Slashdot stories can be listened to in audio form via an RSS feed, as read by our own robotic overlord.

 



Forgot your password?
typodupeerror
Medicine Hardware Science Technology

The Next Revolution In Medicine: Genome Scans For Everyone 126

Posted by Soulskill
from the don't-tell-the-TSA-about-this dept.
the_newsbeagle writes "This year, a biotech company called Ion Torrent will introduce a new chip for its genome sequencing machine, which should enable researchers and doctors to scan a complete human genome for $1000 and in just a couple of hours. Compare that to the effort required to complete the first human genome: $3 billion and 13 years. Ion Torrent has nearly reached the $1000-genome milestone by virtue of a process called 'semiconductor sequencing,' and the company's founder says his chip-based sequencing machine benefits from all the efficiencies of the computer industry. At a price point of $1000, genome scans could become a routine part of medicine. And the price could keep dropping. To test out the technology, and to investigate just how useful genome scans are these days for your typical, reasonably healthy person, the IEEE Spectrum reporter got her own genome scanned and analyzed."
This discussion has been archived. No new comments can be posted.

The Next Revolution In Medicine: Genome Scans For Everyone

Comments Filter:
  • by ColdWetDog (752185) on Friday March 01, 2013 @11:46AM (#43046127) Homepage

    Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table. It will become a very important part of medical research, but in terms of an individual's health, not so much.

    It will be hyped. It will likely end up like 'full body CT scans" - a bragging tool for the seriously hypochondriac but of no help to the routine patient.

    Even the Single Nucleotide Polymorphism (SNP) data which is pretty cheap now (basically what the police use for forensics) helps most people very little. In the context of answering a specific genetic question, perhaps - but not as a routine. When you send someone to a medical geneticist, most of the time and effort revolves around getting the person to understand what you are trying to accomplish and the pros and cons of doing so. Having whole genome sequencing just makes it even harder.

    • by pesho (843750) on Friday March 01, 2013 @11:49AM (#43046177)

      Price isn't the only determinant of whether something is a 'routine part of medicine'.

      yes it is, do you know how much money your doctor can make by adding this to your routine blood work?

      • Consider this is only $1000, which is extremely cheap for a medical procedure, and it is only done once. Compare that to the cost of MRI scans, which run about $3,000 a pop at a hospital, with patients routinely getting multiple scans.
        • by Tarsir (1175373)
          $1000 is what it will cost the hospital. You'll see a $10,000 charge on your bill.
          • Only 10X the cost? The latest Time magazine was devoted to Health Care in the US. Most of it was bringing to light the huge overbillings done for nearly everything. We'd probably see a 25x or 50x cost to this.
          • No different than my medflight that was billed for $67,000.
        • This most definitely will NOT cost $1000 in a US hospital. $1000 might be what gov't run healthcare plans pay for it. Other insurance companies would pay more (maybe $1500). Individuals get to pay the rack rate, maybe $3000-$4000.

        • Re:Pretty little (Score:4, Interesting)

          by ChumpusRex2003 (726306) on Friday March 01, 2013 @02:46PM (#43048355)

          Well, it's $1000 for the consumables for the device, and the operator's time. Then there's the cost of the machine, building, admin, etc.

          In reality though, this is extraordinarily cheaper than what is done at present. Currently, if a physician suspects a genetic disorder, then they the typical process used in a medical genomics laboratory is to use a "matching" technique where the patient's DNA is matched to known mutations. Typically, this costs around $500-700 per mutation tested against. For a number of diseases, this only gives a 75-80% accuracy, because certain genes are prone to new spontaneous random mutations, and have a lot of "normal" functioning variants - so simply checking for a known good gene isn't an option. As a result, these patients end up only with a presumptive diagnosis, leading to difficulties in family and reproductive counselling (i.e. do siblings need to be aware of the risk of passing on a genetic disorder to their offspring?)

          Sequencing is occasionally performed in patients with unknown presumed genetic diseases, where a suspected gene is known - but the cost is very high, and it is infrequently done, unless a whole family are affected, and it is possible to identify which the culprit gene is likely to be.

          Total genome sequencing, while not a panacea, would greatly help the diagnosis and research into newly recognised, presumed genetic diseases. If the total cost of the testing can be brought down to $2000 per analysis, then that would be cheap compared to the current techniques for genetic diagnosis.

          Finally, as to the MRI - the actual cost of an MRI scan including scanner, building, maintenance, staff, admin is about $300-600 depending on scan complexity (or at least, that's the "bulk" price charged by private MRI facilities to insurers or hospitals who have exceeded the capacity of their own MRI scanners).

        • by mspohr (589790)

          The cost may be $1000 but the US health industry will charge you $10,000.
          Of course, then, since nobody knows what most of this means, it will lead to lots more overpriced testing and consultations.
          This is a good way to get lots of money out of patients with no benefit to the patient.

      • by Guppy (12314)

        yes it is, do you know how much money your doctor can make by adding this to your routine blood work?

        If you're seeing an independent family doctor? Not much, and maybe nothing. He/She can charge you for the blood draw (if done at the office), and can charge you for a follow-up office visit to discuss results, if you come back for that. But your family doc doesn't receive any share of the test fee or ensuing referrals, as that would be considered an kickback (illegal).

        Note that there are some situations where the kickback prohibition on tests can be bypassed, however. If your doc's office does the testi

      • Nothing: my doctor's paid the same whether she orders a test, refers me to specialists, or tells me to take ibuprofen, as my HMO (Kaiser [kaiserpermanente.org]) is also the sole employer/owner of the lab, pharmacy, and staff.

    • by bhcompy (1877290)
      It will probably be something more along the lines of medical companies using it for data collection and risk assessment. Actuaries formulating rates and risk assessment would kill for this information
    • by WillAdams (45638)

      The interesting thing will be when we can act on a genome as we can any other set of plans or diagrams. Hal Clement's short story ``The Mechanic'' takes an interesting look at this, the protagonist is a genetic engineer able to create new life forms, or to re-grow / repair parts of existing life forms (incl. people).

      The scary part will be when insurance companies will be able to use such information to determine who is unprofitable to insure --- for that see the movie _Gattaca_.

      • First off, insurance companies in the US are already barred from using genetic data for insurability purposes.

        Second, straight DNA sequencing doesnt give you the keys to the kingdom. Epigenetic factors like methylation are turning out to be extremely important factors in gene expression. Further, there are a number of classes of RNAs that are likewise critical to organism development.

        Basically, the central dogma has been barking up the wrong tree.

    • For the foreseeable future, there is remarkably little utility that an individual's genome brings to the table.

      That's true as long as you treat humans like poor people treat cars and fix them when they break, but it's not true if you treat humans like rich people treat cars and take them in (or have them taken in) for all their scheduled maintenance.

      • by ceoyoyo (59147)

        Yes, in that case you get exactly what the OP suggested - paranoid rich person status symbols like the full body CT (which does more harm than good, by the way - it's a classic example of why screening tests are so limited).

        You can already get tested for various "important" genetic factors and you'll get back a report saying you have the "gene for X," which increases your probability of getting some disease by some small percentage or fraction thereof. Which is where the rich paranoid starts throwing money

    • by Artraze (600366)

      > Price isn't the only determinant of whether something is a 'routine part of medicine'. For the foreseeable future,
      > there is remarkably little utility that an individual's genome brings to the table.

      Technically, yes, it's not so much price and it is value, but realistically price is still a major factor in that calculation.

      As it stands, there are quite a few diseases [wikipedia.org] that we can identify just looking at the genome. For many, sure, there are other tests, but if genome screening was, say, cheaper tha

      • by Rutulian (171771)

        Did you happen to notice the statement,

        The following is a list of genetic disorders and if known, causal type of mutation and the chromosome involved.

        (emphasis added)

        Yes, there are a lot of genetic disorders, but no, there are not many we can identify by simply looking at the genome.

    • Since your genetic markup doesn't change (except for stray mutations but AFAIK not that spread to every cell in your body - single sperm cells are different) the question is can you pay off $1000 over your whole life and medical history? With every advance likely to come 10-50 years down the road? A quick search came up with this from Employer Health Benefits 2012 Annual Survey [kff.org]: The average premium for single coverage in 2012 is $468 per month or $5,615 per year. So over 70 years (probably some of them on a

    • by Anonymous Coward

      The short-sighted folks who maintain views such as this miss a key point. While I'm no fan of this particular company's solution, the ubiquitous sequencing of humans by the medical establishment has the potential to provide researchers ACCESS TO THE VERY DATA THAT WILL PROVIDE THE INFORMATION THAT WILL MAKE GENOME SEQUENCING MORE MEDICALLY RELEVANT. If you stop the process before it gets started in earnest, then what these folks are pouting about becomes a self-fulfilling prophecy. We will not be able to e

  • Either:

    1. Using this data for insurance purposes will be banned, which turns "preexisting condition" into a criterion that can only be applied with eyes closed;

    or 2. Huge numbers of people will be uninsurable, because the likelihood of their future illnesses will be known before they try to buy insurance.

    • by ADRA (37398) on Friday March 01, 2013 @12:00PM (#43046339)

      It works great for countries where health is 'free' (through taxes), and their main goal is to make people healthy, not to extract maximum funds from your pocket. It's too bad that you don't live there.

      • Re: (Score:1, Interesting)

        by gmanterry (1141623)

        Don't forget that when Obamacare kicks in the government will hold all your health records. Now, don't you think that they will submit your DNA info to at least the FBI if not all local law enforcement departments? I do.

    • by compro01 (777531)

      1 is already in place, at least theoretically, in the form of the Genetic Information Nondiscrimination Act.

    • by P-niiice (1703362)
      Mike Huckabee recently compared insuring someone with a pre-existing condition to insuring a house that is already burned down or a car that is already totaled. So I'm sure he'd be all for excluding people based on genetics.
      • by Trepidity (597)

        From an actuarial point of view, it's a reasonable comparison. The difference is that people are born in one body with a lot of things that they can't really do anything about. Sort of like being born in a burnt-down house without any possibility to move to a new one.

        A conclusion could be that insurance for healthcare makes no sense. How do I insure against the possibility of being born with a genetically caused condition? I'd have to buy insurance before I was born.

      • Mike Huckabee recently compared insuring someone with a pre-existing condition to insuring a house that is already burned down or a car that is already totaled.

        Actually, It would be more like insuring a house with insufficient compliance to fire safety regulations. You'd be asked to take precautions as a condition for being provided with the insurance (get your house fixed), or you'd pay some extra insurance premium, or both.

      • by moeinvt (851793)

        It's a fair comparison in many cases. If you go to buy "insurance" and your pre-existing condition is lung cancer, the house has burned down and the car is totaled.

        Insurance is based on pooling risk for unexpected and unlikely events. Calling something an "insurance" policy when dealing with costs related to events which have already occurred is ludicrous. It's also stupid to use "insurance" to cover the costs of routine physicals, contraceptives or pregnancies. That's not "insurance", it's pre-payment

        • by Kjella (173770)

          It's a fair comparison in many cases. If you go to buy "insurance" and your pre-existing condition is lung cancer, the house has burned down and the car is totaled.

          My pre-existing condition is to have a mild case of asthma - occasionally I take some very weak meds for it and I've completed two half-marathons so I'm not exactly a wheezing geezer, but my insurance in case of accident or disease (on top of universal health care) specifically exempts anything and everything lung-related. It's more like they refuse to insure any chassis damage if it has a dented fender.

          It's also stupid to use "insurance" to cover the costs of routine physicals, contraceptives or pregnancies. That's not "insurance", it's pre-payment and subsidy for costs which are totally expected.

          I bet there's a lot of women who'd disagree with you that the pregnancy was not at all expected, lol. If

      • by nedlohs (1335013)

        As any rational person should.

        If you live in a high crime neighborhood your home and contents insurance will cost more (in terms of cost per amount covered) than that of someone living in a low crime area.

        If you have a higher chance of running up large health bills than your health insurance should be more expensive.

        The obvious conclusion is that health care is unsuitable for an primarily insurance model and some other method of allocating health care resources (and allocating resources towards health care

    • Insurance companies can't look at pre-existing conditions in the US anymore. Remember?

    • by moeinvt (851793)

      Or
      3. Their insurance premiums are adjusted based on their risk factors.

      I'm not on the cutting edge of genetic science, but I don't think it's nearly advanced enough to make accurate predictions on an individual basis. Certainly no more accurate than predicting that obese people and smokers are at increased risk for certain conditions.

      IMO, it's only logical to charge people different premiums and to make insurance policies highly specialized for the individual.

      If my risk of getting a brain tumor is 50% and

      • by Trepidity (597)

        I disagree. I think if some people have the misfortune to be born with worse genes, they shouldn't have the double misfortune of also having a significant financial burden piled on top of other burdens such as needing to get surgery. I wasn't born with a congenital heart defect, for example, but that was pure luck, not something I "deserve", and I'm perfectly happy to pay my fair share towards treating those who were less fortunate in their birth.

  • by ceoyoyo (59147) on Friday March 01, 2013 @11:55AM (#43046261)

    Very few diseases are due to simple genetic factors, and those already have dedicated tests. Genotyping may eventually become a big part of medicine, but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.

    • but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.

      Item #2 is what this is about. Items #1 and #3 (uh, redundancy?) are what you get by working with #2.

      • by ceoyoyo (59147)

        No, this story is about using genotyping to treat or diagnose people. Cheap genotyping will definitely help with #2, but it's not going to be useful for treating or diagnosing people for some time. With current trends, by the time that happens actually sequencing your genome will be essentially free.

        #1 and #3 are not redundant. A genome is large and complicated. How to analyze it is a major area of research (#3). Even if you have tools to do that effectively you STILL have a big jump to make to link it

    • Very few diseases are due to simple genetic factors, and those already have dedicated tests. Genotyping may eventually become a big part of medicine, but not until there is a LOT more research done into how to use it, a lot more data available, and a lot better techniques for using it.

      Right now, the genetic tests still cost $1000's, any may not be covered by insurance. (At least for what I might have)

      A sub $1000 test for *everything* could save some people a lot of money.

      The trick is getting the insurance companies to use genetic testing to help people instead of simply excluding the high risk patients. (The most recent bill in congress banned health insurance exclusion, but not life or long term care)

  • by gstoddart (321705) on Friday March 01, 2013 @11:57AM (#43046287) Homepage

    Of course, one of the immediate things people will need to worry about is misuse of this. One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics.

    These kinds of things can have unintended consequences pretty quickly, and the privacy and legal implications of these kinds of tests cheap and routine haven't all been worked out.

    I can certainly see all sorts of potential for abuse of this. I wouldn't be eager to sign up for this, but, I do tend to the tinfoil hat end of the spectrum on these things.

    • by compro01 (777531)

      One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics./quote>

      That base is already covered, at least in theory. The Genetic Information Nondiscrimination Act [wikipedia.org] was passed in 2008 to deal with that.

    • by bitt3n (941736)

      One can easily see the insurance companies making everybody take one of these, and then refusing you coverage based on your genetics.

      one can easily see the individual taking one of these on the sly, then signing up for a full-service insurance plan only if he expects to need it, which then means the company must either do the test on everyone who applies for insurance, or jack up everyone's rate to accommodate such self selection.

    • One more reason to ban/regulate insurance, and make health insurers compete free-market against the free national public health service. As that would require the consent of our Fearless Leaders,

      we're boned.

    • by mange (113241)

      The US Congress has already started regulating some of these misuses. http://en.wikipedia.org/wiki/Genetic_Information_Nondiscrimination_Act [wikipedia.org]

      • by gstoddart (321705)

        The US Congress has already started regulating some of these misuses.

        Sure, but with enough cash and lobbyists, they'll come around -- just like they did for every other industry which asks to be deregulated.

        The Freedom of Genetic Information for Commerical Purposes Act will give them whatever they want ... and then the governments will want the data of course, but all hush hush and without a warrant.

        Now, if you'll excuse me, my hat needs another layer of tinfoil, and I'm contemplating a design for a matchin

  • âoeOur goal,â Rothberg declares, âoeis to really transform medicine.â

    And by that he means HR and the insurance industry.

  • by symes (835608) on Friday March 01, 2013 @11:59AM (#43046321) Journal

    It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK

    • I'm pretty sure you'll still want a raw sample, perhaps in ten years?

    • Re: (Score:2, Funny)

      by Anonymous Coward

      It would be neat to have a nice, light and portable genome sequencer for when I next go eating meat in the UK

      I for one would appreciate some serious commentary on the article versus just horsing around.

    • Its not a full sequencing, but a search for about a dozen genetic markers unique to the equine species. I was trying to find an exact description of the test in google, but the best I could was company called InstantLabs selling a machine [instantlabs.com]. It takes two hours to analyze a sample. Not quite GATTACA yet.

      Unfortunately each test is species specific. So if you want to test for lots of species you have to run lots of tests, assuming they are available.
  • by volvox_voxel (2752469) on Friday March 01, 2013 @12:51PM (#43046987)
    Sequencing has enabled all sorts of medical diagnostics and research that were previously unavailable. It was quite exhilarating to to read in Journals like Nature about people that had late stage cancer being sequenced to find out that they were misdiagnosed with the wrong cancer. Just a few years ago, it was impossible to determine what type of cancer a cancer was before it spread. Once it has metastasized, it was all a guessing game. With sequencing you can know for sure, and give you the right medicine to address that cancer.

    I've always considered biology to be hundreds of years behind physics and the other "hard sciences", because they never had the tools to deal with it.The CPU power, the RAM, the hard-disk space, even the cloud infrastructure are all needed to make DNA sequencer efficient. The last instrument I worked on was a low cost DNA sequencer that could yield a sequence in one day. At the end of a run, to do the basecalling and base alignment of the data, you would need significantly more horsepower than what was on the meager instrument. The cloud allows you access to a supercomputer the the short time that you need it, so the customer is not burdened by the huge computational complexity involved.

    As the cost sequence drops (and continues to drop), whole new fields of research have opened up. Bioinformatics where biology and computer science meet is a pretty hot topic. We have a deluge of data, but we don't yet have all the good algorithms necessary to unlock all the secrets we wish to solve. The Rosetta stone of the 21st century. This is the biggest complaint I hear about from biochemists.. Making sense of the data. Data leads to knowledge leads to wisdom, but data is not knowledge.

    I consider DNA sequencing to be an enabler, just like the steam-engine, or the electric light. It is now possible to look deeply at things we never could, like meta-genomics. Did you know that you have more bacteria in your body then all other cells in your body put together? ..And did you know that you can't grow most of them on a petri dish? We have been to mars, but we don't even know the bacteria in our own gut. Meta-genomics is a form of "shot-gun sequencing" .. In the lab you understand the biology by making millions of replicas of it in the petri dish.Not all bacteria grow on a petri-dsh . With shot-gun sequencing, you sequence enough sample so you can digitally reconstruct what organisms were there to begin with. This has enabled us to [begin to] understand the biochemical messaging between soil bacteria and the roots of plants, understand the biochemistry of food digestion to generate bio-fuels more efficiently, etc .. Interesting times...

    • Data -> information -> knowledge -> wisdom

      There are also non-gene mechanisms that need to be understood as well, since the genome is a blueprint, but what happens when the cell actually starts using that blueprint? Anyone who's had a house built knows that it's the contractors that actually make the house, not the architect, and there are an unknown number of contractors inside individual cells that control what gets built. What makes a particular cell use the "retina" part of the blueprint, and another cell use the "heart muscle" part? I don't believe we know all the answers outside the genome, yet. All those cellular contractors and we don't understand their language (yet).

    • by aaronb1138 (2035478) on Friday March 01, 2013 @05:22PM (#43049845)

      I have generally considered biology so far behind the other hard sciences, especially physics, precisely because for a very long time they failed to consult with the chemists, physicists, and engineers. It has largely been self-induced, and almost entirely a process of falling behind. Heck we have some hacks out there in biology using morphological databases (today - with all the genetic tools they have!) to reverse engineer evolution, when the biologists are well aware that morphology is a good categorizing and search tool (it tells you where to start genetically looking), not an extrapolation tool for real data and conclusions.

      Physics in particular finally just started going the route of butting in wherever they figured out they could be useful to biologists and clinicians especially. CT and MRI are great examples.

      Rothberg's own 6 years of research to sequence 9000 letters of genetic code is a perfect example. After a year or so, a physicist or engineer would have said f--- this, there must be some way of automating this process. I suspect most of the scientists at Ion Torrent are chemists, EEs, and physicists. Probably not too many pure biologists (though some biophysicists are probably around).

  • by Anonymous Coward

    'nuff said.

  • Good that we have PPACA / obamacare or this would or been used to build a nice Pre-existing condition black list.

  • by Cyberax (705495) on Friday March 01, 2013 @01:14PM (#43047227)
    IonTorrent has been promising wonderful new machines _just_ next quarter for almost two years now. So far, they have delivered only a few machines to select customers under NDAs. And they still haven't solved a couple of crippling problems: homopolymer resolution and fairly short read length.

    Also, they haven't showed anything on this year's AGBT (it's like CES, only for biotech) last week. So I won't be holding my breath waiting for $1k genome sequencing machines.
    • TFA was written based on an interview that took place in April of LAST YEAR.

      It shows a graph indicating that cost is decreasing too fast that is also based on data ending at the beginning of last year. Conveniently before 2012 actually happened, where the cost sat completely flat for 12 months and even increased in Q4 as Illumina released new (more expensive) reagents.
      (updated image:) http://www.genome.gov/images/content/cost_per_genome.jpg [genome.gov]

    • It's interesting that Ion Torrent has been getting so much more media exposure than Illumina, the market leader. By all accounts, from actual users, the data quality is better. Getting low error rates may involve much more sampling. This is very much akin to the bit error-rate probability in digital communication, and the number of packets you need to transmit to reduce the error to acceptable levels (but in this case, there is no forward error correction).

      Illumina uses fluorescent labeling which has a m

      • by Cyberax (705495)
        Well, our startup has been recently acquired by Illumina so I might be a little biased. But from our previous experience, IonTorrent produces much worse data and it's not that cheap. Illumina also owns a company producing very nice enzyme (Nextera) that makes life much easier for molecular biologists. Staying quiet is actually a nice feature of Illumina - it just delivers results without much fanfare. IonTorrent in comparison overpromises and underdelivers.

        There are other companies to watch - nanopore-ba
  • So, we could have the full sequences of many many people of different origin, not to mention of many different animals. While it would require quite a bit of data-crunching, I hope that it allows us to look back into our distant past, learning more about evolution.

    Bert
    And if it brings some intolerant religious folks to take their favorite myth book a little less serious, that is a very very nice bonus.

  • The comparison of the cost and time spent to do the first human genome compared to current runs is hiding the very important fact that if you have an existing genome for a species then doing another one is really easy as you can simply map the reads to the genome instead of having to do de novo. Getting a genome as complete as human these days still takes millions of dollars. And you ain't going to just rely on Ion Torrent. Your going to need Illumina for those large number of small reads and PacBio for tho

    • by Rutulian (171771)

      Doing a new genome is very hard and still quite expensive, although technology and techniques have improved things.

      Yes, that and the quoted cost is, I'm assuming, $1000 for a single chip run, which gives you a maximum of 10 Gb or only ~3X coverage (actual will probably be less). That's usually how marketing blurbs work. Even for SNP analysis, you are going to need around 40X coverage, so the cost per genome is much higher than what they are saying, and is still at least an order of magnitude more expensive than Illumina.

  • except you can't easily change the locks...

    Anyone who has your DNA sequence could in theory make a plague targeted just at you (maybe wth some collateral damage). That may be as trivial to do in thirty years as "script kiddie" computer attacks are these days. Our society has not yet thought through the implications of all this...

    See also my essay:
    http://www.pdfernhout.net/recognizing-irony-is-a-key-to-transcending-militarism.html [pdfernhout.net]
    "... Biological weapons like genetically-engineered plagues are ironic because

Invest in physics -- own a piece of Dirac!

Working...