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Genomic Medicine, Finally 64

Posted by Unknown Lamer
from the sorry-you're-defective dept.
Daniel Dvorkin writes "When I first started studying bioinformatics almost fifteen years ago (!) what drew me to the field was the promise that we might soon be able to provide effective, personalized treatments for a wide variety of diseases. There have been some successes along the way, like genetic tests for warfarin dosage, but for the most part our gains in understanding of basic biology haven't been matched by clinical advances. Now it looks like that is at long last about to change, and it's about time.

Too many people suffer and die from too many diseases that we more or less understand, but can't effectively treat. I hated it when I worked in hands-on patient care, and I hate it now in the lab. We are, finally, getting there."
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Genomic Medicine, Finally

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  • by sexconker (1179573) on Friday March 07, 2014 @08:24PM (#46432255)

    Might as well have just done:

    Title: GABBO
    Summary: GABBO is coming!
    Article: Who is GABBO? No one knows, but he's coming soon!

  • Take two genomic pills and call me in the morning. Sounds affordable.

    • The whole point of it being that it won't be.
      Wanna keep on living? That'll be $200k, please!

  • by mi (197448) <slashdot-2012@virtual-estates.net> on Friday March 07, 2014 @08:48PM (#46432339) Homepage

    It is my understanding, that FDA's current stance is that all such person-specific treatments/medicines must be individually approved... And, because the approval process is so horrendously difficult and expensive, few would be willing (nay, able) to do it. Companies do it for mass-market drugs, but for individually-tailored mixtures — where the expected market is numbered in mere scores or, at best, hundreds of people — it just makes no sense...

    • by nurb432 (527695)

      So you just get treatment somewhere else in the world that is less restrictive.

    • by pepty (1976012) on Friday March 07, 2014 @11:25PM (#46432941)

      It is my understanding, that FDA's current stance is that all such person-specific treatments/medicines must be individually approved

      There is already some flexibility on that front. Cancer immunotherapies like sipuleucel-T (Provenge, approved in 2010) are unique to each patient.

      • by mi (197448)

        There is already some flexibility on that front. Cancer immunotherapies like sipuleucel-T (Provenge, approved in 2010) are unique to each patient.

        "Some flexibility" my sore back... Life-saving medicine is still denied patients [myfoxdc.com], because of the FDA's approval cycle. And the additional obscenity of it all, it that the (would-be) manufacturer of the drug is portrayed as the villain...

        • by pepty (1976012)
          One the one hand that's irrelevant to the topic of the thread (approval hurdles for individualized therapies. On the other hand brincidofovir has yet to succeed in phase III trials' it has also failed a phase II (efficacy) trial, so calling it a life saving drug is a bit premature. On a third hand why are you saying this is about the FDA approval cycle and not about ability to quickly scale up production of the drug to support both a Phase III trial and compassionate use, or the difficulty handing out the d
    • by Daniel Dvorkin (106857) on Saturday March 08, 2014 @12:57AM (#46433203) Homepage Journal

      The clinical trials framework that's evolved over the decades isn't really equipped to deal with personalized medicine, but that's starting to change. Where I work [altituderesearch.org], we're starting to understand the genomic basis of altitude sickness and putting together treatment trials on that basis. This is an area where the potential market is pretty large, of course, and for rare diseases that affect small numbers of people it's going to be harder, but if we can develop a generally accepted body of protocols for individualized trials then it should be possible to apply this to smaller groups as time goes by.

  • by Connie_Lingus (317691) on Friday March 07, 2014 @09:36PM (#46432539) Homepage

    move over "X is the year for linux on the desktop"...we have a new contender.

    2014 is the year for medicine on the genome.

  • The Load (Score:2, Interesting)

    by Anonymous Coward

    How many diseases have cheap preventable causes? Many
    How many cheap preventable causes are the medical "science" industry interested in finding? Zero
    What is the likelihood that insurance companies will want to use genetics to exclude benefits? Very high
    How long time will it take for new research to enter into medical practice? As long time as it will take for the practitioner to retire.
    Genetics: Too much knowledge in the wrong hands is a bad thing.

    • Re: (Score:3, Interesting)

      by pepty (1976012)

      How many diseases have cheap preventable causes? Many How many cheap preventable causes are the medical "science" industry interested in finding? Zero

      Well, bullshit. NIH is quite interested in finding them, as are many healthcare providers. Pharmas aren't, but that isn't their job.

      What is the likelihood that insurance companies will want to use genetics to exclude benefits? Very high

      And very illegal. Has been for years.

      How long time will it take for new research to enter into medical practice? As long time as it will take for the practitioner to retire.

      Depends. If it is leading to a new drug, could be 5-12 years. Diagnostics can be much faster.

      • Re: (Score:2, Insightful)

        by Anonymous Coward

        "Pharmas aren't, but that isn't their job."

        Pharmaceutical companies justify their prices and patents by saying that they're performing a public service. No pharmaceutical company needed an fscking patent to develop, test, and sell Viagra, even though they did get those patents. They say they need patents and tax loop holes to develop expensive drugs with small markets and low profit margins.

        But companies aren't pursuing small markets and low profit margins. Big pharmaceutical companies pursue huge markets w

        • by pepty (1976012)

          "Pharmas aren't, but that isn't their job."

          Pharmaceutical companies justify their prices and patents by saying that they're performing a public service. No pharmaceutical company needed an fscking patent to develop, test, and sell Viagra, even though they did get those patents. They say they need patents and tax loop holes to develop expensive drugs with small markets and low profit margins.

          But companies aren't pursuing small markets and low profit margins. Big pharmaceutical companies pursue huge markets with huge profit margins.

          Most genomic science-based drug development is spearheaded by the NIH, universities, and other non-profit centers. Although university labs suck at this because the moment a researcher makes a discovery, he immediately leaves the school to form his own for-profit lab and chase big money. Then some large company buys his company (smelling a publicly financed science windfall). Then, invariably, the research is left to wither on the vine because the company spends 99% of its time chasing weight loss, diabetes, depression, etc. And the CEOs don't care about this ridiculous cycle because as long as they keep buying up small labs at a reasonable pace, they reap asset gains in the stock market because investors equate these deals with progress.

          No biotech or pharma would receive funding from investors to develop drugs without patents to protect themselves. Hate it or hate it, Wall street calls the tune. Companies spent up to $12B per successful drug approval in 2012.

          Last year, about a third of the drugs approved were for orphan diseases (small markets). Most drugs last year were for cancer, but there was also two new treatments for Hep C, one of which will be a cure for many patients. Here's the list:

          http://www.fda.gov/Drugs/DevelopmentApprova

          • by Rich0 (548339)

            If universities are going to develop drugs they will essentially have to be reconfigured as for profit pharmas to get the job done. Is that really what you want?

            I agree with everything you said but this point. There is no reason the NIH couldn't fund drug development (as opposed to drug basic research - which is what they currently fund for the most part). However, it would be very expensive - there is no reason to think that it won't cost them the $12B/drug industry is spending at the moment (on top of whatever they're already spending on research for those drugs).

            The main benefit of having the NIH do it would be that it gets rid of the model where the patient p

            • by pepty (1976012)
              The CRO (contract research organization; research without an ownership stake) model is already a big part of pharma and biotech. The NIH has started translational medicine programs to get things through preclinical trials, but is still planning on handing off to pharmas for the heavy lifting. I think a big problem a public system would have to solve is going from having the wrong cooks (Wall Street) to having too many cooks spoiling the broth. While occasionally something stellar comes along, a lot of the
              • by Rich0 (548339)

                Agree on all. The one advantage of the private model is that there is at least some correlation between medical need and potential dollars to be made. An influential senator might end up having a billion dollars spent on some rare condition that somebody he cares about happens to have, and no private pharma company would do that.

                The other advantage with the private model is that at least there is competition. Nobody blesses one particular research group and says that they're the only ones allowed to work

      • by Rich0 (548339)

        What is the likelihood that insurance companies will want to use genetics to exclude benefits? Very high

        And very illegal. Has been for years.

        Indeed, ACA also made any exclusion of benefits for pre-existing conditions illegal just recently, mandating universal coverage instead (though in a fashion that will probably cause the law to fail unless the tax penalty is significantly raised). I think that this was going to be necessary one way or another, as simply banning exclusion on the basis of genetic testing was not a viable long-term solution.

        If you ban exclusion on the basis of any kind of knowledge (including genetic testing), then it means th

    • Fear not. The most cost effective model if the one based on general practice family medicine. It achieves an 85% resolution rate, with the other 15% of patients being referred to secondary and tertiary health centers. That is the most cost-effective model in the world and even private companies are slowly gearing towards that. All large effective public health systems in the world work like that. Slowly but surely the US will move towards something more like the British or Canadian systems (to give examples

  • by Anonymous Coward on Friday March 07, 2014 @10:51PM (#46432841)

    People need to maintain the distinction in their head from gene finding (which still goes on and is one of the subjects of TFA) and clinical care. The impact of genomic medicine on clinical care is still limited and is likely to remain so for the forseeable future because of what genomic medicine is currently good at predicting.

    There will be some benefits in selection of oncology protocols in the short term, but knowing cancer genomics does not actually lead to new chemotherapeutic agents except in the long term (even if a drug target is discovered today, if there is no currently approved drug on the market it could take 10-30 years to develop a drug targeting a new class of mutation).

    For most other adult disease, the application will be limited to relatively rare outliers like the limb-girdle disease highlighted in the article. Genomic medicine isn't going to change the fact that huge swaths of patients need to take statins, for example. In fact, the 'success' submitter posits (Warfarin) is actually a bust. The actual benefits from pharmacogenetic testing for Warfarin metabolism are swamped by all the other factors which affect Warfarin metabolism (eg diet and other meds). As for Alzheimer's which TFA also mentions, they're still at the stage of recruiting their 40k subjects to sequence at $1000 a pop. The analysis will take thousands of man-hours just to generate some new hypotheses about Alzheimer's which will, in turn, take 10-30 years to lead to new therapeutics (if we're lucky).

    The one area where whole exome sequencing and related technologies are likely to change care in a meaningful way is pediatrics and fetal medicine where there are tons of rare, fatal things due to rare point mutations. In these cases, early molecular diagnosis would reduce the diagnostic odyssey and allow early discussion of the goals of care.

    • by Daniel Dvorkin (106857) on Saturday March 08, 2014 @01:15AM (#46433243) Homepage Journal

      The actual benefits from pharmacogenetic testing for Warfarin metabolism are swamped by all the other factors which affect Warfarin metabolism (eg diet and other meds).

      The FDA disagrees, and so does the evidence [onlinejacc.org]. And there are a whole lot of areas [nih.gov] where pharmacogenetics is starting to have an impact on treatment. In any case, pharmacogenetics is a subset of pharmacogenomics; for example, as I mentioned in another comment [slashdot.org], the lab where I work is working on expression-based tests for prediction of altitude sickness and setting up drug trials.

      • by Anonymous Coward

        as someone working on front line seeing patients as well as doing genetics, genomic medicine remain a niche field and will remain so. most patients cant even get the basics right and you are talking about tweaking drug dosing by a little based on a polymorphism.

    • There will be some benefits in selection of oncology protocols in the short term, but knowing cancer genomics does not actually lead to new chemotherapeutic agents except in the long term

      What about vaccines? Any informed physician that looks at the data can explain to you that bioinformatics has contributed close to nothing in terms of new vaccines. Why is that?

      With regards to cancer genomics, there are a bunch of questions that arise from potential treatment that the pharmacogenomics peddlers never mention

  • Too many people suffer and die from too many diseases that we more or less understand, but can't effectively treat.

    Yes, this is what classical Greek rhetoric describes as a regressive mirage: the more you learn, the worse it gets, no matter how diseases you cure along the way.

    Here's the amazing thing. Understanding tends to outpace effective intervention. Any snooker player can tell you which ball on the table he'd really like to move next. It's rarely the ball he's presently shooting at. In Genomics, w

  • by Stickerboy (61554) on Saturday March 08, 2014 @01:59PM (#46435117) Homepage

    There have been some successes along the way, like genetic tests for warfarin dosage, but for the most part our gains in understanding of basic biology haven't been matched by clinical advances.

    If you're spending thousands of dollars for genetic testing for a $4 a month drug like warfarin, you're doing it way wrong. It's like the proverbial million dollar cure for the common cold. You could either use one of the newer warfarin alternatives with more consistent pharmacokinetic profiles at a higher price or use the old tried-and-true trial and error dosing.

    Either way, you're still doing weekly to monthly lab testing for warfarin dosing. And your warfarin effectiveness (or bleeding risk) is still going to be thrown way off if you vary your diet significantly or start new medications.

    A much better example of genomic medicine payoff would be targeting therapies to specific cancer types, like the EGFR receptor mutations in some varieties of lung cancer [wikipedia.org].

    • If you're spending thousands of dollars for genetic testing for a $4 a month drug like warfarin, you're doing it way wrong. It's like the proverbial million dollar cure for the common cold.

      Right on, brother, right on!

      Do these guys even know the algorithms for warfarin dose adjustment real doctors use for their real patients?

      When you think of a test, you think of them in terms of a large scale. This is thinking in terms of public health (a term unfamiliar to the large American public, but one whose meaning

  • As we know, science has a lot more to do with the sociology of research than we like to think (say hello to Alan Sokal). Bioinformatics has fallen short of its lofty initial goals because it became a prime example of what nefarious effects the struggle for publication can cause, and also of the alienation of a whole field of scientists by another field of...scientists (?)

    The failures of Bioinformatics have to do with it becoming a gold mine for publication-hungry CS PhDs who - if you're familiar with some o

  • I hope people so helped will be labeled. I don't want to marry a GMO person.

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