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Biotech Science

New Tech Promises Cheap Gene Sequencing In Minutes 121

Posted by CmdrTaco
from the but-i-want-it-now dept.
Zothecula writes "Sequencing an entire genome is currently a highly complex, time-consuming process – the DNA must be broken down into segments and replicated, utilizing chemicals that destroy the original sample. Scientists from Imperial College London, however, have just announced the development of a prototype device that could lead to technology capable of sequencing a human genome within minutes, at a cost of just a few dollars. By contrast, when sequencing of the genome of Dr. James Watson (co-discoverer of the structure of DNA) was completed in 2007, it had taken two years and cost US$1 million."
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New Tech Promises Cheap Gene Sequencing In Minutes

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  • Now if we get it down to a second we can use it to control turnstyles...

    • I was thinking more along the lines of Ultraviolet, where a blood sample is used to sign a receipt of sorts: grip pen tightly, it draws a small sample, then sign your signature in blood to confirm identity both via DNA and signature.
      Also, it's used standalone as identification, so maybe we could get unforgeable (or at least VERY hard to forge) IDs.
      • Also, it's used standalone as identification, so maybe we could get unforgeable (or at least VERY hard to forge) IDs.

        Not a problem. I can get lots of your DNA. Without you even knowing it.

        • Also, it's used standalone as identification, so maybe we could get unforgeable (or at least VERY hard to forge) IDs.

          Not a problem. I can get lots of your DNA. Without you even knowing it.

          I'm guessing you're referring to covertly collected hair or skin samples. If someone's watching who touches them and how, those aren't that easy to get. Also, the DNA is likely to be incomplete or deteriorated from exposure, unlike that extracted from a blood sample or a tissue swab.

          • No, he was referring to covertly collected tissue samples contaminated with certain bodily fluids well-known for containing DNA.

            • by Anonymous Coward

              And that's why I always eat the evidence. You just can't be too safe.

      • by CCarrot (1562079)

        Also, it's used standalone as identification, so maybe we could get unforgeable (or at least VERY hard to forge) IDs.

        Sure, as long as the reference database is un-hackable and there's no way to sniff and spoof the digital signature generated from the DNA anywhere along the communication path from the reference database to the end device...oh, wait...

        But true, this would make low-tech identity theft much more difficult.

      • by icebike (68054)

        Simply sequencing a gene is a far cry from matching.

        If anything this leads to a whole raft of kitchen table scientists making ridiculous claims of paternity or crimes based on the assumption that because there exists a fast cheep tool to do part of the job, suddenly everyone is Horatio Cane.

        YEEAAAAAAAHHHHHH!
         

        • Add big cloud of computers and a cheap 100MBPS line and you can match in two secconds against a database.... or how many megabytes does a genome take? I dont think too many. I think its already well compressed.

          • Three billion base pairs, two bits per pair, four pairs per byte... About 750 megabytes.
            • Don't need to check the whole thing though. Could use something like a checksum. Or just check 1 random MB at a time...
      • by kurokame (1764228)

        Forgery is almost trivial, particularly when many people assume it's impossible. I can already hop online and order an arbitrary genetic sequence for delivery. Normally, this is used to create short sequences for insertion into a larger genetic strand, but the same tech would let a patient researcher forge an arbitrary DNA sequence under any conceivable test.

    • by gstoddart (321705)

      Now if we get it down to a second we can use it to control turnstyles...

      I'm more worried about them using it in airports. That will mark the last time I ever fly.

    • by kurokame (1764228)

      The emergence of MEMS devices for performing PCR and doing chemical analysis makes the development of portable DNA scanners more or less inevitable at this point. The only question is who will get the patent.

      The odds are fairly high that in a maximum of 20 years, I will be able to hop on Digikey and buy a DNA scanner IC for a few dollars. Given that it could integrate an appropriate sample collection modality and immediately begin PCR may also significantly broaden what constitutes a viable sample compared

  • Let's hope we heed the warnings of sci-fi [imdb.com].
    • Go figure: My main complaint about the movie was that ultrafast DNA analysis was unrealistic. What's next?. A device that transmits the sound of explosions in space?
      • by Monkeedude1212 (1560403) on Wednesday December 22, 2010 @02:31PM (#34643622) Journal

        You know what they say... In Space, no one can hear you complain about Science Fiction.

      • as in, every time- no matter how bad the power situation ever is, especially when 'shutting down to be electronically insignificant to detection' artificial gravity is always a constant.

        Millenium Falcon, Jetstar 1, enterprise, firelfy, pigs in space, hitchikers, galactica, dr. who, farscape, stargate atlantis & Universe, starship troopers, tripping the rift....

        • by omnichad (1198475)

          Artificial gravity is never even different on alien spaceships where the alien planet probably had different gravity...

        • Babylon 5?
          • Partial: Areas of different gravity were spoken of, but no scene was ever shown on a non-earth-gravity station, ship or planet. Fighter ships cleverly avoided a problem by strapping the pilot into a harness tight enough that it's impossible to tell from image alone if they were experiencing gravity or not.
      • by gilleain (1310105)

        Go figure: My main complaint about the movie was that ultrafast DNA analysis was unrealistic. What's next?. A device that transmits the sound of explosions in space?

        The worst part was when they get their DNA analysis results, and its like several sheets of "GAGATTATATGAGAGATAGAGATAG...". Firstly, it would be more like several telephone directories, or perhaps just a list of single mutations. Secondly, it would be meaningless without some extra analysis on top (annotations, basically) even to a geneticist.

        • I'm going to have a Kinkos print this GCTA crap from my genome into a big holy book for everyone to study once I get around to setting up that religion where everyone worships me which is going to be after they set up an app to read your genome with a smartphone. I'm hoping to have it start with the book of AAAAAA.
    • Because I always go to Hollywood for policy advice! It must be the tremendous respect they show for the truth.

    • "Warning?"

      That's an instructional video!

    • by Anonymous Coward

      Fun Fact: The DNA helix used on the box art is left handed rather than our typical right handed B-DNA.

  • by Anonymous Coward

    If they can build those in bulk, the CSI episodes are becoming much more realistic

  • by jfengel (409917) on Wednesday December 22, 2010 @02:26PM (#34643582) Homepage Journal

    I can't get too enthused about a prototype of something that might one day lead to another prototype, "up to ten years away".

    But the article in the sidebar titled "Breakthrough raises possibility of genetic children for same-sex couples" is at least amusingly illustrated with a picture of Bert and Ernie.

    • NOT gay (Score:2, Insightful)

      by snookerhog (1835110)
      they are not gay! otherwise Bert would have been in the tub with Ernie instead of the duck.
      • Re: (Score:2, Funny)

        by d'fim (132296)
        The duck was male and so was the other duck with Bert in the bedroom and besides it's none of your business what gay couple they swapped partners with anyways.
        • ... the other duck with Bert in the bedroom...

          That was no duck! That was Big Bird! And, now, Bert knows why he's called "Big".

  • have just announced the development of a prototype device that could lead to technology capable of

    The prototype could lead to technology, which could lead to discoveries that could lead to clues that could lead to a one-armed man who could lead to some funding...

    What problem were we trying solve again?

    I hate over-hyped article titles and summaries.

  • by Anonymous Coward

    I hate scientific journalism. "New tech promises cheap gene sequencing in minutes" is complete bullshit. When I read interesting news on scientific research, I try to track down the actual research to compare. Usually what's in the media is something like "SCIENTISTS ONE YEAR AWAY FROM CURING CANCER!!!" and the research reads "Behavior of protein XYZ under high pH"

    For those of us here that actually care about this kind of stuff, here is the real information: http://pubs.acs.org/doi/full/10.1021/n

  • Article citation (Score:5, Informative)

    by brteag00 (987351) on Wednesday December 22, 2010 @02:34PM (#34643664)
    It drives me nuts when the popular media article doesn't include a citation back to the original research. Here's a link to the article on the Nano Letters website: http://pubs.acs.org/doi/full/10.1021/nl103873a [acs.org]
    • Re: (Score:2, Funny)

      OK, Take a Popsicle stick, scrape it inside your cheek and send the DNA sample to them. They will analyze your DNA and tell you the source of the "anxiety about source less news story syndrome". Hurry, if you are the first, they will name the disease after you.
      • by brteag00 (987351)
        It's a constant old-media gripe of mine. They linked back to the Nano Letters front page - how much harder would it have been to link straight to the article?
    • Hmmm... My quick scan of this failed to turn up any mention of progress toward differentiating between the 4 bases (A,C,G,T) as the DNA strand exits the pore. That's going to be quite a challenge, especially with unlabeled DNA, but it's pretty fundamental to this being used directly for sequencing. Looks like it might be great for fragment sizing in the shorter term, though.

      • by brteag00 (987351)
        Yeah, the article just talks about the fabrication and characterization of the nanopores, and demonstrates that they can detect the translocation of single nucleotide pairs. If they had actually been able to identify the nucleotides, it would published somewhere bigger than Nano Letters.
        • On the other hand, fragment sizing is exactly how traditional Sanger sequencing is done. If you could use this to rapidly size a sufficient sample of fragments from each of the four sequencing reactions -- instead of waiting for them to separate electrophoretically -- it could still be quite useful.

    • Thanks for the citation. The most striking thing about the device is that it is non destructive and is reading one DNA/RNA strand at a time one base pair at a time. When you have that level of non destructive access, we could do manipulation at base pair level. Initial break through would be in cutting out the head or tail of a strand by ramping up the tunneling to cut the strand. Then at some point they could come up with devices to snipe out a section of DNA out or splicing DNA from two different strands.
      • Not sure which part of that is scary. I did that yesterday, just not with a nanopore machine.
  • Sounds plausible. (Score:4, Informative)

    by chemicaldave (1776600) on Wednesday December 22, 2010 @02:45PM (#34643774)
    FTFA

    At the heart of the Imperial College device is a silicon chip, with a 50-nanometer nanopore bored through it. DNA strands are propelled at high speed through this hole, and get their coding sequence read by a “tunneling electrode junction” as they come out the other side. This junction consists of a 2-nanometer gap between two platinum wires, with an electrical current passing between them, across the gap. The current interacts with the unique electrical signal given off by each of the DNA strand’s base codes, and the resulting data is then processed by a computer to determine the complete genome sequence. The chips are reportedly quite durable, standing up to repeated uses and washings with no loss in performance.

    Doesn't sound too outrageous. I suppose this is one advantage of only two base pairs.

    • by Zouden (232738)

      Four base pairs.

      • I thought there were four bases that made two pairs. Or does their orientation count? Or am I completely forgetting my high-school biology?
        • by Zouden (232738)

          Yes, the orientation counts because the pairing is (temporarily) broken when the DNA is read by the cell. Only one strand is read.

        • Orientation does indeed count.

          http://www-jmg.ch.cam.ac.uk/tools/magnus/molecules/nucleic/dna1.jpg

          Look closely. Notice assymetric. One of the helixes is not like the other.
  • Dr. OneEye: "We have a match on the Genome of the DNA we found and its a HUMAN"

    Detective BRassBalls: "How did you find it that fast?"

    Dr. OneEye: "With this new Instant Genome from As Seen on TV". "We can solve cases in minutes instead of 40 minutes with commercials and it only cost 19.95 with S&H".

    Detective BRassBalls: "You total NERD. Do you know what you have done?"

    Dr. OneEye: "No What?"

    ---- Later ----

    Detective BRassBalls: "Now we solve cases in 5 minutes with 55 minutes worth of commercials and

  • by nospam007 (722110) * on Wednesday December 22, 2010 @02:57PM (#34643904)

    The first one was also done in 'minutes', 1,051,897 of them.

  • Moore's Law of DNA (Score:5, Insightful)

    by Fractal Dice (696349) on Wednesday December 22, 2010 @03:01PM (#34643956) Journal

    Ignoring any one specific advance in technology, the cost per base pair of sequencing DNA has dropping exponentially. The cost to sequence an entire human genome has gone from billions of dollars in 1990 to about $40,000 in 2010. By 2015, it will probably cross the $1000 barrier.

    By 2020, it will likely be under $100 - at which point it might as well be a standard part of a person's medical file.

    By 2030, it could under $1 - amateur biologists could start collecting genomes like poleroids while hiking.

    By 2040, it could be a fraction of penny - cough on a sensor, get a readout of all the microbes in your lungs, what strain they are and, by looking at the specific mutations between generations and comparing to a database of everyone else's microbes, the likely person who infected you.

    • by swb (14022)

      By 2040, oil will be, what, $500 a barrel -- if there's any "open" market at all and its not all locked up as part of a handful of nations' strategic military reserves.

      Meaning the machine will be so ridiculously expensive to make due to even small dependencies on oil & oil-based products that it will never get built.

      • by omnichad (1198475)

        Oil is what $50/barrel or not far off? Going to $500 is a 10fold increase. Multiplying GP's numbers by 10 doesn't make the huge change that you claim.

      • Energy remains constant at about 10x the minimum wage per "barrel of oil" worth of energy.

        There are many alternatives waiting to come on line at 12x the minimum wage. Some of them are dropping in cost.

        If it is $500 a barrel in 2050, then the minimum wage would be $125 an hour.

        Energy costs have roughly doubled since the mid 80's.

        At current rates (~$8->$16->$32), $32 is a likely rate so a likely cost would be ~$300 a barrel.
        That also fits using oil costs ($80->$160->$320).

        Any time oil gets too ex

      • I imagine a lot of those oil-based products can be done without. Remember there was a time when even electronics came in wooden enclosures. Substitutes would be needed for insulation, component packaging, etc... but it's doable. Natural rubber is not derived from oil, and gets you half way there already. Just need to mix in the right additives.
      • That doesn't make any sense. The economic viability of many different energy sources (which in turn can be used to make plastics) occurs when oil reaches $100 / barrel. At $200 / barrel, there's lot of different sources, and at $400, almost anything will be cheaper.
    • by brteag00 (987351) on Wednesday December 22, 2010 @03:33PM (#34644312)
      I don't argue that the cost-per-base of sequence is dropping dramatically - but comparing the output of an Illumina sequencer [illumina.com] (the tens-of-thousands of dollars pricepoint) to the Human Genome Project is misleading. The reason the HGP cost so much is the quality of the reference sequence they produced - the so-called Bermuda standard [genome.gov], of one error in 10,000 bases. The HGP researchers assembled all those individual sequence reads into an almost unbroken reference of astounding quality and utility.

      In comparison, the sequence data people are producing today is crap. The individual reads are 30-80 base pairs and get put together into contiguous runs of only several thousand bases of length, on average. This is good for some kinds of work, but it doesn't give nearly the same picture of the genome that made the original human genome sequence such a masterpiece.

      (I'm a genomics grad student. Can you tell?)

    • by Plekto (1018050)

      One step closer to the technological singularity.

    • by RandCraw (1047302)

      Make that $1000 for a genome NEXT year, not 2015. The current cost for a genome (at maybe 5x ocersample) from the Beijing Genomics Institute is about $5000 in bulk, and dropping fast. Speed, reagent cost, oversampling, and completeness (e.g. over 95%) are all improving at super linear rates.

      For more, read "The $1000 Genome", printed in mid-2010. It makes clear that gene sequencing technology is The Next Big Thing, and imminent. The question that remains is, how useful will the info prove to be until tec

      • by gringer (252588)

        For now, genomic data is almost entirely a novelty -- mostly good for entertainment value.

        I suspect that it'll get cost-effective for drug companies a bit before it becomes popular for the general public. 'Sequence once, test for ever' is quite an attractive proposition.

        • I imagine a whole lot more attractive to insurance companies - thus the attempts to prohibit the practice before it even comes into use. There are already fears of a future where some people are uninsurable due to genetic predispositions that no insurance company wants to risk playing out.
          • by gringer (252588)

            Everyone has a few hidden DNA defects [independent.co.uk] that would severely impact their health if ever triggered. If insurance companies took this at face value, no one would be insured, and they'd be out of business — a silly position for the companies to take. I would expect that it'd just be factored into their risk analysis, which already includes things with a high heritability (like family history of particular diseases).

            I don't think it's a good idea to give an insurance company your entire genome sequence, but

    • by ignavus (213578)

      Ignoring any one specific advance in technology, the cost per base pair of sequencing DNA has dropping exponentially. The cost to sequence an entire human genome has gone from billions of dollars in 1990 to about $40,000 in 2010. By 2015, it will probably cross the $1000 barrier.

      By 2020, it will likely be under $100 - at which point it might as well be a standard part of a person's medical file.

      By 2030, it could under $1 - amateur biologists could start collecting genomes like poleroids while hiking.

      By 2040, it could be a fraction of penny - cough on a sensor, get a readout of all the microbes in your lungs, what strain they are and, by looking at the specific mutations between generations and comparing to a database of everyone else's microbes, the likely person who infected you.

      So when will it become an iPhone and Android app?

  • 2 years @ $500,000 a year doesn't sound like a lot. In fact it sounds completely implausable for something as valuable as the results they produced. Maybe in the 50's or something.

    I wonder how they came up with that figure? I imagine the lab + scientists alone cost that much to outfit and rent; not to mention lawyers and research assistants

    • by Anonymous Coward

      whats missing is all the RnD to get their
      Like, it costs a billion bucks, give or take, to build a new intel fab plant, but they sell an individual cpu chip for 100 - 1000 order of mag
      So, you are right, this is sort of a reagents +salary cost
      In any event, it is way, way outdated - the newest instruments like the illumina Hiseq gets a genome for 100K (I think)

      However, you really have to ask what is a "complete genome" even today, there are large stretches (sub telomeric repeats, cnetromeres, etc) that are un

  • by glwtta (532858) on Wednesday December 22, 2010 @03:18PM (#34644128) Homepage
    By contrast, when sequencing of the genome of Dr. James Watson (co-discoverer of the structure of DNA) was completed in 2007, it had taken two years and cost US$1 million.

    Yeah, but nowadays it can be done in a few hours and costs under $10,000. May as well say that the Human Genome Project took 13 years and cost $3 billion - true, but not very relevant.

    And we're well on-track for sub-$1,000 genomes in a year or two (without any new breakthrough technologies); which is basically "good enough" for research purposes. As Lincoln Stein pointed out in a recent paper, we're already almost at the point where it costs less to sequence a base pair than it does to store it for computational analysis.
    • by Arcquist (1100065)
      I seem to remember looking into this a while ago and the human genome isn't really as big as I thought it was. According to this nature page [nature.ca] there are 3.4 billion base pairs and since each is only one of 4 values it takes 2-bits per base pair to encode so the entire genome is only 850,000,000 bytes which is 810.6MB (1,048,576 bytes/MB). I don't know about you but the cost to 'store' this in my mind is essentially nothing. There are a ton of places on the web that will easily offer 1GB of storage for free, 1
      • Wouldn't need even that much: almost all of it's the same in every human. All you need to do is agree on a single 'reference human,' and then store genomes as the difference between this reference and the individual. The reference would be 800-ish meg, but after that each person will only be a couple of megabytes extra.
      • by RDW (41497)

        '...the entire genome is only 850,000,000 bytes which is 810.6MB'

        That's about right - the reference assembly from UCSC is 778Mb in their standard .2bit format. That's just a single sequence for each autosomal chromosome plus one each of X and Y, though - you'll need to allow about double that to store your full dipoid genome, so better buy a 2Gb flash drive. On the other hand, if you take the reference sequence as a given and only store the differences between it and yours, you only need about 4Mb!:

        http://w [nih.gov]

      • by glwtta (532858)
        so the entire genome is only 850,000,000 bytes which is 810.6MB

        You'd have to include the sequencing data, not just the final call: a single Solexa run generates about 1TB of data (if memory serves) and you need a couple of those for a full human genome at some reasonable coverage.

        And it was sort of implied that you're doing something useful with the data, not just sticking it on a thumb drive, which means (relatively) expensive SAN disk space, which is still in the dollars per GB area (including backup
  • No more long lines at the gene sequencing place!
    No more frantically pulling everything out of the glove compartment looking for $1 million in change.
    - sigh, that's all I got

  • The base pair sequence is nice, yet there is much more to gene expression than that. Two cloned cats can look and act remarkably differently. In embryology, it is known that the same gene can act differently depending on the timing and circumstances of that gene's activation. So bravo for cheap fast sequences, but we will need to know more about gene expression for genomics to bring big changes to medicine.
  • Last weeks issue of Nature mentions gene hackers [nature.com] who study newly posted human genomes for interesting DNA. We are somewhere in the "third decade" of sequenced human genomes- that is between 100 and 1000 fully sequenced genomes published so far. There are interesting things remaining to be discovered in this huge mass of data.
  • Here's a small detail that the article leaves for the last paragraph:

    “The next step will be to differentiate between different DNA samples and, ultimately, between individual bases within the DNA strand,” said study co-author Dr. Tim Albrecht. “I think we know the way forward, but it is a challenging project and we have to make many more incremental steps before our vision can be realized.”

    In other words, they can zip DNA through this device quickly and measure some signal as the DNA passes through, but no one knows yet whether it is possible to extract accurate sequence information from the signal they get. Similar implementations (that admittedly have a less sensitive way of getting a signal from the different DNA bases) have so far failed to see significant enough differences between the DNA bases to be useful for sequen

  • Nanopore sequencing has been around for at least a decade in the lab. They admit that their method of using tunnel junctions to detect the DNA cannot even distinguish between different base pairs.

    For background, here's the basic idea of a classical nanopore sequencer:

    1. Make a solution with ions in it with a very thin membrane separating two different compartments each containing an electrode. The membrane has a very tiny hole (nanopore)

    2. Apply a voltage. This will either attract or repel the
  • Keep your eye out for Ion Torrent's Personal Genome machine. Reviewed on the same site http://www.gizmag.com/ion-torrent-personal-genome-machine-launched/17330/ [gizmag.com]
  • Membrane - very thin sheet or plate
    Pore - a small hole in the sheet
    current - ions (atoms such as sodium or chloride) per second; in a salt solution, current is carried between the electrodes (usually Platinum wire, or graphite) thru the liquid by ions; these ions have a size of roughly 1 angstrom, so they are, compared to electrons, really big.
    when we measure the current, we are simply measuring the number of ions/second going thru the pore; if the pore has ~ the size of a DNA moleucle, then it seems obv
  • According to [1] the cost of sequencing Watson's genome in 2007 was $2 million, not $1 million! Costs of the "original" genome sequences are often misquoted as well as $3 billion when that was the cost of the entire HGP which included the yeast genomes, the mouse genome and the development of a lot of technology that enable the sequencing of larger genomes. For an estimate of the actual cost of sequencing the original genomes (circa 2001-2003) a better source of information is the total amount of capital

  • If you read TFA, it turns out what they have done so far is drill a tiny hole.

    Everything else is still TBD. Things like:

    (1) Figuring out how to get a thread of DNA to enter the hole.

    (2) Figuring out how to push it through the hole.

    (3) Figuring out how to read the bases, which are electrically equivalent and somewhat shielded by the phosphorous backbones..

    (4) Figuring how to keep DNA and other crud from getting wedged in this nanometer-width hole.

    Somehow I think they're doing this all ba

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