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Biotech Medicine Science

100,000 Californians To Be Gene Sequenced 176

Posted by Soulskill
from the homing-in-on-the-prius-gene dept.
eldavojohn writes "A hundred thousand elderly Californians (average age 65) will be gene sequenced by the state using samples of their saliva. This will be the first time such a large group has had their genes sequenced, and it is hoped to be a goldmine for genetic maladies — from cardiovascular diseases to diabetes to even the diseases associated with aging. Kaiser Permanente patients will be involved, and they are aiming to have half a million samples ready by 2013. Let's hope that they got permission from the patients' doctors first."
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100,000 Californians To Be Gene Sequenced

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  • by jamstar7 (694492) on Wednesday October 21, 2009 @11:37AM (#29824787)
    I don't live in California. Just what I need, some company taking and patenting my genetic sequence and suing me for using it.
    • by interkin3tic (1469267) on Wednesday October 21, 2009 @11:57AM (#29825095)

      Don't consider yourself safe just yet:

      "This is a force multiplier with respect to genome-wide association studies," says Cathy Schaefer, a research scientist at Kaiser Permanente, a health-care provider based in Oakland, CA, whose patients will be involved...
      Kaiser Permanente is meanwhile trying to expand its collection of biological samples to 500,000 by 2013.

      While the scientists running the experiment are clearly doing this to actually advance research, and it will, I'm thinking someone at Kaiser is hoping this will pave the way for "You want health insurance? We just need to sequence your genome first. Oh, sorry, you're going to get Huntingtons disease. Good luck with that."

      • by SUB7IME (604466) on Wednesday October 21, 2009 @01:13PM (#29826269)

        This is why we passed GINA: http://www.genome.gov/24519851 [genome.gov]

        • Can you assure me that there are absolutely no loopholes or ways around GINA that insurance companies could exploit? Can you assure me that insurance companies won't just disreguard GINA? If there is a loophole, insurance companies certainly have an incentive to find it and exploit it, and I know they would have no moral problem with doing so.

          It's somewhat reassuring to know it won't be quite as obvious as my scenario, but one law doesn't make me trust insurance companies.

        • by madcow_bg (969477)

          Well, a lot of wasted efforts to circumnavigate the obvious solution - universal healthcare...

      • by icebike (68054)

        From TFA: " University of California, San Francisco (UCSF), with a $25 million, two-year NIH grant that tapped federal stimulus funds ".

        That would seem to me to make all this research public domain, and prevent Kaiser from patenting any genes, holding any information proprietary, or selling it to drug companies.

        While you can't legally discriminate (see GINA in this subtread), there are many other ways this study could end up benefiting Kaiser alone, or Kaiser in cahoots with some drug company unless there i

      • ...hoping this will pave the way for "You want health insurance? We just need to sequence your genome first. Oh, sorry, you're going to get Huntingtons disease. Good luck with that."

        At least for this group, doesn't matter. At age 65+, they're all eligible for the kind of can't-be-turned-down everyone-pays-the-same-premium government-operated socialized health insurance that Congress seems to think would be a disaster for the rest of us.

        • At least for this group, doesn't matter.

          Right, they do a pilot program first to determine how useful this will be before they do it on a widescale. Or they could.

      • by ShakaUVM (157947)

        >>I'm thinking someone at Kaiser is hoping this will pave the way for "You want health insurance? We just need to sequence your genome first. Oh, sorry, you're going to get Huntingtons disease. Good luck with that."

        The nice thing about my health insurance through Kaiser is that they don't screen applications. You're charged an amount based on your age, and that's it. I think you have to fill out a thing about your existing conditions (they won't cover cancer if you have it already, I think) but that's

  • Not sequencing (Score:5, Informative)

    by Anonymous Coward on Wednesday October 21, 2009 @11:38AM (#29824813)

    This not (gene or genome) sequencing. Rather, it picks up single nucleotide changes (SNPs). Still valuable information, but no new mutation will be discovered with this method.

    Sequencing would be a couple of orders of magnitude more expensive.

    • Re:Not sequencing (Score:5, Informative)

      by SUB7IME (604466) on Wednesday October 21, 2009 @01:20PM (#29826409)

      Anonymous coward is correct. This is genotyping, which is orders of magnitude less resource-intensive than gene sequencing.

      Genotyping | sequencing || driving down the highway | Lewis and Clark's journey

      Sequencing is pathfinding (they are not doing this). Genotyping is exploring the path that you already know is there (this is what they are doing). On the sequencing front, there is currently a 1000 genomes project - a massive collaboration of worldwide importance due to its difficulty and expense. On the other hand, genotyping 100,000 people is done all the time (heart attack GWAS, etc). The two concepts are enormously different.

      • Re: (Score:2, Informative)

        by Anonymous Coward

        Parent is absolutely right. Just to illustrate the difference, here are some approximate costs for doing this in one patient:

        Genotyping: $100
        Sequencing 80% of coding genes: $10000
        Sequencing entire genome: $60000

  • by LUH 3418 (1429407) <maximechevalierb@@@gmail...com> on Wednesday October 21, 2009 @11:43AM (#29824887)
    The good thing is that this kind of data will help us develop tests to predict the occurrence of many diseases, and perhaps understand their causes better.

    The bad is that private insurance companies are likely to eventually *require* you to get a DNA sample, and possibly reject you if they determine your genes predispose you to old-age diseases.

    Where it gets ugly, is that this will be yet another tool that could allow screening of unborn fetuses, and potentially selective abortions. I'm not personally against this. We're overpopulated anyways, but some people clearly don't like that idea.
    • Re: (Score:2, Insightful)

      by Anonymous Coward

      Which is one of the big reasons for single payer insurance and insurance that can't be denied. Single payer system would negate the benefits of excluding people based on their DNA, and instead would allow people who might have a chance of something going wrong to actually get insurance.

      • by element-o.p. (939033) on Wednesday October 21, 2009 @12:59PM (#29826059) Homepage
        Awesome. I can see it now: those who actually need health insurance will be unable to get any. Those who will be making payments for the next n decades, but rarely -- if ever -- actually obtaining any benefit from the insurance will be the only ones who will qualify for coverage.
        • Those who will be making payments for the next n decades, but rarely -- if ever -- actually obtaining any benefit from the insurance will be the only ones who will qualify for coverage.

          Why would anyone want that kind of coverage? What fool would buy it?

          • That was my point: if health insurance companies are able to sequence and/or access DNA information on individual applicants, the only people who would have access to health insurance would be those who are unlikely to need it. Perhaps I should not have omitted the "lt;sarc> tag at the end of my post ;)

            A slightly more pragmatic answer would be that people who were worried about acute problems -- accidents, the occasional cold, etc. -- might still buy insurance.
        • by HiThere (15173)

          Well there are still accidents and other environmental hazards. There will be SOME utility in health insurance. Just not as much.

            <humor>So of course they'll reduce their rates because their expenses have gone down. </humor>

      • by TheCarp (96830) *

        Of course, in reality, this is just a good argument for ANY sort of "group insurance". Thats kind of the problem with one-off single insurance. You go to the ins company, and ask for insurance. They look at YOUR risk to insure you.

        When I got my job, I got insurance with it. Working at this company is the criteria by which I got onto my plan. So there is no reason for the insurance company to see me as a greater risk than anyone else at the company, since they have nearly everyone here, its all about average

      • by bkr1_2k (237627)

        Thank you. I was wondering if I'd have to be the first to mention that.

    • by MBGMorden (803437)

      The bad is that private insurance companies are likely to eventually *require* you to get a DNA sample, and possibly reject you if they determine your genes predispose you to old-age diseases.

      Look at it on the positive side: consumers can get the same data too, and I'm sure that if they get accurate enough the people who don't actually need the insurance can either skip it completely, or go for cheaper "accident only" coverage. If the insurance companies tighten their grip too much and try to only sell to people who absolutely don't need it, they may find that they end up eliminating their customer base.

    • by Idiomatick (976696) on Wednesday October 21, 2009 @12:09PM (#29825271)
      God I hope you guys get your healthcare shit together before that happens. In a modern country the data could be used to save lives... In the US I can only see it saving money and costing many thousands of lives.
    • Re: (Score:2, Insightful)

      by BlowHole666 (1152399)
      Prove we are overpopulated. Did someone find an Earth manual someplace that says only 7billion humans can be supported? I am sure wise ass will come back and say "We are overpopulated because people are starving in ". Well people starve in American and Americans are considered some of the fattest. So I think maybe we are not overpopulated we just have a food delivery problem.
      • by jhfry (829244)

        First, define overpopulated.

        To me, a population is too large when its environment can no longer sustain the population. So, in many parts of the world, where people die of starvation especially, they are overpopulated. To argue that its a logistics problem is a fallacy. What if the entire earth were starving, would it be a logistics issue because we are not consuming the resources of a planet in a nearby solar system?

        I personally think that we have already significantly overpopulated the earth, because w

      • by 1s44c (552956)

        Prove we are overpopulated.

        I can't prove we are overpopulated right now, but I can prove we are either overpopulated now or will be in the near future.

        Exponential growth is not stable in any finite system.

    • by Rich0 (548339)

      Yup - insurance only works in the absence of knowledge. If you could predict with 80% accuracy whether somebody's house would burn down, then almost everybody could get dirt-cheap fire insurance (which they wouldn't buy anyway since they wouldn't need it), and a small number of people wouldn't be able to afford it and would lose everything they have in a fire. The insurance companies would go out of business since nobody would bother buying insurance either way.

      The only thing that would work once genetic

      • If you could predict with 80% accuracy whether somebody's house would burn down, then almost everybody could get dirt-cheap fire insurance (which they wouldn't buy anyway since they wouldn't need it), and a small number of people wouldn't be able to afford it and would lose everything they have in a fire.

        Rather, the houses likely to burn down would be unoccupied, and probably demolished, and the remaining houses would be be insurable at much lower rates. Everyone wins. Well, some people would be out the cost of a house and need to find new shelter, but at least they won't be caught in a fire.

        In the medical case, of course, you can't leave your "house"—but you can take steps to mitigate any diseases you may be genetically predisposed to. Analogies aside, however, by the time your genetics have been det

      • by TheSync (5291)

        here is no reason that a poor person without insurance should have to pay $100 for a doctor's visit that costs $30 for Aetna (even if the poor person can haggle them down to $50 - assuming they are in the condition to haggle BEFORE the services are rendered).

        FYI, a CVS Minuteclinic [minuteclinic.com] exam costs $62. You need no appointment, and they are open evenings and weekends.

    • "Predisposition to death." I'm really surprised that some insurance company hasn't tried this one yet.

      "So, your great grand mother, how healthy is she?"
      "Well, she died about 30 years ago"
      [checks off box]
      "And your grand mother?"
      "She died just last year."
      [checks off another box].

    • by Sir_Lewk (967686)

      A possible upside to private insurance companies doing this is that if they accept you, you know you probably don't need it so bad after all!

  • Consent (Score:2, Interesting)

    I didn't see it in the article, but was consent obtained from each of these patients to use their DNA in this study? Or is this one of those OPT-OUT programs that companies think consumers like?
  • Yeah, let's hope they got the doctors' permission, because, you know, it's not like the patients have a say in it or anything...

  • Let's hope that they got permission from the patients' doctors first.

    I would think that getting the patients' permission would be a little more important.
  • California needs samples of saliva. If you live in California, proceed directly to the capital and spit on the front door. Your state is counting on you.

    At least that way they can get saliva samples of conservatives. Of course, in California, that's a sample size of about four, but it's a start...

  • by ianbean (525407) on Wednesday October 21, 2009 @12:16PM (#29825341)
    Maybe everyone should read the article. They're being genotyped (700,000 SNPs by Affymetrix array) not sequenced. There is a significant difference...
  • by Manip (656104) on Wednesday October 21, 2009 @12:21PM (#29825441)

    The article seems to gloss over this BIG question.... Did they get the patients permission before they scan in their DNA and link it into their medical records?

    If they didn't or aren't, then that is a big privacy violation with perhaps huge negative ramifications for those individuals (if any diseases are identified that aren't treatable but will impact their ability to get insurance).

    Also breaks the doctor/patient trust entirely since your doctor is more or less stealing from you...

    • Re: (Score:3, Insightful)

      by SecurityGuy (217807)

      Or for the patients children. I can see being in my later years and really not caring, since I'll presumably be on the federal dole (Medicare/Medicaid/Whatever) by then, but this data is also predictive of the patients children and grandchildren. Much as I can see the value in the research, this is a monstrous can of worms. Patient consent should be required at a minimum, and prohibitions on genetic discrimination are going to be required as well.

    • by BobMcD (601576)

      If they didn't or aren't, then that is a big privacy violation with perhaps huge negative ramifications for those individuals (if any diseases are identified that aren't treatable but will impact their ability to get insurance).

      This depends entirely on the proper collection and use of the data. If they're looking for trends across a huge dataset, HIPAA rules allow them to de-personalize the data. Thus the sample comes from Male03241, whose identity is stored in a discrete location used only for specific purposes.

      Thus, they'll know that someone has the gene for Parkinson's, but will not have access to who that person is outside their own study. And with a set of data this large, there's a solid chance they don't really need that

    • Re: (Score:3, Informative)

      by CupBeEmpty (720791)

      It would be completely illegal without informed consent. They would have had to go to their Internal Review Board (IRB) and get approval and would be required to follow federal guidelines. This is a highly regulated part of medical privacy and IRBs do not screw around with the rules because the institutional consequences are massive. They range from massive lawsuits to federal crimes. The scientists doing the SNP arrays would also be forbidden from knowing any patient information. Only the doctors involved

  • The article keeps repeating how diverse the participants in the study will be. But I'm going to guess that they won't find very many people who have genetic diseases which cause a person to die before they reach oh, say their 65th birthday.
  • "Mr. elderly Californian, I'm afraid I have some bad news for you . . . you have cancer."

    "But I also have some good new for you, it's treatable."

    "But yet again I have some bad new for you: you have the QZURVN gene, which our research indicates that you will die of heart disease in a few years anyway, so why should we bother treating the cancer?"

  • Other countries (Score:2, Interesting)

    by FenixBrood (760690)
    I live in Sweden and here we take DNA samples of all newborn and put the samples with SSN and parents name in a national database. The database can then be accessed by scientists for study. We have done this for decades. I haven't heard anybody here really care about being in the database.
    • Re: (Score:3, Informative)

      by BlueParrot (965239)

      I haven't heard anybody here really care about being in the database.

      a) Listen harder

      b) They only tell your parents about it and by the time you are old enough to care chances are your parents have forgotten.

    • Re:Other countries (Score:4, Insightful)

      by Schickeneder (1454639) on Wednesday October 21, 2009 @12:50PM (#29825901)

      You have universal healthcare in Sweden, so all the citizens should theoretically get equal/fair treatment anyway. People in America aren't generally afraid of having that "personal" information known, rather they worry about the possible consequences of private healthcare providers and employers accessing that data and discriminating.

    • by HiThere (15173)

      In Sweden you aren't likely to die because someone else knew what your genetic codes were. In the US...well, it's illegal to discriminate because of a person's genetic variants, but it could be quite profitable if you're a health insurance company. Of course nobody worries about that because we all know that the health insurance companies are all ethical and law abiding.

      So you aren't hearing any worries or complaints. You aren't. You aren't. You aren't hearing any worries or complaints.

  • Bad summary (Score:2, Informative)

    Of note, this is single nucleotide polymorphism (SNP) genotyping, and NOT sequencing. Only 700K common variants will be genotyped. While individuals could certainly be identified in the database by their SNPs (as few as 24), this project does not employ high-throughput sequencing. The title of the summary is misleading.
  • by idontgno (624372) on Wednesday October 21, 2009 @12:58PM (#29826049) Journal
    "Well, it appears that DNA analysis proves that you are actually a Streptococcus mutans [wikipedia.org] bacterium. I recommend against antibiotics or toothbrushing in order to extend your lifespan."
  • by CupBeEmpty (720791) on Wednesday October 21, 2009 @01:20PM (#29826401) Homepage

    This is not the same as sequencing their genomes. This will not provide a full sequence of each person's genome. It will look for specific mutations that have already been identified and tell us who has certain point mutations.

    Think of it as the difference between having the full text of the file in the case of sequencing and having a count of the number of times the writer wrote "teh" instead of "the"

    This is not to say that this study is without merit but it is not gene sequencing or genomic sequencing.

    For more information on SNP arrays wikipedia is helpful [wikipedia.org] and if you really want details you can talk to Affymetrix [affymetrix.com] (I bet these are the arrays they will use).

  • Getting ready for real world Gattaca I see.
  • I can say without a doubt that Kaiser Permanente is hated...for many reasons. All of the worst things you've heard about managed care/hmos, etc crystalled in one company.

    • by TheSync (5291)

      I can say without a doubt that Kaiser Permanente is hated...for many reasons. All of the worst things you've heard about managed care/hmos, etc crystalled in one company.

      I bet the "public option" will look very much the same...a "public option" will, like Kaiser, insist you take the "blue pill" that costs half the price.

  • ...that your State Governor will activate Skynet and nuke the site from orbit.

  • I do not think that anyone has pointed out that even with samples sizes that big, we can only figure out the genetic architecture of complex disease to an extent that makes it no better than family history for predicting disease. In fact, I hazard it will still be an order of magnitude worse. Obviously, the researchers did not point that out to the health insurance companies paying for it because I am sure that they will still find many interesting things.
  • Why in the world would you think they should have permission from the patients doctor, and not from the patients themselves?

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