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Medicine Biotech Science

Personal DNA Sequencing Machine One Step Closer 65

Posted by timothy from the who-the-hell-are-you? dept.
oxide7 writes "A new, low cost semiconductor-based gene sequencing machine has been developed and may unlock the door to advanced medicines and life itself. A team led by Jonathan Rothberg of Ion Torrent in Guilford, Conn is working on a system which uses semiconductors to decode DNA, dramatically reducing costs and taking them closer to being able to reach the goal of a $1000 human genome test. The current optical based system costs around $49000 and is already on the market and being used in over 40 countries."
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Personal DNA Sequencing Machine One Step Closer More

Personal DNA Sequencing Machine One Step Closer

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  • It's about time.

    • and life itself.

      Agreed! Finally, LIFE!

    • You know it's coming: it'll be an attachment for the iPhone. (not an iPhan)

      • No, no. This is DEFINITELY an Android app...

      • Re: (Score:1)

        by luceth ( 2407120 )
        Actually, the Ion Torrent PGM has an iPod dock. In fact, it comes with an iPod in the box. Yes, really. See, for example, this link. [slashgear.com] Sadly, they don't have an iPod app yet - they were more focused on getting the product to market. (Yes, my lab has one.)

        • Re: (Score:2)

          by RDW ( 41497 )

          The world's most expensive iPod dock and it doesn't even come with speakers :-)

          How are you finding it? Looks useful for smaller -scale (subgenomic or bug) projects where the capacity of a bigger machine would be wasted. And the concept of a 'massively parallel pH meter' is certainly cool.

          For human whole-genome stuff there are already relatively cheap options. Illumina now offers a genome service for $4000 per sample in quantity:

          http://www.bio-itworld.com/news/05/09/2011/Illumina-announces-five-thousand-doll [bio-itworld.com]

          • Re: (Score:1)

            by luceth ( 2407120 )
            Well, it was just installed a few weeks ago - hasn't seen a whole lot of use yet, so not too many experiences on which to base an opinion. A single run costs ~$400 (an order of magnitude less than an Illumina Hi-Seq run!), but only gets you 10-20 million bases of sequence. (A human genome has ~3 billion bases, and you need ~10-fold coverage to make sure you get each base. In the Nature paper, they sequenced Gordon Moore's genome - and it took about 1000 chips to do it.) There's some talk of using it to
  • From the short video on their site [jivesoftware.com] (youtube alternate [youtube.com]), it appears that this technology relies on a DNA template across thousands or millions of wells on a chip that emits hydrogen ions every time a base is incorporated into a DNA strand by a polymerase. I'm not a biologist but it looks like a pretty neat idea and I certainly hope it works as well as they say it does. I guess even if your sensor isn't that great at classifying between A, G, C or T then you can just build more wells on the chip and look at the statistics. I'm not sure how they ensure that one process is going on in each cell but I'm hoping this yields some cheap and fast accuracy. This would be a huge boon for research -- hell you could start up some hobby work very quickly and (relatively) cheaply since it's such a straight forward process.

    • hell you could start up some hobby work very quickly and (relatively) cheaply since it's such a straight forward process.

      They're hoping to get the cost down for a total organism sequence to around $1000. That's one hell of an expensive hobby even before you start asking yourself what you plan to do with that rather impressive amount of information. I suppose you could use it to blackmail your family and friends by turning up all sorts of paternity issues - whatever floats your boat.

      Researchers, OTOH, should be very happy about the trend.

      • Re:Essentially a Proprietary Hydrogen Ion Sensor (Score:4, Interesting)

        by fuzzyfuzzyfungus ( 1223518 ) on Saturday July 23, 2011 @08:55PM (#36860232) Journal
        You can already do most paternity and forensics stuff, to a quite usable degree of confidence, with much smaller snippets. Trying to do so on the very cheap might well get you results from a lab that can't be bothered with minor stuff like negative controls or not fucking up on a regular basis(luckily, this never, ever, ever happens at crime labs); but you can get it today, cheap. Here's an over-the-counter option for $150 [cvs.com](no particular endorsement implied, of course, just an example of what you can find in totally mainstream shops with 30 seconds of searching...)

        Whole-organism sequencing will likely remain a research tool for quite some time. The snippet-based stuff is already as or more accurate than the people doing it, and whole-organism for medical purposes will be largely snake oil(although there will certainly be people selling it) until we actually have the knowledge necessary to make meaningful inferences from those sequences.

        • and whole-organism for medical purposes will be largely snake oil(although there will certainly be people selling it) until we actually have the knowledge necessary to make meaningful inferences from those sequences.

          It's called statistics. Research is an important part of medicine. Really cheap whole genome analysis will let you more easily and cheaply find the short sequence test you want to make as a diagnostic, and if lucky clue you into the metabolic pathway involved leading to a place to start with drug design or which drug to try for off-label treatment of rarer genetic diseases or deficiencies. Or you can test to see what genetic factors are associated with side effects or particular efficiency of a drug compoun

      • Re: (Score:2)

        by Xemu ( 50595 )

        They're hoping to get the cost down for a total organism sequence to around $1000. That's one hell of an expensive hobby even before you start asking yourself what you plan to do with that rather impressive amount of information.

        www.meet-your-genetic-match.com

        You heard it here first.

    • Time to view all news through an Evil filter.

      Nice try for these guys coming up with tech. Now the Insurance companies will require one so they can save $50,000 per "hit" on a "predisposed condition".

      Hello, Gattaca.

    • Re: (Score:1)

      by Anonymous Coward

      The problem at this moment is that no machine is able to meet all of the criteria set by the gold standard Sanger technology. Sanger gave long reads with high accuracy which gave good assemblies but was terribly expensive and slow. The new technologies tend to focus on high throughput (gigabases of raw sequence) at the expense of read length and accuracy. Imagine trying to assemble a 4 Gb genome from 200 Gb of 100 bp fragments (or less) and suddenly it doesn't look quite as cost effective. Some of the n

    • Each well is just large enough to allow one microsphere in it. This microshpere has copies of the DNA to be sequenced attached to it. Each of the 4 bases are then added to the chip one at that time and the pH is measured. When a nucleotide is incorporated it changes the pH and the signal is recorded. The $50K pricetag is a little decieving, you also need the machinery to produce the DNA coated microspheres and a hefty server to process the millions of ~100 base reads form the machine and assemble them into

    • Re: (Score:1)

      by mlvlvr ( 617395 )
      The technology deposits DNA fragments, many copies of a single fragment, in each of millions of wells on a chip. A, G, C, or T are flooded over the chip sequentially, and if one is incorporated by the polymerase, the reaction, not the chip, emits a proton and the sensor beneath each well picks up the change in voltage. The cycle is repeated hundreds of times, until the end of the fragment is reached or the quality of the reads falls off. Lets say you get a few million fragments of a few hundred basepa

  • Gaaa the numbers are all wrong (Score:1)

    by Anonymous Coward

    it does not cost $49000 to sequence a human genome. it's cheaper than $1000. this system is more expensive than current models. The difference is that this has some hope of having more headroom to mature. But eventually it's going to come down to whichever method has cheaper pre-processing. in the long run the machines will be cheap.

  • ... police cars near you.

  • This sounds great and all, but can someone please explain to me what this will mean for those that get the test done and have their genome on a flash drive? I can understand yeah you might have male pattern baldness or increased risk of cancer, etc but there are other ways of determining that currently including yearly blood tests and the like.

    What will having your genome sequenced actually do for you, today, right now? Why should I pay $1k or even $50k for something like this?

    • Re:Sounds great? (Score:4, Insightful)

      by ColdWetDog ( 752185 ) on Saturday July 23, 2011 @08:49PM (#36860210) Homepage

      What will having your genome sequenced actually do for you, today, right now? Why should I pay $1k or even $50k for something like this?

      Virtually nothing. There have been several companies that have tried to cash in on the 'personal genomics' craze (23andMe comes to mind) that actually didn't do a whole sequence, just SNP [ornl.gov] (single nucleotide polymorphisms) that purported to help you determine your risk of various diseases. Except that they found precious few diseases that had clear links to SNPs. Whole genome sequencing will be even harder to figure out.

      So other than bragging rights, it does you little good. For research purposes, getting fast, accurate (and see the AC's post above concerning the Sanger Method and accuracy) and cheap sequences will be very useful. For personal use, not so much.

      • Re: (Score:2)

        by Rich0 ( 548339 )

        In the 1950s computer scientists speculated on the creation of computers that wouldn't cost millions of dollars and fill entire rooms. Imagine what such power in the hands of the individual consumer could bring!

        However, this was completely silly thinking. As anybody who actually had access to a computer knew, being able to program one was far beyond the reach of individual consumers. No, computers are strictly the domain of research, and have little practical use for individuals.

        Or, perhaps what is the d

        • Re: (Score:2)

          by Urkki ( 668283 )

          If we ignore that GPP talked about "today, right now", then home gene sequencing alone will be of very little use, just like home computers alone were of very little use except as a hobby for a decade or so. However, once we have molecular construction machinery available, then we can have customized drugs (including, but not limited to the medicine kind...) made at home. But that's quite a few decades away, possibly not happening in this century, and most likely will be illegal as long as corporations rule

          • Re: (Score:2)

            by Rich0 ( 548339 )

            Well, you don't need to make your own drugs to benefit - we already have some knowledge about the correlation between genetics and response to commercially-available drugs. If this were expanded there would probably be a greater variety of drugs on the market, since it would be easier to get them approved (once you figure out who gets the side-effects vs the benefit you can just make the indication "... in people with SNPs x,y,z").

            Home chemical synthesis is an entirely different technology, and might somed

    • Testing for genetic differences that lead to well characterized diseases are better done methods other than sequencing. Methods such as real time PCR and microarray analysis costs large amounts of money to set up and validate but are much cheaper once they are up and running. This is why places like 32andme are $400 and not $1000s. The power of next gen sequencing like ion torrent is that you can go fishing for things you don't know about. Deep sequencing is a good example. Many cancers result from spontane

    • Re: (Score:2)

      by julesh ( 229690 )

      There are two things:

      1. Full genome sequences are useful for research. Lowering the cost opens up new avenues of research (e.g. comparing genomes of thousands of individuals, rather than the much smaller samples used today). Imagine performing automated correlation tests on, say, ten thousand sufferers of a particular disease versus ten thousand control subjects. The results could be quite interesting.

      2. Patented genetic tests normally work by patenting a method of isolating a particular gene and determi

  • There are at least 8 bases in the DNA sequence and this will be only looking for 4 of them
    http://www.sciencedaily.com/releases/2011/07/110721142408.htm [sciencedaily.com]
    • Your article talks about methylated bases [wikimedia.org] - the basic DNA base pairs that have been modified AFTER replication. And you are correct, non of the sequencing methods (AFAIK) can determine the extent of methylation or demethylation of a given base. This is likely to be rather important although the mechanism and the level of importance has yet to be determined.

      • If by "sequencing method" you mean the whole process from wet lab to assembly, then we can indeed detect methylation. Look up, for example, methylation-specific PCR.

    • Re: (Score:2)

      by julesh ( 229690 )

      Yes, but as methylation of DNA is not preserved when the DNA is duplicated, any effects of these additional bases are only localised. AIUI, different cells in your body will have different methylation states. This means that the information about which precise bases are methylated is not especially useful for most things you would want a gene sequence for. It's important for those studying internal cell processes, especially DNA repair, but otherwise not really interesting.

  • Not sequencing of course, but checks a whole lot of SNPs. I've been quite happy with the information you can get, and you can download all the data yourself.

    Problem is, once you get the sequence, it's hard to know what to do with it.

  • the dawn of hype itself! (Score:3)

    by tverbeek ( 457094 ) on Saturday July 23, 2011 @09:25PM (#36860312) Homepage

    "...may unlock the door to ...life itself"

    Well, it's about time! The universe has been sitting lifeless for so long, and here we sit, unable to make any!

  • Personal DNA Machine (Score:4, Funny)

    by hyades1 ( 1149581 ) <hyades1@hotmail.com> on Saturday July 23, 2011 @11:32PM (#36860654)

    For the love of god, don't let one of those machines find its way into the southern United States. Can you imagine what damage it would do to the family trees if they had ironclad proof of how many hillbillies didn't understand that even if they got divorced, they're still brother and sister?

    • Here it is, bigotry and hatred, right out on display in public and modded funny. Disgraceful.

    • For the love of god, don't let one of those machines find its way into the southern United States. Can you imagine what damage it would do to the family trees if they had ironclad proof of how many hillbillies didn't understand that even if they got divorced, they're still brother and sister?

      After divorce, your wife becomes your sister?

  • Gattaca, Gattaca, Gattaca !

  • The summary says:

    A team led by Jonathan Rothberg of Ion Torrent in Guilford, Conn is working on a system which uses semiconductors to decode DNA, dramatically reducing costs and taking them closer to being able to reach the goal of a $1000 human genome test. The current optical based system costs around $49000 and is already on the market and being used in over 40 countries.

    Unfortunately this summary is missing two crucial sentences (between the above two) from the article:

    Typical DNA sequencing machines use optical technology instead of semi-conductors. While fast, optical technology is expensive and complex.

    Without the above sentence, the summary sounds like Ion Torrent sells "[t]he current optical based system" which they do not. (However, it is true that Ion Torrent is part of another company (Life Technologies) that does in fact sell an optics-based system called SOLiD.)

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