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Biotech Science

X Prize Foundation Encourages DNA Decoding 100

Posted by Zonk
from the who-doesn't-love-a-good-sequence? dept.
Carl Bialik from the WSJ writes "The X Prize Foundation, the group behind the $10 million prize for human space flight, 'plans to offer a $5 million to $20 million prize to the first team that completely decodes the DNA of 100 or more people in a matter of weeks, according to foundation officials and others involved,' the Wall Street Journal reports. 'Such speedy gene sequencing would represent a technology breakthrough for medical research. It could launch an era of "personal" genomics in which ordinary people can learn their complete DNA code for less than the cost of a wide-screen television.' But don't set aside that TV purchase just yet: Foundation officials don't expect the prize money to be claimed for five to 10 years."
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X Prize Foundation Encourages DNA Decoding

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  • Costs? (Score:3, Interesting)

    by I_Strahd (791299) on Friday January 27, 2006 @09:37AM (#14578250)
    Wouldn't it take more than the prize money to accomplish this task? If so, does this really give people incentive or am I missing something?

    Thanks!
    • Re:Costs? (Score:4, Insightful)

      by Pyrowolf (877012) on Friday January 27, 2006 @09:39AM (#14578271) Homepage
      I think the technology that would come from this would easilly pay for itself regardless of the R&D costs. There would be an immediate need for this technology in various industries.
    • Wouldn't it take more than the prize money to accomplish this task? If so, does this really give people incentive or am I missing something?

      10 years ago yes. Today it would take a $10,000 DNA type of sequencer machine and a "super" computer to process the data. And a by super computer this could just be a couple thousand volunteers like SETI, but one would have to put together the effort.

      Not like you can share all that money with the volunteers...
      • You can not sequence a genome this cheap. The reagents cost more than this. The point is that it would require new technology, new chemistry (or better, no chemistry). There are at least 4 or 5 methods on the horizon though.

        Phil
    • Yes, of course, it would cost much more than this. 5 million dollars is nothing at
      all in R&D. People are very expensive. And, unlike human space travel, there are
      quite a few fairly immediate applications for this technology and lots of people
      who will pay for it.

      It's great advertising for the X foundation though. Someone else does all the work,
      they get to appear visionary and it only costs 5 million. Pretty clever.

      Phil
      • Phil,
        That was my initial thought as well. I know that the X foundation (no relation to the professor) will look great in the end, but I think that the result of this could help us all. I know private industry is already pursuing things such as this just like the first non-government/military trip to space. It will be done sooner or later. Why not take some credit for it?

        Perhaps I would like to see them offer $50 Mil to go to the moon. Then I can start construction on my super-slingshot. I just nee
        • Because the people who are attempting to do this already, could almost
          certainly not care less about 5million dollars either way. If you the X foundation
          were venture capital offering 5 million dollars no one would have noticed either
          way. Or better still a philanthropic research charity. They should try sponsering
          research, rather than living in it's reflected glory.

          Phil
          • Ah. Just read the article. It appears that the prize was the idea of the one J. Craig Venter. My initial impression that it is all the work of self-serving, egotistical, self-publicists seems to have been born out.

            Phil
    • Re:Costs? (Score:3, Insightful)

      by BiggerBoat (690886)
      It cost Paul Allen (with Mojave Aerospace Ventures through Burt Rutan and his Scaled Composites) more to win the original X-Prize than the prize awarded him. They won $10 million, but reportedly spent more than $20 million.

      For them, it wasn't (just) about the X-Prize and its money. That was just icing on the cake; the "real money" will probably come afterwards (we'll see how well Virgin Galactic does). I could very easily see the same thing happening with this new prize and the people who are already int
    • Richard Dawkings claims that the cost of genome sequencing mimic's Moore's Law -- meaning that it is decreasing exponentially. However, he goes much further than that, claiming that the computing power of a few more decades of Moore's Law will provide the ability to not only analyze millions of genomes collectively, but to manipulate them. Since this can also be easily done for chimpanzees, too, Dawkins has made a bold prediction: that by the middle of this century, the ability to create the "missing lin
    • An important factor in innovation is the constraints applied. If you have infinite time, or infinite money, or infinite ingenuity, then you will not need to innovate.

      Instead, what will happen here is that innovators will be focused on doing it in timely and a relatively inexpensive manner, which is probably one of the prize's hidden goals.

    • People were already working on this before this prize was announced. I know a friend who is working in a lab that's trying to design tiny little nanomachines or something that can run along a piece of DNA and sequence it. This would just be a little bonus for them I guess.
  • by TripMaster Monkey (862126) * on Friday January 27, 2006 @09:40AM (#14578276)


    While there's no disputing that speedy, accurate genome sequencing will have a significant positive impact, being the pessimist I am, I can't help but dwell on the possible downsides:

    • Cheap and accurate gene sequencing in the hands of insurance companies could make it difficult for a person with a genetic predisposition to disease to obtain health or life insurance.
    • Cheap and accurate gene sequencing in the hands of corporations encourages said corporations to discriminate in their hiring practices on the basis of genetic predispositions to everything from coronary disease to psychological problems.
    • Cheap and accurate gene sequencing in the hands of people searching for a spouse could lead to rigorous screenings of prospective mates for evidence of genetic 'undesirability'.
    • Cheap and accurate gene sequencing in the hands of governments could lead to governments investigating citizens on the basis of 'questionable genetic heritage'.


    Brave new world, indeed.
    • Cheap and accurate gene sequencing in the hands of insurance companies could make it difficult for a person with a genetic predisposition to disease to obtain health or life insurance.

      Chances are with this level of technology, health concerns will start to be a moot point. Predisposed to being over weight or having cancer... Well why not just use gene therapy to fix that.

      Cheap and accurate gene sequencing in the hands of corporations encourages said corporations to discriminate in their hiring practices on
      • Chances are with this level of technology, health concerns will start to be a moot point. Predisposed to being over weight or having cancer... Well why not just use gene therapy to fix that.

        Sure, and if you have a fast disassembler, all software bugs can be immediatly fixed. Right?
      • Chances are with this level of technology, health concerns will start to be a moot point. Predisposed to being over weight or having cancer... Well why not just use gene therapy to fix that.

        There are only a few successes of gene therapy. Getting the minute details of human physiology is hard. The results from mouse metabolism studies do not always carry over to humans. Researchers are make some progress on understanding the basis of obesity (i.e., leptin, ghrelin, etc.) that lies beyond the obvious "overea
    • Brave new world, indeed.

      I have CF and Celiac. Trust me, it's the Old World, brother. You're just about to emigrate is all. Being stripped and deloused is just part of the deal.

      KFG
    • Cheap and accurate gene sequencing in the hands of corporations encourages said corporations to discriminate in their hiring practices on the basis of genetic predispositions to everything from coronary disease to psychological problems.

      I hope there isn't a gene that says "I probably will only stay here for 6 months."
    • by RichDice (7079) on Friday January 27, 2006 @11:15AM (#14579208)
      Cheap and accurate gene sequencing in the hands of insurance companies could make it difficult for a person with a genetic predisposition to disease to obtain health or life insurance.
      What you're describing here is the concept of adverse selection [wikipedia.org]. It's an endemic problem in the insurance industry, but more generally is a phenominon of economics in the realm of information asymmetries.

      This kind of genome sequencing technology would bring it into the foreground so that the whole American population would suddenly talk about and understand the concept, and perhaps do something about it, in the same way that high interest rates in the early 1980s had everyone suddenly talking about "time value of money" and "cap rates", terms previously only used and understood by economists and MBAs. (Of course, people seem to have forgotten these things since.)

      I mention this because America currently practices a kind of strategy against adverse selection in health care by linking health care provisioning to employment through employer-provided health insurance. I'm not sure if this is why the system was set up initially (probably not, as economists didn't have a good theory regarding adverse selection until the 1970s) but the idea here is that if you're healthy enough to be employable, then you're probably healthy enough to be worth insuring from the perspective of the insurance companies. By being employed, you help level the information assymetry that you hold in your advantage over the insurers.

      Of course, if everyone (insurers and would-be subscribers to insurance) held perfect knowledge, the whole industry would collapse. Insurers wouldn't bother insuring people who needed it, and the people who were super-healthy wouldn't bother buying insurance.

      Other countries (e.g. Canada) solve this problem by making health care universal. It's quite egalitarian, which some people would consider a good thing. It's also very efficient, because now you don't have to put all kinds of resources into a system to check to see if people are good candidates for insurance. (You also don't have to have billing departments or big beefy accounting departments.)

      If there's any kind of sanity in the US, this kind of technology will (finally) provide the political impetus for a real, substantial universal health care system there, too. Whether or not such a system develops can be used as a proxy to determine the hidden (or at least unobservable) information regarding the presense of sanity in the US.

      Cheers,
      Richard

    • by Anonymous Coward
      ... being the pessimist I am, I can't help but dwell on the possible downsides: ...

      I understand these concerns. But we--as in you and me and everyone else on earth--wouldn't have the capabilities we do now if it hadn't been for natural selection. Leave the system alone--through policy and other conscious efforts--and the system will regulate itself; people will evolve into better, more advanced bio-machines.

      Darwin's survival-of-the-fittest applies to all living creatures, including us humans. I'm so tired o
      • and the system will regulate itself; people will evolve into better, more advanced bio-machines.

        Umm.... Actually we threw the proverbial monkey wrench into human biological evolution years ago. Once humans were able to sit on a couch and not be eaten by a lion is pretty much when natural selection no longer applies.

        Take a look at humans... People with born with imperfect vision (ie requiring contacts and glasses... no offense, since I don't have perfect vision either) won't go away with our current way of e
    • You know... that was a great post, because, yes, what you said is so true, i can see it coming 10 miles away.

      Although you are right, my optimistic self cannot help but point the followings :

      Cheap and accurate gene sequencing would help detect babies with genetic disorder before their birth, possibly allowing the correction of the defective genes prior to the baby's birth.

      Cheap and accurate gene sequencing would most certainly be helpful curing uncurable diseases such as AIDS or Cancer

      Cheap and accurate gene
      • "Cheap and accurate gene sequencing would help detect babies with genetic disorder before their birth, possibly allowing the correction of the defective genes prior to the baby's birth."

        One thing that scares me about this scenerio: "Correction" might mean kill off the fetus before its born. Thats the cheap option right?

        (I am not advocating that through any means! I am a Transsexual, but I don't want to be "corrected". Why cannot I live my life the way I want?)
      • What if Pasteur had never created the vaccine ? lots of people would have died of course. But if he hadnt created the vaccine, our body wouldnt have learned to protect against those viruses and if the body hadnt learned to protect itself, the viruses wouldn't have mutated in even more virulent forms of viruses.

        Not quite. If we haven't been able to learn to protect against those viruses in millions of years of evolution, I really doubt we would have learned in the 100 years since he created the vaccine.

        A

    • You mean like in "Gattaca"?
  • by LiquidCoooled (634315) on Friday January 27, 2006 @09:41AM (#14578289) Homepage Journal
    Folks, make sure you obtain a large polythene sheet before "decoding" peoples DNA.

    I tried it once and apart from a blood stained carpet, I'm serving 12 years for my trouble.

  • by oni (41625) on Friday January 27, 2006 @09:42AM (#14578295) Homepage
    I'm sure that the same companies who fire employees who dare to smoke on their own time would NEVER dream of sequencing the genes of employees and fire any who have a 2% change of heart desease. Oh no. That will never happen. And if it did, I'm sure that congress, who does not receive enormous donations from the companies, will pass laws that will protect us.
      1. There are laws in place already to protect against various forms of descrimination.
      2. One, I've never heard of any company firing someone who smokes. Could you provide a source.
      3. However, even if they did, smoking is a choice, having a gene that puts you more at risk for heart disease is not a choice. Firing someone for their personal choices is somewhat defensible, but firing someone for things they cannot help or change (for example handicaps, race, gender) has been generally frowned upon by congress and the
    • Yes another good example of why having health insurance attached to your job is a Really Bad Idea and another argument in favour of universal health care provided by government.

      But then, you guys could just head North to see how it works in Canada if you want to see it in action

      • Are you NUTS?

        The reason government feels that it can pass laws about what we can smoke and eat is because it sees itself as paying for you hospital bills. (Even though we pay those bills through taxes.)

        Do you really think the government would give a damn about you hurting yourself if it didn't have to foot all the hospital bills you can't afford?
    • Sequencing individual's genome doesn't mean that you'll be able to tell if a person has 2% chance of heart disease - you have to analyze the sequence data to find out which diseases you might have - the gene expression might tell you that. These kinds of analysis (eg microarray-genechips) are expensive as well, so people should figure out how to do this cheaper at the same time with sequencing (nanotech is promising, but still costly, and would remain so for maybe at least 10 years).
    • I wonder how many genetically perfect people there are? Would there be enough genetically perfect people for companies to hire, so that they could ignore the imperfect ones?
      • I wonder how many genetically perfect people there are? Would there be enough genetically perfect people for companies to hire, so that they could ignore the imperfect ones?

        Nah, you miss the point, when a company hires you they do a simple calculation.

        Money you will generate for the company - Money you cost the company = Your worth to the company

        Theoretically, they do this calculation for all applicants and then hire the person with the highest number after the equals sign. In practice, much of it is based
        • Good points, and of course, even if everybody has one defect or another, there would always be situations where one applicant would win over another because of genetic dispositions.

          Still, it seems to me with more information available, it should in the end be possible to handle things more efficently, to everyone's benefit? Not that I am not concerned about privacy issues etc., but their might be solutions, too.
  • What about this screams, "good idea?!"
    • Everything. I for one would like to know what potential problems I have waiting for me in the future. Plus parents would like to know the genetic disposotion of their children. Sure it will possibly be used for dubious purposes too but the same can be said for just about anything.
  • by Daniel Dvorkin (106857) * on Friday January 27, 2006 @09:44AM (#14578314) Homepage Journal
    The usual problem with science reporting, particularly in biology. The article says "... the first team that completely decodes the DNA of 100 or more people ..." No; the prize winner will sequence the DNA. That is a looong way from "decoding" the human genome, or even the genomes of any particular 100 people. Sequence information is valuable, but it's not "decoded" in any meaningful sense of the word. Imagine looking at an enormous program written in a language you've just started learning, and full of function and variable names like "do_stuff()" and "x1".
  • This is a $10 million prize for a several billion dollar technology. It'll be nice for sparking interest in the field, but it shouldn't make any more Celera Genomics-types. "The plan for a genomics X Prize fell into place last year after Google Inc. co-founder Larry Page joined the foundation's board and then recruited Dr. Venter to become a director." (Dr. Venter is the Vietnam vet who started Celera Genomics [comes from "Celerity"]) Well, that just took the idea from "unrealistic" to "unnerving." I see
    • Venter's scientific enemies (like Lander and Sulston) have tried to convince the public that Venter aims to be the Bill Gates of biology. That isn't, and never was, true. You need to understand the history of Craig. He started out at NIH and then started the non-profit institute TIGR (where I work today) when the NIH was too shortsighted to support sequencing in the early 1990's. He joined Celera when it was clear the public effort wasn't using modern methods and would take forever to complete. Take a look
    • "Don't be evil motto..." Huh? Why is it that people fear any new technology they don't fully understand? People are so negative when speaking about any new biotech(genetic) breakthrough. Remember all the BS people talked about (and still do) about cloning? Come on people should do some research into something before panicing.
      • The "don't be evil" line was a reference to Google's hand in censorship for the Chinese government (this is recent news). Try checking out www.google.cn before flinging mud.
        I'm a skeptic of this prize because the technology is so valuable that a million dollar incentive shouldn't change the decision of whether a company or individual should pursue a billion dollar technology.
        If I offered you twenty million dollars to develop a fully functional AI, that certainly wouldn't be your incentive, would it?
  • ordinary people can learn their complete DNA code for less than the cost of a wide-screen television.

    Coincidentally, once these ordinary people get their code sequenced, they find out that they have highly-evolved genetic tendencies for couch potato-ness, eating crunchy foods and better wide-angle vision.
  • Is the prize for sequencing or for sequencing and assembling?

    Some companies like 454 [454.com] have got the technology to quickly sequence large genomes but assembling them is a completely different problem. And anyway we understand (roughly) about (roughly) 30% of the genes of any species that has been completely sequenced (mostly bacteria). I wish there was a prize for technics to annotate genomes accurately.
    • The assembling of sequences obtained from so called shotgun sequencing are hard to assemble, because you don't know where each piece of sequence belongs. (shotgun sequencing chops th DNA in random chuncks, isolates single chunks and sequences these) But once you know where a chunk belongs, and that is pretty easy if you have more than 1000 bases, you can just put it on the map. There will be viariation in the sequence as people do not have 100% the same sequence, but this is very small compared to the simil
  • while having my Wheaties, I poured the toasty goodies into a cereal bowl and out fell a cellophane wrapped prize. Wahoo, it was a secret DNA decoder ring... Yes, come to papa you lovely $10 million!

    I just couldn't resist!
  • DNA decoding uses nano-technology and supercomputer, both of which are on Moore's law curve. This means costs decrease an order of magnitude every five years. So if it costs a million bucks to decode a mammal's genome today, it will cost $100 in 2025.
    • Throw in the ability to use donated computer cycles to do the sequencing (like SETI@home), and this may be doable sooner rather than later; however the potential for the abuse of this type of personal information is at least as great as any benefits and it should not be done.
  • ..because DNA doesn't come with an EULA. This kind of reverse-engineering is allowed!
  • HapMap (Score:2, Informative)

    by derniers (792431)
    the first draft of the human haplotype map (HapMap) is already done: http://www.hapmap.org/ [hapmap.org] for a short commentary see N Engl J Med. 2005 Oct 27;353(17):1766-8.
  • I know very little about the specifics of DNA sequencing, but everything I've read says that the genes that make individual humans different are less than 1% of the total.

    So... you don't sequence the known quantity and just sequence the 1% that is different.

       
    • But you don't know in advance which 1% are different, so you still need to do all the sequencing. The "1%" figure you cite is just an estimate, based on a very small sample of individual genomes. In order to get a large sample, you need much cheaper and faster sequencing technology. Hence the prize.

      Furthermore, you are missing the point of the prize, which is to promote advances in sequencing technology. If they made the challenge easier then there would be no point.

      -- Anonymous Pedant
  • . . .when reading about the X-Prize Foundation rewarding all this work in DNA sequencing was: "I guess they're doing that so it will be easier to identify and differentiate the remains of the tourists who get blown up while flying in experimental spacecraft."

    Just part of a morning of disturbing thoughts. . .
  • supercomputer$> diff myDNA chimpanzeeDNA
    supercomputer$>


    D'Oh!

    • supercomputer$> diff myDNA chimpanzeeDNA
      supercomputer$>

      D'Oh!

      supercomputer$> ldd /usr/bin/diff
      libmono.so.1 => /lib/libmono.so.1 (0x00002aaaaabc2000)
      [...]

      perhaps the supercomputer is somewhat biased, afterall. Thank-you Miguel :-P.

  • I saw it done on CSI!
  • I think this challenge is pointless. The race for speeding up genome sequencing has been going on for several years and this price will not change anything. It will not bring in new players and the ones that are already there are working fiercely on the problem anyway. Just this summer there were two different papers in Nature, I think, that introduced nano-scale sequencing techniques with a speedup of 100x compared to "traditional" techniques. The foundation should spend its prize money on some other nobl
  • by Baby Duck (176251) on Friday January 27, 2006 @12:47PM (#14580388) Homepage
    In the ten years it takes to develop "turbo-sequencing", we will have find that very little of the sequence will now NOT be copyrighted by some corporation. So any possible research "cures for what ail ya" will be slowed down by having to take the time to bribe the copyright owner.
  • Is this a hoax? (Score:1, Insightful)

    by Anonymous Coward
    Is there really a prize for this? I can show anyone how to sequence their entire DNA structure in a matter of minutes with some basic electronics. And NO I'm not talking about DNA matching for evidence, I'm talking about full blown DNA sequencing of a single strand. It's very easy. I don't understand how something like this could be overlooked... How do I claim the prize?
  • The concept of being able to archiave my DNA is just so amazing that I am perfectly willing to wait 20 years before I can afford it. Not even having children offers this level of hereditary legacy. One day there may even be a library where everyone can submit their DNA for archive. It's very exciting.
  • NimbleGen (Score:1, Informative)

    by Anonymous Coward
    I bet this could be accomplished with a reasonable cost using technologies like those provided by NimbleGen [nimblegen.com]. They make custom DNA microarrays within weeks. They could pump out enough chips for 100 people's worth of DNA. This prize sounds like a good way to pump interest into DNA related sciences, and could spark new development.
    • Not really - NimbleGen's technology - while powerful - would not allow for sequencing of the Entire Genome. Affymetrix for example makes a set of 100 arrays that would sort of allow you to obtain sequence information (still not quite - not enough detail) from only 1/3 of the genome. With the NimbleGen technology it would take 1000s of arrays to reach this level - and still you do not have detailed sequence of the whole genome for even one person.

      If I had to take a guess I would say a technology like 45

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