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Biotech Science

New Method To Revolutionize DNA Sequencing 239

Posted by ScuttleMonkey
from the start-saving-up-to-buy-a-clone dept.
An anonymous reader writes "A new method of DNA sequencing published this week in Science identifies incorporation of single bases by fluorescence. This has been shown to increase read lengths from 20 bases (454 sequencing) to >4000 bases, with a 99.3% accuracy. Single molecule reading can reduce costs and increase the rate at which reads can be performed. 'So far, the team has built a chip housing 3000 ZMWs [waveguides], which the company hopes will hit the market in 2010. By 2013, it aims to squeeze a million ZMWs [waveguides] onto a single chip and observe DNA being assembled in each simultaneously. Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.'"
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New Method To Revolutionize DNA Sequencing

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  • 99.3% accurate? (Score:5, Insightful)

    by Valdrax (32670) on Monday January 05, 2009 @01:28PM (#26332679)

    That's, what, 28 incorrect base pairs out of 4000? I'm not a biologist, but is this considered an acceptable error rate? Even the hopes of 99.999% accuracy seems really awful when there are about 3 billion base pairs in a human genome.

    I realize that we aren't going to be trying to make a cloned copy from this data, but what uses is this "good enough" for?

  • Re:99.3% accurate? (Score:5, Insightful)

    by imamac (1083405) on Monday January 05, 2009 @01:31PM (#26332727)

    I realize that we aren't going to be trying to make a cloned copy from this data...

    What makes you so sure? Who knows where this will lead?

  • Re:99.3% accurate? (Score:2, Insightful)

    by aoeusnth (101740) on Monday January 05, 2009 @01:34PM (#26332787)

    That's, what, 28 incorrect base pairs out of 4000? I'm not a biologist, but is this considered an acceptable error rate? Even the hopes of 99.999% accuracy seems really awful when there are about 3 billion base pairs in a human genome.

    I realize that we aren't going to be trying to make a cloned copy from this data, but what uses is this "good enough" for?

    More than good enough for forensic work at least, I'd wager.

  • by djupedal (584558) on Monday January 05, 2009 @01:35PM (#26332809)
    > Company founder Stephen Turner estimates that such a chip would be able to sequence an entire human genome in under half an hour to 99.999 per cent accuracy for under $1000.

    I think this qualifies as a true 'technological singularity' [wired.com] :)
  • Re:99.3% accurate? (Score:5, Insightful)

    by ccguy (1116865) on Monday January 05, 2009 @01:37PM (#26332825) Homepage
    Well, depends if those 28/4000 errors are the same in each run or not.

    If they can sequence the whole thing in less than 30 minutes one time with a 0.001% "read" error rate, my guess is that they can get it probabilistically near 100% correct in 2 hours or so.

    By the way, what's the current error rate? Is it 0? (just asking)
  • error correction (Score:3, Insightful)

    by bugs2squash (1132591) on Monday January 05, 2009 @01:39PM (#26332859)
    Is there not some form of error-correction in the sequence itself that could be exploited ?

    Something like the error correction on an audio compact disk ?
  • Re:99.3% accurate? (Score:2, Insightful)

    by Anonymous Coward on Monday January 05, 2009 @01:45PM (#26332947)

    Re: mistakes and inaccuracies...

    You run two or three trials and do "a check sum" ...a la Raid inter leafing...errors stand out and are discarded..

  • Re:99.3% accurate? (Score:5, Insightful)

    by scorp1us (235526) on Monday January 05, 2009 @01:53PM (#26333061) Journal

    There is a saying from the old sailing days. "Never set sail with two compasses". One is ok, three is better. But never two. The paralysis from not knowing which is right is far worse than being wrong and correcting later.

  • by Hurricane78 (562437) <deleted@slashd[ ]org ['ot.' in gap]> on Monday January 05, 2009 @01:58PM (#26333151)

    Yes. It's called "natural selection". :P

  • Re:Bad summary (Score:3, Insightful)

    by damn_registrars (1103043) <damn.registrars@gmail.com> on Monday January 05, 2009 @02:13PM (#26333393) Homepage Journal

    Using 454 sequencing you get average read lenghts of ~400-500 bp

    I suspect someone had confused 454 with the other popular next-gen sequencing technique from Illumina, which does give very short reads.

    Read lenghts around 20 bp would be pretty much useless. At least for de novo sequencing..

    Not necessarily. If you can drive the cost/base down far enough, you can make short reads worthwhile if you use a shotgun approach and try for large-scale coverage. Especially if you can produce the short reads at a lower rate of time/base.

  • by timeOday (582209) on Monday January 05, 2009 @02:36PM (#26333795)
    This is entirely reasonable and desirable if you replace "spider-thing" with "cancer" or "aids," or even "common cold." Gene sequencing your disease and taking the right medicine for what you *actually* have - instead of today's educated guesswork - will be a HUGE advance. Thousands die every year because they have to guess a year in advance which flu strains will be prevalent and usually guess wrong.
  • Re:Bad summary (Score:3, Insightful)

    by nodrogluap (165820) * on Monday January 05, 2009 @02:42PM (#26333863) Homepage

    The use of short reads for de novo assembly only makes sense if you want a rough draft of a genome, not the complete thing. There are way too many transposable elements, repeats, variation, etc. to accurately reconstruct even a bacterial genome with short reads. Nowadays, people don't even bother trying to piece it all together. They get down to a few dozen large fragments and say "good enough". It just costs too much to get the last 1-2% with a random sequencing approach.

  • Re:99.3% accurate? (Score:2, Insightful)

    by m93 (684512) on Monday January 05, 2009 @02:48PM (#26333941)

    I realize that we aren't going to be trying to make a cloned copy from this data, but what uses is this "good enough" for?

    It's most likely good enough to deny you health coverage. Pre-existing condition? Now risk can be assessed on pre-existing genes.

  • by nwf (25607) on Monday January 05, 2009 @02:54PM (#26334039)

    Although humans differ from one another in about 0.1% base pairs for a total of 3 million, the number of difference that describe human variability may be vastly smaller than this. First you discard non-coding DNA which gets you done to 30,000.

    Except that when our differences are so small, the non-coding regions are even more important. They control what genes are active and to what degree. That's nearly as important as the genes themselves.

    Genes are only part of the puzzle. You need to know what to do with them, and non-coding regions provide some of that along with the cellular machinery.

    Scientists used to call them "junk" DNA where junk == "I can't figure it out". Why would cells spend all that energy maintaining something useless? Not very likely.

  • by Anonymous Coward on Monday January 05, 2009 @03:09PM (#26334227)

    [Suspects] that come up positive can ask for the more accurate test.

    Umm... kind of like getting a lawyer for free if you need legal representation and lack funds, if you come up positive, it should be the default that they run the more accurate test.

  • Re:Gattica... (Score:1, Insightful)

    by Anonymous Coward on Monday January 05, 2009 @03:21PM (#26334427)

    Unless we perfect gene therapy, there are going to be a few billion people who find little consolation in that.

    Fixed that for you. Cloning wouldn't help the people who are alive now.

  • Re:Gattica... (Score:1, Insightful)

    by Anonymous Coward on Monday January 05, 2009 @03:35PM (#26334577)
    Sorry... but, "Gattica"?! Did you completely fail to understand the meaning of the name of the movie? (since when was there an "i" nucleotide?)
  • Error Correction (Score:2, Insightful)

    by LUH 3418 (1429407) <[maximechevalierb] [at] [gmail.com]> on Monday January 05, 2009 @03:48PM (#26334739)
    Many people seem concerned about the reading error rate. However, as it's been pointed out, it should be easy enough to read a DNA sequence multiple times (or read the whole genome multiple times) to decrease the error rate significantly. If you have one chip that can read the entire human genome in 30 mins, you can have the same chip read it twice in an hour, or four chips reading four copies in 30 mins.

    Furthermore, if you're using a technique like this to map a person's genome, you can be clever about it. Base pairs code genes, which is something you can take into account. For example, if you're reading the eye color gene, and your machine somehow consistently makes mistakes in that area, you can compare your reads to the few possible known eye color genes, and pick the most likely based on the genetic sequences of the entire gene.
  • Re:99.3% accurate? (Score:1, Insightful)

    by Anonymous Coward on Monday January 05, 2009 @03:59PM (#26334911)
    > 1.) Rapidly sequence a suspect's DNA > 2.) Find a cheap way to make "good enough" copies > 3.) Plant evidence Huh?! Step one only works if you already have a suspects DNA, and if you do, you can plant it. Why use millions of dollars of equipment to clone a suspect? Just plant the cells you already have, or (for the mad scientists only) encourage the cells you have to grow a bit so you have more. No need EVAR to sequence a suspect's DNA if you want to plant it.
  • Re:nitpick (Score:3, Insightful)

    by TheMeuge (645043) on Monday January 05, 2009 @04:45PM (#26335659)

    One base-pair does not a gene make.

    But a one base-pair change can unmake the gene pretty well.

    Tons of major debilitating mutations are due to a point mutation.

  • by CrankinOut (629561) on Monday January 05, 2009 @04:54PM (#26335795)
    If the article had stated that the cost were $1,000,000 to do the sequence, then the potential applications of the technology would be severely limited. Getting the cost (not the charge for the service) down creates the opportunity for more studies to be performed, more financial accessibility for patients, and less resistance for insurance companies or Medicare to deny charging for the study when it's indicated.

    In medicine, the cost of a study, as well as its reliability, availability, and predictive value, enters into the decisions made in clinical management.

  • by CrankinOut (629561) on Monday January 05, 2009 @05:03PM (#26335921)
    Just as seeing the moon doesn't require the same amount of effort as landing on it, reading a DNA sequence doesn't mean that selective modification is "just around the corner."

    Real applications of this, however, include looking for gene sequences in adults which predispose them to diseases (e.g. breast cancer) and then providing counseling and monitoring commensurate with that risk, a far less expensive effort than monitoring everyone for the same disease, even if they aren't at risk. Also, one could use this on embryonic cells obtained through amniocentesis to screen for hereditary diseases is families where there are risk factors.

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