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Biotech Technology

Matching Cancers With the Best Chemical Treatments 68

Posted by samzenpus
from the the-machine-says-take-pill-a dept.
Roland Piquepaille writes "When oncologists meet a new patient affected by a cancer, they have to take decisions about the best possible treatment. Now, U.S. researchers have devised an algorithm which matches tumor profiles to best treatments. They've used a panel of 60 diverse human cancer cell lines from the National Cancer Institute — called NCI-60 — to develop their "coexpression extrapolation (COXEN) system." As said one researcher, "we believe we have found an effective way to personalize cancer therapy." Preliminary results have been encouraging and clinical trials are now planned."
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Matching Cancers With the Best Chemical Treatments

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  • Whats next? (Score:1, Funny)

    by ZachMG (1122511)
    now that they are personalizing the treatment can you get any other flavors of kemo?
    • Graviola is shown to be upto 10000 times more effective than chemo on some cancers, but you are unlikely to find anyone recommending it as the drug companies are more interested in finding the active component and patenting it than helping cure people.

      A friend of mine has cancer that was so bad she was warned that the treatment was more about managing the progress of the disease than curing it. After 6 months her doctor could not explain why her cancer was in remission. The reason she gives is the gaviola c
      • by dmpyron (1069290)
        WHAT A CROCK! And I suppose this will also enlarge my penis. You make the claim that it's "shown to be up to 1000 times more effective". Cites, please. And don't go trotting out the supposed study from Johns Hopkins. That's an urban legend that they have been trying to kill for a while. http://www.snopes.com/medical/disease/cancerupdate .asp [snopes.com]
        • "WHAT A CROCK!" !! well its nice of you to dismiss it so quickly and easily. My friend was relieved to know that her delayed funeral was just a figment of her and my imagination.

          I also said upto 10,000 times more effective, not just 1,000! This is the claim that outrages you so much. I can understand that as it does seam to good to be true, but then ketchup was reported in the national press (UK) earlier this year to be a very effective treatment for prostate cancer. Sadly I cannot remember the study they b
  • Insurance (Score:5, Interesting)

    by ChromeAeonium (1026952) on Thursday July 26, 2007 @01:56AM (#19993103)
    Lets just hope that doctors who use this algorithm still throughly examine every patient before beginning treatment, because, while probably useful, I doubt its as effective as a full examination by a professional. I kinda wonder if this would be used in lesser insurance policies to substitute extensive examinations. Premium insurance plan gets a full examination prior to treatment, the plans that cost less have the cancer run through an equation, and a treatment is printed out.
    • Re:Insurance (Score:4, Informative)

      by Daniel Dvorkin (106857) on Thursday July 26, 2007 @02:37AM (#19993297) Homepage Journal
      The application of the algorithm will come well after the "full examination by a professional" stage -- they'll be using it once the cancer has been diagnosed, and they're deciding on which of several specific treatments to use.
      • Re: (Score:3, Informative)

        In addition, since this program requires microarray gene expression profiling analysis, which is somewhat more complicated than a lot of lab work (AFAIK), you wouldn't do this test in the first office visit, but more likely much later, and for cancers that don't have or aren't responding to standard treatments.
    • Re:Insurance (Score:4, Informative)

      by piojo (995934) on Thursday July 26, 2007 @04:15AM (#19993763)

      Lets just hope that doctors who use this algorithm still throughly examine every patient before beginning treatment, because, while probably useful, I doubt its as effective as a full examination by a professional.
      Actually, if I remember correctly, an algorithm is better than doctors at diagnosing heart attacks... something about doctors being too human, and being unable to ignore statistically unimportant factors such as age (that is, being younger makes you less likely to experience a heart attack in just the same way that being younger makes you less likely to experience the symptoms of a heart attack--a given set of symptoms is equally to indicate a heart attack, regardless of age). My source? Blink, by Malcolm Gladwell. I'm probably misremembering a some of the details, but the point is there.

      You may be right about its effectiveness in some cases, but its correctness, once it's perfected, will most likely be statistically better than the judgement of doctors.
    • Re:Insurance (Score:5, Interesting)

      by _14k4 (5085) <sullivan.t@gmai[ ]om ['l.c' in gap]> on Thursday July 26, 2007 @08:12AM (#19994851)
      My wife is a breast cancer survivor (people are survivors from day one) and we are in the process of finding out that, hopefully, it has not spread to her bones. I can tell you, with 100% certainty, that cancer patients and caregivers do not care what the insurance companies say. The doctor can bill me personally and take the money right out of my paycheck if you need to. I will also say that, in my own experience, the oncology centers we have used have cared less about insurance than my PCP! One of the first things they ask is, "Do you need money to help pay bills during all of this?"

      I would hope that this is used in conjunction with other treatment options - not as a "failsafe to lower level insurances"...
  • by r00t (33219) on Thursday July 26, 2007 @02:07AM (#19993159) Journal
    Imagine this. You go to the supermarket. Right there, next to the pork chops and sirloin steaks, is a cancer. A real human cancer. No creature was ever killed for it, so it's even vegan and PETA would love it.

    You take it home, grill it up, and... well how does it taste? Do different types of cancer have different flavors? Which ones are good?

    The stuff is damn easy, too easy even, to grow. We might as well make use of it.
    • by Torodung (31985)
      Oh man, Joe Jackson [lyricsfreak.com] would have a field day with that...

      --
      Toro
    • by B3ryllium (571199)
      Some tumors contain teeth, hair, and other wacky fun items.

      I'd rather not taste it, thank you very much.
      • by Anonymous Coward

        Some tumors contain teeth, hair, and other wacky fun items.

        Marge: But the grocery store sells meat for 35 cents a pound.
        Lisa: And it doesn't have teeth and hair in it.
        Homer: Those are prizes.
      • by dubbreak (623656)

        Some tumors contain teeth, hair, and other wacky fun items.

        Had I read that a month ago I wouldn't have believe it, but my fiance is a perioperative nurse (she works in the OR) and recently described tumors with hair and/or teeth inside.

        I'd rather not taste it, thank you very much.

        Me neither. I almost gagged when I had it visually described to me. I'd be full on projectile if someone put a steaming hair and tooth pile on my plate.

    • Re: (Score:2, Informative)

      by bersl2 (689221)
      Aren't there supposed to be a few dogs that have been trained to smell the difference between healthy tissue and cancerous tissue? Or was that a bust? Or am I making it up?

      Not that a dog can communicate the olfactory properties of tumors to us.
    • by raddan (519638)
      Wow. Easily the most fucked up thing I've read on Slashdot. Just... wow.
  • Ooo dirty (Score:2, Funny)

    by Null Nihils (965047)
    I bet you they're running the COXEN in some boxen.

    I bet you the COXEN is a big... application, and the boxen are tight...ly... integrated... if they run Linux. Otherwise the boxen are hosen. Or something.

    *ducks*
  • by syousef (465911) on Thursday July 26, 2007 @03:06AM (#19993443) Journal
    Most doctors won't even use computers to help them make diagnoses because they feel they should always be able to do better. What tends to happen is that if a rare condition presents they can miss it quite easily. I'm no doctor but I believe it has to do with the medical profession's heritage, culture and the politics of their licensing institutions. Doctors are taught that every diagnosis can be life or death. Using an aid like a computer to make the decision therefore is seen as a sign of weakness.

    When you think about it that's insane. There's no way any doctor can know every medical condition that presents, even the rarer ones. What's needed is a system whereby the doctor can check his diagnosis against what comes up with a computer search against the same symptoms. There needs to be no stigma in doing this. If something comes up that's rare but could fit the doctor then needs to have a think about whether it's worth addressing. Systems like this have been rejected by the medical profession time and again which is unfortunate because to get good at diagnosis they'd need to be honed with a lot of feedback, particularly where multiple conditions present. However they have the potential to help pick up serious conditions earlier than what even the best doctor might without them.

    Same goes for this system except we're talking treatment choice not diagnosis. One hurdle is getting other doctors to accept it. Another is making sure the control and final say remains with the doctor and patient not some machine. There'd be great temptation for the medical insurers to use such a system to avoid providing treatment that a doctor believes is necessary.
    • Re: (Score:3, Insightful)

      by Ihlosi (895663)
      Using an aid like a computer to make the decision therefore is seen as a sign of weakness.



      It also opens a floodgate for all kinds of interesting liability issues. No medical device manufacturer wants to be hit with an avalanche of lawsuits - which is what's going to happen when they make a device that does anything more advanced than making trivial diagnostic or therapeutic decisions (i.e. "patient has ventricular fibrillation -> administer defibrillation shock").

    • by macklin01 (760841) on Thursday July 26, 2007 @05:06AM (#19994007) Homepage

      Don't forget that the gap needs to be bridged from both sides: while it will indeed take some cultural changes in the medical community to use computational / predictive tools in choosing therapy, it will also require cultural changes in the modeling community to facilitate this. Furthermore, doctors' trust in computational tools must be earned by a well-validated track record of results by the mathematical / engineering community. Interestingly, these cultural changes are underway and can already be observed.

      My primary field of research is developing computational tools for modeling cancer progression and angiogenesis, primarily using a PDE point of view where I model nutrient transport within the body and uptake by tumor cells, some simple biomechanics, the degradation and remodeling of the extracellular matrix by the tumor, and the resulting motion of the tumor boundary within the tumor. In fact, this was my dissertation topic just a little over a month ago; the interested reader can see my publications here [uci.edu] and some animations of cancer simulations here [uci.edu].

      In the several years I've been doing this work, I've seen interesting changes on both sides of the aisle. The mathematical models of cancer have grown in sophistication and realism at an incredible speed. Five or six years ago, models would only examine a single, isolated aspect of cancer growing in homogeneous tissues that were more idealized than even simulated in vitro petri dishes; today, they model many aspects of cancer and the interaction between those aspects. Several years ago, the models were little more than interesting mathematical objects with simplified, spherical solutions that weren't very interesting outside the mathematical community; today, we're simulating complex tumor shapes in fairly realistic tissues, and the results are shedding light on current problems in cancer biology that are otherwise difficult to understand.

      Several years ago, it was difficult to even get doctors, oncologists, and others to even look at our research (in our field in general). Today, we're building a track record of results that makes the work easier to trust. Mathematicians and engineers are also realizing the need to acquire the "vocabulary" and biological background necessary to communicate with doctors and biologists, and they're making moves to bridge the gap and collaborate. In the meantime, more cancer biologists are realizing that it takes more than studying isolated cells to understand cancer systems, and they're reaching out to mathematicians to model these complex systems.

      The result: very rich and exciting collaborations between doctors and mathematicians to develop helpful predictive tools. My group (at the UT Health Science Center in Houston, with the M.D. Anderson Cancer Center) is doing exciting joint work with oncologists, biologists, mathematicians, and engineers to combine experiments with well-calibrated models of glioblastoma, an aggressive form of brain cancer. Sandy Anderson and Vito Quarnata are doing similar joint mathematical/biological work on breast cancer at Vanderbilt and the University of Dundee, and their work has been featured on slashdot before.

      So, it really requires growth toward collaboration from both sides, but fortunately, the need for this has been recognized by both communities and is occurring as we speak. It's a very exciting time in cancer systems biology and computational / predictive oncology! -- Paul

    • by bwen (675669) on Thursday July 26, 2007 @05:08AM (#19994021)
      As a physician, I resent your inaccurate and uninformed response. "Doctors are taught that every diagnosis can be life or death" - where did you hear that? You are making sweeping generalizations and accusations. The ASSUMPTION that physicians resist using a computer to research a medical problem is ridiculous (at least in the US.) I do not know a MD that is not comfortable with a computer nor with researching a medical problem online. We often have resources that the general public does not use, and due to lack of an additional 7-11 years of post-grad training, would not understand. You seem to typify the person that turns to herbs from China that mostly consist of grass/dirt and expound how modern science is ignoring it. We very much appreciated you in the dark ages, thanks for your insight!
      • Re: (Score:2, Interesting)

        by UbuntuDupe (970646) *
        Oh really? So doctors have hastened the end of the hand-scrawl prescription so they can replace it with a computerized database that automatically checks for possible excessive dosage or condition interaction? So doctors quickly change to empirically validated methodologies that sidestep their "expertise" for a rote checklist? So doctors are interested in lifting the artificial limits on MDs granted? So doctors never wait until a patient "asks his doctor about NewMeda" to research it, and never change th
        • by bwen (675669)
          I'll try to address your points (some of which are valid) First, the vast majority of doctors do not possess programming skills to create the database/program for computerized prescriptions. Most are happy to use it as it is usually quicker, more legible, goes on file automatically and checks against allergies to the medication. I have not met a doctor who thinks he is completely infallible- although some have a "God complex" Second - doctors do rely on their "expertise," which does not mean ignoring "empir
          • First, the vast majority of doctors do not possess programming skills to create the database/program for computerized prescriptions

            My complaint was NOT that "every doctor has not written a database program to replace prescriptions"; it was that that doctors resist such a change to one.

            I have not met a doctor who thinks he is completely infallible- although some have a "God complex"

            I haven't seen an unsecure operating system -- although I have seen Windows.

            Second - doctors do rely on their "expertise," which does not mean ignoring "empirically validated methodologies" - do you think there is a conspiracy to actively participate in bad medicine when there is typically no benefit to it.

            I think that doctors do resist transparency in their occupation for fear of bringing failures to light and having to conform to methodologies that imply the irrelevance of (a large part) of their "expertise", absolutely. This is a human failing, in which doctors are far from a

            • Re: (Score:2, Informative)

              by bwen (675669)
              I haven't found a resistance to using computerized prescriptions where they are effectively implemented- there are good programs and bad ones. Power failures and system freezes are 2 of the problems with the present ones. If a program is more efficient, reliable, easy to use and codes/bills effectively, you can be sure that doctors will not resist it. There are a few subpar programs out there that i have used that are not effective. The lack of transparency is, I believe, less a matter of pride and more one
          • That said, the artificial limits (largely circumvented by foreign medical schools but still limited by residency slots) do keep the quality of MDs up as it is fairly competitive to get into med school

            The Osteopathic profession is also helping to meet the (artificial) doctor shortage. As you might be aware, Allopaths organized in the mid-1800's to exterminate their competition. The problem was that they were getting their clock cleaned by health care providers who used more effective modalities than bleeding, mercury and surgery. 100 Years of Medical Robbery [mises.org] covers how the AMA managed to shut down 1/2 the country's medical schools between 1910 and the 1960's (also read the followup, 'Real Medical Free

      • If I had a dollar for every time a doctor almost killed me because they were to certain of themselves to do the proper testing (an X-ray) and research (PDR), I would have 3 dollars.

        That, my friend, is 3 dollars too many.

        I fear the day I get a serious disease, because I can't trust doctors with a sinus infection.
      • Re: (Score:2, Informative)

        by edsyc (1088833)
        I wouldn't be so quick to get on your "I'm a physician" high horse. Of course physicians use computers in their work. But when it comes to making diagnoses, there is plenty of evidence that physicians resist using computer aids:

        Kaplan B. Evaluating informatics applications: Clinical decision support systems literature review. Int J Med Inform. 2001;64:15-37.

        Overhage JM, Tierney WM, McDonald CJ. Computer reminders to implement preventive care guidelines for hospitalized patients. Arch Intern Med. 199
      • by syousef (465911)
        Well truly I don't care that you resent the response. Your profession is full of some very shonky people.

        As a patient I've received some extremely bad treatment from doctors, and so have my loved ones. Some examples:

        - A loved one repeatedly got seizure causing medication increased despite seizures clearly being listed as a contra-indication. This is by a neurologist as well as GPs. In the end she was having a seizure every day or 2. I looked it up and brought this to their attention at which point he said y
    • by QunaLop (861366)

      I think that you make some valid points, however, i wanted to expand on the fact that "no one knows everything" - People seem to have limited memory, this system may be a key component in a general "diagnosis AI." I imagine someday a system where a physician enters your symptoms and test results, the system would then provide the user with possible diagnoses and medical tests to perform to further reduce possible diagnoses/confirm a diagnosis.

      I was originally diagnosed with an "infectious tumour" (not ca

    • by vegiVamp (518171)
      IANAA (I am not an American), but if the way the American lawsuit-culture is perceived here is anywhere near accurate, then I can imagine MDs are quite reluctant to use this kind of tech.

      Imagine someone going for an examination, and the MD deciding to dismiss the software's suggestion that the patient may have some rare disease. If the patient later does turns out to be suffering from that disease, or even dies from it, the malpractice lawsuits will soon be flying, even though the doc's decision may have be
    • Well, COXEN will generally be used (at least at first) to suggest treatments for cancers that have either failed or don't have first-line treatments. So presumably the doctor has already tried or doesn't know which drug to use. In addition, since chemotherapeutic agents are generally administered in combinations, and because there are quite a few cancer drugs out there, the number of different combinations can be quite high, so hopefully this can be used to predict a few drugs that a) haven't been used, b)
    • by abushga (864910) *
      What five idiots moderated this post "insightful?"

      I'm still around to write this because my oncologist kept such a clear focus on my disease stage and response to treatment. His knowledge, experience, intuition, and talent in asking the right questions achieved a miraculous outcome. Like a true /.er, I burned a lot of bandwidth researching the etiology of my phenotype; my long-suffering oncologist patiently fielded my unanswered questions, even though they were often beyond the scope of his practice. It was
  • Variations exists, so its not that straight forward, however Algorithms like these act as a wonderful reference.
  • Not a new idea (Score:3, Interesting)

    by Crashbull (1133163) on Thursday July 26, 2007 @03:19AM (#19993511)
    There is a lab in Germany that's been doing that for years now. This isn't a new idea. I'm just really surprised and a bit disappointed that no one in the US has bothered to do something like this before.
    • America, behind another country in $(SCIENCE)? SHOCKING! :P

      -:sigma.SB

    • by AngryDad (947591)
      All I can say - good luck with that. I did this in 1995 for CHD (coronary heart disease) patients. We analyzed 5-years of data for ~2500 patients in order to identify the best suitable treatment. It did not go very well - factor analysis revealed too many variables and although we identified several trends and patterns, they were inconsistent and unlikely suitable to be used clinically.
      • Well, COXEN works by examining patterns of genetic deregulation for each individual cancer tissue sample, and so this should be a more direct measurement of the causative factors than the situation you've described.
  • by Anonymous Coward on Thursday July 26, 2007 @03:22AM (#19993537)
    int drug_choice_algorithm(){
       int our_most_expensive_drug = 1;
       int other_cheaper_option = 0;

       if(patient_has_insurance()){
           return our_most_expensive_drug;
       }
       else {
           if (patient_is_rich()){
               return our_most_expensive_drug;
           }
       }
       return our_most_expensive_drug;
    }

     
  • by DrZZ (138100)
    To see all the underlying data, go to DTP Human Tumor Cell Line Screen [nih.gov] data page on the National Cancer Institute's Developmental Therapeutics Program web site [nih.gov]. There's a lot more data listed here [nih.gov].
  • Good news (Score:3, Interesting)

    by wamerocity (1106155) on Thursday July 26, 2007 @06:18AM (#19994333) Journal

    I work at the Huntsman Cancer Hospital, a division of the University of Utah hospital. I draw blood on dozens of patients every day and see the same pattern of treatment as we see similar cancer patients come in. I can only see this as a good thing to help diversify and specialize treatments.

    As someone who won the lottery and was treated in a cancer hospital myself, I found my doctor seemed to put me on a fast track to treatment, straight out of the books, which involved removing an important part of my anatomy (not THAT part). With much resistance on my part, I got him to investigate other options and I actually got to keep my spleen.

    From a doctors POV, I know it can be difficult as well as uneconomical to see every patient as a super-special-individual-with-their-own-needs-and- feelings, but with the type of stigma surrounding the C-word (not THAT C-word) it is pretty much a necessity, at least from my experience. If this new system requires doctors to spend a little more time with a patient and yield a higher success rate, then it is an all-around win.

    • by bcolflesh (710514)
      I ruptured my spleen when I was a kid (fell out of building) - I can tell you that it's not important at all and has had no effect on my health in my 25+ years since the accident.
  • A good article on the cancer industry--> http://www.newstarget.com/021892.html [newstarget.com]
  • Can you say 'Licensing Fees'?

    John Coxen
  • From TFA "Another issue is that the 60 cell lines did not include all important cancer types (for example, certain bladder cancers, lymphomas, and small cell lung cancers were not among the 60 lines studied)."

    Soooo. My wife (Lymphoma when she was 32) and me (Small cell Lung Cancer at 37) aren't included. My treatment was with chemo drugs that have been in use for 30+ years (VP-16 & Cisplatin) with Chest Radiation. It really sucks that there aren't any new treatments for anything except Breast Cancer t
    • I don't want to sound sour but everytime I see a cancer story on /. I hope it will eventually help someone to not go through the hell that is cancer treatment because it doesn't do anything for me

      The "normal" way of treating cancer (and heart disease, and diabetes, and arthritis, and ...) is way too profitable to make it anything but losing proposition for the patient. First they fleece the patient for all they're worth (even better if they've good insurance or Medicare), then the patient frequently dies anyways. The medical-industrial complex likes this state of affairs because it's good for their bottom line.

      Effective cancer therapies are unprofitable because the patent has expired, or is by its

  • we did things like this over a decade ago at SUGEN. i did some stuff like this in the years after SUGEN too, just for fun, but took a completely different approach. the main caveat is that some of the NCI screening data is questionable, so extrapolating from those particular zones would likely be bogus. if anyone is really interested in this stuff, there is a nice 1997 article where NCI reviewed its efforts in _Science_, volume 275, number 5298, pages 343-349, (DOI: 10.1126/science.275.5298.343)

    there

    • I'd be interested in hearing about some of the work you did (and also what SUGEN is--I'm sorry but I'm not familiar with it).


      The NCI-60 data can be spurious, but maybe some confidence assessment can be made based on the number of times any individual compound has been tested.

  • OK, I don't see anybody else here posting to this point, so I thought that I would jump in here.

    The thing that is really striking about this study is that this is the first example that I've heard of that uses genetic information about an individual patient to customize treatment. Most treatment decisions simply look at individual phenotypes (ie, apparent, external traits) to help make the decisions, but by starting to look directly at genotypic information, we are getting much closer to the point of a

  • where I can go to a hospital, have my life-threatening ailment reduced to a few numbers and receive "personalized" treatment by plugging them into a cold, unfeeling math equation.

    While the story uses a poor choice of language, the ability to cut-down arbitrary treatment plans would be a step in the right direction. More surgical strikes instead of carpet-bombing.

There is no distinction between any AI program and some existent game.

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