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100,000 Californians To Be Gene Sequenced

Posted by Soulskill on 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."

40 of 176 comments (clear)

  1. Damned sure glad... by jamstar7 · · Score: 2, Insightful

    I don't live in California. Just what I need, some company taking and patenting my genetic sequence and suing me for using it.

    --
    Understanding the scope of the problem is the first step on the path to true panic.
    1. Re:Damned sure glad... by interkin3tic · · Score: 3, Insightful

      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."

    2. Re:Damned sure glad... by Idiomatick · · Score: 3, Informative

      At least get your racist history right. China had circled the globe in 1300s created the great wall of China, the still current largest man made channel, and the forbidden city, while they mapped the sky. At this time they didn't bother even trading with the Europeans because they were so much more advanced that they seemed like dirty savages. The largest fleet that Europe had at the time were Venician longboats armed with bows. Would have been easy for China to conquer them and the anchors of their ships weighed more than the European ships and the fact that they had bombs at the time.

      Oh and if you go back further. Africans built great civilizations and had lots of math that the europeans stole from them. Some cities were very well educated. Timbuktu rivaling Alexandria in some respects.

      Or further forwards, the inuit haven't fared nearly as well as america. Even though they are an offshoot of americans. I'm sure you made a mistake in your calculations somewhere.

    3. Re:Damned sure glad... by Anonymous Coward · · Score: 5, Funny

      That depends on how you define "publish." I know I have many copies of my DNA, and I've even distributed some of them.

    4. Re:Damned sure glad... by SUB7IME · · Score: 5, Informative

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

    5. Re:Damned sure glad... by CrimsonAvenger · · Score: 2, Informative

      China had circled the globe in 1300s

      Citation?

      In general, other than somewhat exaggerating the capabilities of non-European nations, you're correct - Europe wasn't the height of civilization back then. But don't undermine your own arguments by adding items of questionable veracity.

      Also, note that even if China had been inclined to conquer Europe then, they'd have been unable to do so - the logistics situation would have been impossible.

      --

      "I do not agree with what you say, but I will defend to the death your right to say it"
  2. Not sequencing by Anonymous Coward · · Score: 5, Informative

    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.

    1. Re:Not sequencing by SUB7IME · · Score: 4, Informative

      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.

    2. Re:Not sequencing by Anonymous Coward · · Score: 2, Informative

      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

  3. The Good, the Bad, the Ugly... by LUH+3418 · · Score: 4, Interesting

    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.

    1. Re:The Good, the Bad, the Ugly... by Anonymous Coward · · Score: 2, Insightful

      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.

    2. Re:The Good, the Bad, the Ugly... by Red+Flayer · · Score: 5, Insightful

      That's only "bad" if you turn out to be predisposed, in which case your higher risk will no longer be subsidized and you'll have to pay fair premiums in proportion to your risk.

      Thereby making the cost of insurance prohibitive to those with genetic predisposition to serious, expensive-to-treat maladies. This works out exactly the same as denying those people insurance coverage, unless they are very wealthy.
      This defeats the general purpose of medical insurance (which IS for the healthy to subsidize the sick).

      From a libertarian standpoint (yours, I'm assuming, from prior discussions), why not just get rid of health insurance altogether? That's the only way to ensure that everyone pays their "fair" costs into the system. That seems to be what you're getting at, so why mince words?

      --
      "Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
    3. Re:The Good, the Bad, the Ugly... by Idiomatick · · Score: 3, Insightful

      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.

    4. Re:The Good, the Bad, the Ugly... by moogied · · Score: 2, Informative
      ...except that congress passed a law making this illegal?

      http://www.genome.gov/24519851

      --
      So basically, -1 troll/offtopic is really slashdots way of saying "I hate that you thought of something before me."
    5. Re:The Good, the Bad, the Ugly... by element-o.p. · · Score: 4, Insightful

      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.

      --
      MCSE? No, sir...I don't do Windows. Yes, I am an idealist. What's your point?
    6. Re:The Good, the Bad, the Ugly... by bzipitidoo · · Score: 2, Insightful

      Knowledge is power. All in all, it's good that we are learning about ourselves. Ultimately it gives us more choices.

      But power always cuts two ways. Insurance companies won't be able to resist the temptation to abuse this knowledge. Though they aren't qualified, they'll pass judgment on genes, deciding which ones are "bad" and "good". They'll take a lot of shades of gray and paint them black and white, and they won't get it right. Suppose they find something like a correlation between baldness and skin cancer? Suddenly, being bald might be "bad". There's too much chance that those of us so unfortunate as to have "bad" genes will be punished for it. Also possible is the use of it to make certain no one can be right. Those who've had a bit of bad luck-- injured in an accident, say-- might suddenly be informed that they've been found to have some genetic condition that voids their coverage. For those whose conditions really are debilitating, that's punishment enough without some faceless committee sitting in judgment and further reducing their chances because they've been judged not a good bet.

      We so need a system where such judgments are not needlessly harsh and incentives needlessly perverse. Too many cures are overlooked in favor of much more profitable chronic care needed to handle symptoms. For instance, the standard treatment for high blood pressure is to take medication-- daily, for the rest of your life. Life and evolution are quite harsh enough, we don't need Neo-Eugenics.

      --
      Intellectual Property is a monopolistic, selfish, and defective concept. It is "tyranny over the mind of man"
    7. Re:The Good, the Bad, the Ugly... by sjames · · Score: 2, Insightful

      You can claim Godwin if you want, but the topic is so close to eugenics and eliminating the untermensch anyway, it's hard to avoid.

      What do you propose that those people whose premiums woud be impossibly high (or who are insurance pariahs) should do? Euthanasia? (illegal anyway).

    8. Re:The Good, the Bad, the Ugly... by ishobo · · Score: 4, Insightful

      From a libertarian standpoint (yours, I'm assuming, from prior discussions), why not just get rid of health insurance altogether? That's the only way to ensure that everyone pays their "fair" costs into the system. That seems to be what you're getting at, so why mince words?

      Bravo. Any free market libertarian should not be using any type of insurance. Afterall, insurance is a form of wealth redistribution.

      --
      Slashdot - The great and glorious cluster fuck of Internet wisdom.
    9. Re:The Good, the Bad, the Ugly... by JesseMcDonald · · Score: 4, Insightful

      Any free market libertarian should not be using any type of insurance. Afterall, insurance is a form of wealth redistribution.

      This demonstrates a profound misunderstanding of both the concept of "wealth redistribution" in respect to libertarian philosophy and the concept of insurance itself.

      First, insurance is not "wealth redistribution" even in the limited sense described below, at least when it's not actually being turned into some sort of forced-"charity" scheme via regulation. The projected value of an insurance subscription is equal to the projected value of the premiums being paid (less overhead and the insurer's profit margin, of course, just as with any other service). You're neither subsidizing nor being subsidized by your fellow insurees. What you get from insurance—what makes it worthwhile enough to justify the overhead—is that people tend to prefer that their future costs be predictable. Insurance takes a high-cost, low-probability future event and, by pooling it with many similar events, turns it into a low-cost, predictable event in the form of periodic insurance premiums. Critically, risk is conserved with respect to each insuree; no one pays extra to subsidize anyone else's above-average projected cost (risk). In retrospect, of course, some will be compensated more than others depending on the actual circumstances, but ex ante no insurees can be said to benefit at others' expense.

      Second, "wealth redistribution" is only a problem when it's involuntary. Donating to charity is perfectly consistent with libertarian philosophy, and something many libertarians do frequently. When libertarians speak negatively of "wealth redistribution" they're referring to redistribution by force, involuntarily, which is an entirely separate matter. The force is what makes it wrong, not the redistribution.

      --
      "The state is that great fiction by which everyone tries to live at the expense of everyone else." - Bastiat
    10. Re:The Good, the Bad, the Ugly... by Red+Flayer · · Score: 2, Informative
      Emphasis mine:

      No, the purpose of insurance, medical or otherwise, is for like-risk individuals[1] to form a pool and trade assessed risk for equivalent, but predictable[2], premiums. Subsidies have nothing to do with it.

      1. The 'like-risk individual' qualification -- I believe this to be an incorrect assumption on your part. There is no such thing as 'like-risk' -- the question is to what extent we can factor known risk factors into premiums.

      2. Yet when you proposed adjusted premiums for ascertained variable risk, that contradicts your definition of the purpose of insurance.

      3. Effectively, those who incur reimbursable expense are subsidized by those who don't. That's the nature of the system, and how it operates when operating as intended. Those who do not make claims subsidize (through their premiums) those who do make claims. Not sure how you could claim it operates any differently than this.

      We have very different philosophical stances, and we'll never agree on those foundations. But I think if you want to split hairs on terminology, you need to be very careful.

      --
      "Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
    11. Re:The Good, the Bad, the Ugly... by sjames · · Score: 3, Informative

      Unfortunately for the social Darwinists in the crowd, they DO have one last option available. That is, attack the society that told them to just kindly go away and die quietly somewhere and take what they need. It's not as if they would have anything to lose is it?

      The same philosophy of social darwinism that tells you it's OK to just let them die also tells them it's OK to kill you so they and their family might live. The difference is that at some point they will face a 100% chance of death if they DON'T attack and a significant but lesser chance of death if they do.

      Disenfranchise people en-mass long enough and soon enough they will form their own society. If the parent society interferes with that, they will eventually become an enemy.

      Alternatively they become a diffuse source of discontent and the society unravels from the inside out.

    12. Re:The Good, the Bad, the Ugly... by HiThere · · Score: 2, Insightful

      And no company would ever break a law to increase it's profits.

      --

      I think we've pushed this "anyone can grow up to be president" thing too far.
    13. Re:The Good, the Bad, the Ugly... by bluej100 · · Score: 3, Insightful

      Insurance is for amortizing risk over time and population. Knowing the degree of risk makes it better insurance, not worse--it's not illegal to charge higher car insurance rates to people who are bad drivers. It's the role of the government to redistribute wealth to those who've gotten a crappy start, not the role of insurance firms. (And I dispute the notion that those unfortunates who share our nationality should be our first moral responsibility.)

    14. Re:The Good, the Bad, the Ugly... by JesseMcDonald · · Score: 2, Interesting

      There is no such thing as 'like-risk' -- the question is to what extent we can factor known risk factors into premiums.

      The idealized model of insurance places individuals into different "pools" depending on their individual risk, with each pool corresponding to a specific risk and equivalent premium. It is assumed that there are sufficient individuals within each pool for things to average out. However, that's just an abstraction. In the real world risk is a continuous variable, so every individual would be in a separate pool (with no averaging). Instead, everyone pays into a single pool in proportion to their respective risk. It works out the same in the end.

      Effectively, those who incur reimbursable expense are subsidized by those who don't.

      When you look at things from an ex post cost basis, yes. However, that's an artificial point of view; when considering whether to invest in insurance you don't know the shape of future events. The whole point of insurance is to take that uncertainty and turn it into a stable situation from an ex ante point of view, where risk, not cost, is the determining factor. And in terms of risk there is no subsidy; given all the information known ex ante there is no reason for any insuree to believe they are subsidizing anyone. All insurees within a given pool are equally likely to be compensated. (Or, avoiding the "pool" abstraction, all insurees have a probability-weighted projected compensation which is proportional to their premium.)

      No one willingly joins an insurance program expecting to pay in substantially more than their individual risk—not when competitors are free to offer them lower premiums—and no insurance program could survive for long without balancing risk if low-risk individuals are permitted to opt out. Ergo, no voluntary insurance program can retain ex ante subsidies over the long run.

      --
      "The state is that great fiction by which everyone tries to live at the expense of everyone else." - Bastiat
    15. Re:The Good, the Bad, the Ugly... by NeutronCowboy · · Score: 2, Interesting

      No. What I said and what you said are fundamentally different. You assume like-risk, I don't. Furthermore, I don't assume that pools are formed by individuals. I merely assume that a demand exists, and that there is a product to fill that demand.

      You also misunderstand the reason that insurance works. It works BECAUSE cost is externalized onto all the people who pay for more insurance than they need.

      If people would pay for exactly the insurance they need, they could just as well pay a regular amount into a savings fund, and draw down from there once something happens. That's the only thing they need. If they encounter a situation that exceeds the monthly amount they're paying, they're directly being subsidized by others - who could be paying less if they wouldn't be subsidizing others.

      Let me repeat that: the entire point of insurance is to overcharge a lot of people a little bit so that a few people don't go bankrupt. Plus generate profit for the insurer.

      Finally, you also seem to misunderstand my last comment. There is a total cost to society as a whole when people and companies go bankrupt. There are the obvious ones (layoffs, unemployment benefits being paid out, etc) and the less obvious ones (kids being raised in a worse environment, and being a bigger drain on society down the road). Sometimes, it is cheaper for society as a whole to subsidize the prevention of catastrophic events (such as a medically-related bankruptcy) rather than mop up after it.

      It has nothing to do with it being cheaper because it doesn't come out of my pocket. Absolutely nothing. It is cheaper because in the balance sheet of a society, it is less expensive.

      --
      Those who can, do. Those who can't, sue.
    16. Re:The Good, the Bad, the Ugly... by causality · · Score: 3, Insightful

      From a libertarian standpoint (yours, I'm assuming, from prior discussions), why not just get rid of health insurance altogether? That's the only way to ensure that everyone pays their "fair" costs into the system. That seems to be what you're getting at, so why mince words?

      Bravo. Any free market libertarian should not be using any type of insurance. Afterall, insurance is a form of wealth redistribution.

      Many others have corrected you in basic terms of what insurance actually is, and when the redistribution of wealth is undesirable (i.e. when it's done by force).

      I wanted to add one thing. Insurance of any kind is based on the principle of indemnity. This is a fundamental concept behind all forms of insurance. To summarize indemnity, it means restoring you to where you were (i.e. after a loss). It means that a policyholder does not profit from filing an insurance claim. If your car takes $5000 in damages from an accident, and your insurance company pays $5000 for your car, X dollars to cover your rental vehicle while your car is being repaired, etc., your net gain is zero. You are only paid because you incurred a covered loss, and are only paid the amount that the covered loss has cost you. That's indemnity.

      --
      It is a miracle that curiosity survives formal education. - Einstein
  4. Consent by kidsizedcoffin · · 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?

  5. The doctors' permission?! by icebrain · · Score: 2, Insightful

    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...

    --
    The meek may inherit the earth, but the strong shall take the stars.
  6. s/Sequenced/Genotyped by ianbean · · Score: 3, Informative

    Maybe everyone should read the article. They're being genotyped (700,000 SNPs by Affymetrix array) not sequenced. There is a significant difference...

  7. With or without permission? by Manip · · Score: 2, Insightful

    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...

    1. Re:With or without permission? by SecurityGuy · · Score: 2, Insightful

      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.

    2. Re:With or without permission? by CupBeEmpty · · Score: 2, Informative

      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 with patient treatment would know any identifying information.

      Now one of the interesting caveats to this is that the doctors involved with the patient's care are privy to the results of the SNP array. Presumably they would be told "Patient X Y and Z have mutations correlated with early onset Alzheimers and Huntington's Disease. They would be obligated to tell their patients and begin any appropriate care. My guess is that is why they decided to study patients around 65 years old. Any genetic predispositions would already have manifest themselves. I am curious if it was done to avoid any ethical concerns with "diagnoses" arising from the study.

  8. Re:Illegal to Discriminate by irondonkey · · Score: 2, Insightful

    And of course, nothing illegal is ever done.

  9. Other countries by FenixBrood · · Score: 2, Interesting

    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.

    1. Re:Other countries by BlueParrot · · Score: 2, Informative

      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.

    2. Re:Other countries by Schickeneder · · Score: 4, Insightful

      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.

  10. Re:nice by Red+Flayer · · Score: 2, Funny

    and maybe they can make SENS work so we'll all be "effectively immortal"

    If you want to get SENS working right, you have to blow on the cartridge, but that's ridiculous. Who'd want to make SNES work when they could get the N-64 working and play Goldeneye instead?

    --
    "Trolls they were, but filled with the evil will of their master: a fell race..." -- J.R.R. Tolkien on Olog-hai
  11. Bad summary by neurogeneticist · · 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.

  12. Overheard in the doctor's office... by idontgno · · Score: 2, Funny

    "Well, it appears that DNA analysis proves that you are actually a Streptococcus mutans bacterium. I recommend against antibiotics or toothbrushing in order to extend your lifespan."

    --
    Welcome to the Panopticon. Used to be a prison, now it's your home.
  13. NO NO NO... not gene sequenced by CupBeEmpty · · Score: 2, Informative

    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 and if you really want details you can talk to Affymetrix (I bet these are the arrays they will use).