    In their movie it looks like the DNA has to be single-stranded to be read by the chip. One of my friends has been working on a way of doing the reading with double stranded DNA, which is easier to work with:
    http://pubs.acs.org/doi/abs/10.1021/nl9020232

  26. It won't be good by Anonymous Coward · · Score: 0

    IBM Researchers Working Toward Cheap, Fast DNA Reader

    Cheap, Fast, Good. Pick any two.

  27. Similar projects already exists... by cHeR2 · · Score: 1

    For example, Pacific Biosciences:
    http://www.nytimes.com/2008/02/09/business/09genome.html
    ``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."

  28. Pacific Biosciences by slave_to_coffee · · Score: 1

    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.

  29. How to solve the DNA migration rate problem! by Scubaraf · · Score: 1

    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 relative to the scanning frequency, but then you couldn't differentiate between a sequence of 3 G's in a row or a single G getting scanned three times.

    If you design your DNA reader with multiple reading points in series (i.e. read the strand simultaneously at multiple points along it's length), this problem would go away. Here's how it works:
    1. You assume that the entire strand moves at the same rate (this rate can vary, but must be slow compared to the scan rate of the base readers).
    2. If any of your serial DNA readers record a change in base, you interpret this to mean that the DNA molecule has moved down the pore by one base height. Any detectors that did not record a base change are likely reading their next base as well, but it just happens to be the same kind as the one they read just prior.

    By allowing for multiple scans per base, you increase the likelihood of making a correct call. In fact, you may be able to distinguish a C from a methyl-C from a hydroxymethyl-C and get epigenetic information at the same time you get sequence information! By using multiple detectors in series, you are able to detect when the DNA strand has moved one base height and get another crack at making sure you read the right bases.

    If anyone from IBM sees this and thinks it might work - drop me a note. I would be very interested in participating in the development/testing of this technology. - Cancer genetics researcher / clinician.