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Biotech Medicine Hardware Technology

A DNA Sequencer Cheap Enough For (Some) Doctors' Offices 136

Posted by timothy
from the soon-next-to-blood-pressure-booth-at-the-store dept.
cylonlover writes "Until recently, DNA decoding machines — fitting in the US$500,000 to $750,000 price range — would take weeks or even months to sequence a human genome, and the whole procedure would cost $5,000 to $10,000. That could be about to change, however, as Life Technologies introduces the Benchtop Ion Proton Sequencer — a machine that may finally deliver the power of genetics into the hands of ordinary doctors thanks to its $149,000 price tag and ability to decode a human genome in one day at a cost of $1,000."
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A DNA Sequencer Cheap Enough For (Some) Doctors' Offices

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  • by bonch (38532) * on Saturday January 14, 2012 @01:49AM (#38695404)

    Warning--side effects may occur [imgur.com].

    • by grantek (979387) on Saturday January 14, 2012 @01:58AM (#38695432)

      This is a completely different machine, it's not the one that TSA agents will use to remotely scan your DNA...

      • by AHuxley (892839)
        Give blood for a US visa? They can look for the strength of your VMAT2 (God Gene, spiritual experiences) gene.
        If you light up, your fanatic potential is noted.
        • In Dead Space 2 the Unitologists would do various physical and psychological tests on prospective members to weed out the skeptics.

      • by justforgetme (1814588) on Saturday January 14, 2012 @03:06AM (#38695642) Homepage

        omg, the days of GATTACA are finally here! Now I'll never fly to mars ${sadface}

        • You may still fly to Mars! But best give up on Jupiter; your heart is crap.
        • Weren't they going to Titan in Gattaca?

          FWIW, $1000 is still somewhat expensive and it's just scanning genes at the moment. It's not actively messing with the genes of a zygote as was happening in Gattaca.

          For the moment, anyway.

          • by zippthorne (748122) on Saturday January 14, 2012 @10:37AM (#38697330) Journal

            Half of what was happening in Gattaca. Not even the interesting half.

            Messing with genes was the logical response to the first half, though, which was gene discrimination. Or did you not notice that the main character was smart enough and driven enough to become a rocket engineer, but because of a chance of a flaw in other areas was relegated to menial labor.

            It's not just that they wouldn't let him be an astronaut, either. They wouldn't even hire him as an engineer at all, as a "bad risk." And his love-life was implied to have suffered as well, with the matchmaking sequencers on every street corner....

            The movie was about the horrors of discrimination, and the virtue of overcoming them, not gene manipulation, which is not a necessary precondition to gene discrimination. Regardless, I think it was probably supposed to be an allegory to present-day race discrimination, but with a narrative trick to make the character white, so white people wouldn't have any preconceived notions getting in the way of the message, rather than a direct prediction of the future, however prescient it may appear to have been.

            • That's a very good post. Someone mod parent up, please!

            • by mrops (927562)

              Gene discrimination has been happening for ever, some call it Evolution.

            • Whie I like your general points on the movie, if Gattaca's biotech was so advanced, why could the protagonist not just alter his own DNA etc.? Or maybe Gattaca's biotech was not really as advanced as one might think?

    • It turns you into Jeff Goldblum?

    • They also conveniently forget to mention the "side effect" that you need a $75,000 computer setup to analyze the data the $149,000 machine spits out. So in reality, this is actually a $225,000 machine, plus an IT person to manage the hardware.

  • Hospitals (Score:2, Insightful)

    by Anonymous Coward

    I predict that the first buyers will be University research hospitals, and the Mayo Clinic.

    It needs to drop a bit more before seeing it at your local pediatrician's.

    • by jamstar7 (694492)
      Love to scam one of these puppies up when the price drops to a couple K. Especially if it has a 'write mode' as well.

      Think 'gene hacking' as the next 'nerd' occupation...
    • Re:Hospitals (Score:5, Interesting)

      by bill_mcgonigle (4333) * on Saturday January 14, 2012 @03:37AM (#38695756) Homepage Journal

      It needs to drop a bit more before seeing it at your local pediatrician's.

      And I'm not sure that it ever will. How long has generating a CBC been a solved science? But the pediatrician will still send you over to the hospital's phlebotomy lab to get one.

      I guess they do do instant strep tests in the office. When a DNA sequence costs $15 including equipment perhaps they'll do it.

      • by cperciva (102828)

        The only reason they do instant strep tests at MD offices is that they want to know the results before you walk out the door. The same goes for rapid STD tests: If you walk out the door and have to come back to get the results later, there's a chance you won't return.

        A DNA test is the ultimate in non-urgent tests, and is going to remain something you head off to the phlebotomist to get done... right up until the day where they are done routinely at birth and you leave the hospital jugging a baby, birth cer

        • by RDW (41497)

          ... right up until the day where they are done routinely at birth and you leave the hospital jugging a baby, birth certificate, and a flash drive containing its DNA sequence.

          Which might happen sooner rather than later:

          http://www.forbes.com/sites/matthewherper/2012/01/10/not-quite-the-1000-genome-but-maybe-close-enough/ [forbes.com]

          "Yale geneticist Richard Lifton, who was the first to document the use a DNA sequence to diagnose a disease, is looking at utilising the Proton for clinical work. In the state of Connecticut, where Yale is based, infants are tested for 43 different genetic mutations that need to be detected early in infancy. The Proton could be a better way to do that that tradit

        • by timeOday (582209)
          Why wait until birth? If your DNA doesn't pass muster, you'll probably be rejected as a zygote and head off to the incinerator with 99% of your siblings.
  • by Anonymous Coward on Saturday January 14, 2012 @02:25AM (#38695504)

    There are two unfortunate challenges that the Ion Proton approach hasn't yet solved. The first is that the steps required to get the DNA out of human cells and into the sequencer (DNA extraction and especially library preparation) are still frustratingly complex. Their OneTouch device simplifies parts of the library prep but there are still many steps that require highly skilled people doing hours to days of work.
    The second major issue is that the genome is being read out in fragments of 200-400 nucleotides, then needs to be assembled. The human genome is full of repetitive regions that are much longer than 200-400nt and when one gets a sequence read from one of these regions, it's can be very difficult to determine which of the copies of the repeat region that sequence came from. Better statistical models and algorithms for genome assembly may solve this to some extent, but there are fundamental limits to what can be done with short sequence reads. Other sequencing technologies don't suffer the short read problem, Pacific Biosciences' hardware for example can read several thousand nucleotide fragments. Mate pairing strategies might be used on the Ion instrument but the library prep for these involves considerably more challenging and manual lab work.

    • by ColdWetDog (752185) on Saturday January 14, 2012 @02:41AM (#38695560) Homepage

      The third problem (once you solve the first two) is what the hell you do with all that information. At present, having a complete readout of your genome doesn't get you very far. Even after you've figured out what diseases that you are more at risk for, what do you do? Well, you keep an active, healthy lifestyle, drink in moderation, don't smoke etc. You didn't need all of that info for me to tell you that.

      I don't see this in doctor's offices (except for the boutique practices that do everything to / for you for the specific purposes of lightening your wallet). Maybe it will allow smaller research groups to tackle projects that they couldn't afford to do. But it's a long way to clinical utility.

      • by Samantha Wright (1324923) on Saturday January 14, 2012 @03:11AM (#38695670) Homepage Journal
        You archive it until you need it. A situation-specific microarray might cost a hundred dollars; those tend to stack up with every hospital visit. With whole exome sequencing like this, you pay the fee once, and have all* the data medical science will ever need about you.

        * Not counting repetitive elements, promoter regions, UTRs, spacer DNA, or the epigenome, all of which are known to describe at least a few diseases.
      • Re: (Score:2, Informative)

        by Anonymous Coward

        The third problem (once you solve the first two) is what the hell you do with all that information. But it's a long way to clinical utility.

        Well, if by "long way" you mean five years, then yes, it's a long way.

        On the other hand, in five year when this technology gets of the ground, it will transform diagnostic medicine in the same way that the automobile transformed personal transportation.

        One huge application is diagnosis of infectious disease. Not only will you know whether what you have is viral or bacterial, if it's bacterial you'll know exactly which antibiotics will work. And you'll probably even be able to correlate you infection with kn

        • by Rutulian (171771)

          One huge application is diagnosis of infectious disease. Not only will you know whether what you have is viral or bacterial, if it's bacterial you'll know exactly which antibiotics will work. And you'll probably even be able to correlate you infection with known outbreaks: "There's been 50 other infections with this pathogens in the northeast corner of this city over the last two weeks."

          I think you're overselling this a bit. Sequencing a human genome is not going to tell you whether you are infected with a pathogen, and it won't identify the pathogen. To do that, you will need to isolate the organism and sequence it that way. Also, having the genome of an organism does not automatically make it easier to determine things like antibiotic resistance. In some ways it makes it more difficult, because you have too much information. High throughput sequencing is definitely a great advance for th

          • by Pseudonym (62607)

            Sequencing a human genome is not going to tell you whether you are infected with a pathogen, and it won't identify the pathogen. To do that, you will need to isolate the organism and sequence it that way.

            Actually, you may not need to isolate the organism at all. If you really had a "just stick a sample in the machine"-type reader (which this box isn't), and copy of a few human reference genomes and a library of known pathogens, you could separate the reads just using simple statistics. We do this today with mixtures such as gut flora samples or cancer xenografts with varying degrees of success. The statistical models are getting better every day, though.

            Of course, what constitutes an "infection" is partly c

      • by cthlptlk (210435)

        There is a very real use case for genomics in the treatment of disease: drug-gene interaction. Just as certain mutations suggest a higher risk for certain diseases, certain mutations also reduce the probability that certain drugs don't work. For example, plavix must be metabolized, so the 15% (or so, can't remember) of people who can't metabolize it should take something else. And there's a well known genetic marker for that.

        Of course, that doesn't mean that the test should happen in a doctor's office, and

    • by Samantha Wright (1324923) on Saturday January 14, 2012 @03:09AM (#38695658) Homepage Journal
      Pacbio promises a trillion unicorn farts per second. It's hard to take them seriously. As far as medical applications are concerned, the read length in the Ion Torrent system is ten times the size it needs to be, since most (known) diseases occur due to mutations in the very specific and non-repetitive exome, or in its close vicinity. No one (that I know of) has ever seriously proposed using this hardware for de novo sequencing of large eukaryotes, especially since the machine currently on offer doesn't have the well capacity to sequence the whole human genome!

      That being said, there's always paired-end reads. I'm guessing the protocol for doing so with this system doesn't exist yet, but they tend to solve most of the repetitiveness problems for shorter read lengths.
      • by backslashdot (95548) on Saturday January 14, 2012 @03:49AM (#38695794)

        "the read length in the Ion Torrent system is ten times the size it needs to be"

        Uh no. Not at all.

        "most (known) diseases occur due to mutations in the very specific and non-repetitive exome"

        The problem is that if it does occur outside of this, there's be no way to tell where exactly it is. Second, even if it is within the non-repetitive region .. a mutation could make matching the sequences difficult since it wouldn't be certain if you're dealing with an overlap or a mutation. The reason most known diseases occur due to mutations in non repetitive areas is because those are the easiest areas to detect. The unknown diseases probably occupy the other spots.

        For disease specific mutations such as cancer the only way to detect the mutations is with long reads. If you want to cure cancer there needs to be a way to do long reads with single cell sequencing.

        • by RDW (41497)

          For disease specific mutations such as cancer the only way to detect the mutations is with long reads.

          This really isn't true. Though it would be nicer to have longer reads, short read sequencing (exomes or whole genomes) is actually proving to be very successful at picking up many novel mutations in cancer. Discovering tumour-specific somatic mutations is a particularly nice application for this technology, as you can often do a direct pairwise comparison with the patient's normal germline DNA (e.g. blood DNA if you're working with solid tumours). Typically results will be validated by another technique (e.

        • As I said in my journal, I think the gains from the Ion Torrent read length vs. the SOLiD read length (about 10x) don't do as much to probe the depths of repetitive regions as is necessary to be super-useful. Most of what's lost can be made up for with increased coverage. (Insert theoretical and inauthentic-sounding statement about combinatorial magnitude here.) Of course, it only takes one example of two genes a few hundred bp apart with a couple of SINEs in the middle to prove me wrong. :)
          • by Pseudonym (62607)

            I am not a biologist, but I am a bioinformatician. So I can BS about combinatorics slightly more convincingly.

            Even though de novo assembly for most medical diagnostic purposes is a waste of time, I should point out that most de novo assemblers (including ours) split up long reads into short reads for error correction, then piece the reads back together. In that sense, if all you want to do is find SNPs or other small variants, read length is irrelevant given the same coverage, especially compared to the bia

            • Yeah, I'm a bioinformatician too, not really a biologist, but I figured I should keep it obvious for my signature. :) And yeah, you raise a very good point about de novo techniques; velvet will go as short as 5 bp when it wants to really get something done, as I recall.
    • by lbbros (900904)

      There's another problem to bear in mind: coverage. What is coverage exactly? In terms of "next generation sequencing" (to which this machine belongs to) is how well a part of the genome is covered (sequenced), and that in turns means that the number of fragments (100-150 in the case of Ion Torrent) read for a specific region must be high as possible (those are called "reads").

      A good coverage allows you ensure that what you're seeing is real and not some sequencing errors (all technologies suffer from certai

    • by mapkinase (958129)

      PacBio produces a lot of errors.

    • by Pseudonym (62607)

      You're completely right about sample prep. It's not like you can just bleed into the machine and results an hour later.

      On read length, though, a few hundred nt is probably fine for 90+% of diagnostic tasks, given that we have lots of reference human genomes already. Unless it's a cancer biopsy (and sometimes not even then), any sample processed in a doctor's surgery or consumer pathology lab doesn't need to be assembled de novo. Alignment plus statistics will probably do the job just fine.

      Another applicatio

  • The Ion Proton Sequencer uses analysis software called Ion Reporter to analyze the data of a single genome on a single server. This speeds up the process considerably and removes the IT-related bottlenecks

    Genius! A cluster of computers is an obvious bottleneck and they have made the step of getting a single server to do all the work. I hope they have a patent on that idea.

    However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation of Ion Torrent semiconductor chip technology.

    Oh. Right. So this is really just using _better_ hardware to do the job.

    • by lbbros (900904)
      In fact, I think it's just hype. To do proper analysis runs you *need* parallel computing, as these tasks are primarily CPU bound. But a whole load of RAM doesn't hurt, either, especially if you analyze more than one genome at once.
    • by RDW (41497)

      Reports elsewhere suggest they'll be selling a "$75,000 server" with this machine, which will apparently be able to spit out a fully processed whole genome in a day, and lets them market the whole thing as an 'appliance'. This will be enough for many labs. But if the Proton is anything like their previous sequencer, the unaligned sequence data will just be in a standard text file format that can be uploaded to the local cluster (if you have one) and processed any way you like. Large genome centres may go th

      • Yes, and I'm betting that $75k server has just a few processor cores in it, which really takes care of the parallel computing problem nicely.
        I'm guessing for that kind of money, it's probably a quad core, 4 CPU machine, at least. I can't imagine it needing enough storage to burn through $60,000+ worth of hard drives, so it's got to be a monster processing machine.
        My wife (yes, there are married slashdotters!!!) currently works with the previous instrument that Ion Torrent released, about a year ago. It us

  • by jcr (53032) <[jcr] [at] [mac.com]> on Saturday January 14, 2012 @02:34AM (#38695534) Journal

    A hundred and fifty grand doesn't sound like a whole lot of money for medical equipment.

    -jcr

  • Yay, progress! (Score:3, Insightful)

    by martin-boundary (547041) on Saturday January 14, 2012 @02:37AM (#38695546)
    Patient: "So, snif, bhat dh'you bheckon I habh, snif, bhoctor?"

    Doctor: "Well, it looks like you have a common cold. But let's be sure, shall we? I just got this new DNA sequencing machine. Come back tomorrow."

    The next day...

    Patient: "Hebho bhoctor, bhat dho I habh?"

    Doctor: "Well, it looks like you have a common cold. That will be $1000."

    • by guttentag (313541)

      Patient: "Hebho bhoctor, bhat dho I habh?"

      Doctor: "Well, it looks like you have a genetic predisposition to paying exorbitant sums of money for things you don't need. It's called Gullibility. Don't be so sad, it's very common in this country, like a cancer! Just remember that even though it eats some people alive, some people survive! You just need to have balls like Lance Armstrong, avoid drugs and wear yellow shirts in the summertime. That will be $1000. Now that I know what to look for, I can zero in on this and accurately determine the likeliho

    • Huh? In what way does the cold virus alter your DNA, such that a DNA sequencing machine could be used to diagnose it? And you know, doctors currently have all sorts of diagnostic tests at hand that could be used unnecessarily, yet I've never heard of doctors using an x-ray, EKG, MRI, or anything of the sort to diagnose a cold.

      Yeah, I know, it was probably a joke and not meant to be taken seriously, but your score was +3 Insightful, not +3 Funny.

    • by timeOday (582209)
      Alternately, "I'm afraid you have Bird Flu, please come with me!"

      The reason "the common cold" hasn't been cured is because "it" is actually hundreds of different virii. If only there were a way to tell which is which...

      In the future the doctor will swab your throat, upload some markers, and the next day the correct prescription (from hundreds) will be FedEx'd to your door.

  • by nbauman (624611) on Saturday January 14, 2012 @03:06AM (#38695640) Homepage Journal

    Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

    "What am I supposed to do with that?"

    Years ago, people thought that we could find Mendelian genes for all the important things in health and disease. Now it turns out that most of the important things we want to know are controlled by hundreds or thousands of genes, each of which increases the risk by 1%, sometimes less. That's for things like cholesterol, autoimmune diseases, cancer susceptibility, etc.

    For the most part, your family history is a better predictor than any genome screening. Gene tests usually aren't useful unless you have a particular gene in your family and you want to find out whether you have it, like the BRCA genes for breast cancer. If your mother died of breast cancer at age 40 because of the BRCA1 gene, and you don't have the BRCA1 gene, you don't have to worry.

    • by EnsilZah (575600)

      Well, obviously you don't bring the raw data to your doctor.
      How about you run it through some statistics software and it gives you a list, 5% increased chance for breast cancer, 7% chance of heart attack by age 50, then your doctor can suggest more frequent checkups, changes in diet.

      How about this, your government subsidizes a sequencing for every individual (I know getting into Gattaca territory here, also Americans would scream 'socialism!'), say in reverse order, oldest to youngest until you can do one a

      • by nbauman (624611)

        OK, you run it through this wonderful statistics software and it gives you a list.

        Your doctor says, "Normally you would have a 10% chance of getting breast cancer (when you're still young enough that treating it would make a difference), so you should get a mammogram every 2 years. But you have a 5% increased chance for breast cancer, so you have a 10.5% chance of getting breast cancer. You *really* should get a mammogram every 2 years."

        There is an increasing list of mutations that really do make a signific

    • by pesho (843750) on Saturday January 14, 2012 @03:52AM (#38695802)

      Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

      "What am I supposed to do with that?"

      You hit the nail on the head. There is very little if any useful information for a doctor in full genome sequence, and most of it can be obtained with much cheaper genetic tests. ABI is ramping up the hype because they really need this instrument to be a good seller. Their first bet in the field was on a sequencing by ligation machine (SOLID) which did not sell very well.

    • Yes, you bring your doctor a thumb drive with 3 billion base pairs of your genome, coding for 23,000 genes. Do you know what he says?

      "What am I supposed to do with that?"

      Maybe you should get a doctor that knows what an USB thumb drive is?

      Then you can move onto the next problem.... (who's your daddy?)

  • I know someone who (was) married to a guy who's only 26 and he makes six figures selling some sort of medical machine. Apparently he plays video games all the time and is lazy and just works sparingly and travels a few times a month. You have to wonder about how much mark up is on these medical machines if a guy who works only only a few days a week or month with little schooling can earn 6 figures in commissions

  • FTFA: "However, the most important factor in reducing the sequencing speed so dramatically is the introduction of the next generation of Ion Torrent semiconductor chip technology."

    Shouldn't it be increasing sequencing speed, or reducing sequencing time?
  • by JustNiz (692889)

    Now my doctor can make some interesting mutant fish for the aquarium in his waiting room..

  • we are about to be served with a "let's look at your DNA" at every visit for completely unrelated diseases in every possible scenario possible. This is going to get annoying very fast

  • Just curious since I remember reading, admittedly on a blog, somebody take that "It takes X dollars to do 1 MRI" statement on. Basically the idea was that MRI's have a huge fixed cost. (IE you have to pay for the machine and tech before you do even the first MRI) However the additional cost from each MRI was basically nothing.(Since the machine has to be already there, it's going to use the same amount of power no matter what and the tech has to be there.) So from an economic point of view it didn't make se
    • by RDW (41497)

      'Is the deal the same with this sequencer? (IE once you have the machine and the guy to run it a single sequence basically costs nothing.)

      No, the $1000 (or whatever the figure turns out to be) is just for consumables. You need to spend this on every run.

    • by alphatel (1450715) *

      Just curious since I remember reading, admittedly on a blog, somebody take that "It takes X dollars to do 1 MRI" statement

      The DNA sequencing table [dnasequencing.org] shows a precipitous drop in costs down below $10,000 and under .10 per genome or check the latest genome chart [genome.gov]. However this cost only calculates raw full human sequence not just a particular strand or some desktop device that does limited work.

  • A DNA scan of all bacteria/virus from patients with infections would be boon to public health. I can think of two good reasons it should be free to do DNA scans on every patient with an infection. Tabulating the data to watch for the spread of a desease. Studying the changes in bacteria/virus DNA as they develop resistances to treatments. I can also think of three good ways to pay for it. The government wanting to control desease outbreaks. Researchers wanting data for research. Pharmaceutical companies w

  • It's nice that the price of using DNA sequencing technology is coming down, but I have a question:

    So what?

    Doctors aren't trained to use DNA sequencing equipment. And even if they were, how many disorders can be diagnosed by gene sequencing? Other than confirmation of genetically carried disorders, gene sequencing would never even be able to help diagnose anything.

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