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Hope and hype in genomics and “personalized medicine”

“Personalized medicine.” You’ve probably heard the term. It’s a bit of a buzzword these days and refers to a vision of future medicine in which therapies are much more tightly tailored to individual patients than they currently are. That’s not to say that as physicians we haven’t practiced personalized medicine before; certainly we have. However it has only been in the last decade or so that our understanding of genomics, systems biology, and cell signaling have evolved to the point where the vision of personalized medicine based on each patient’s genome and biology might be achievable within my lifetime.

I was thinking about personalized medicine recently because of the confluence of several events. First, I remembered a post I wrote late last year about integrating patient values and experience into the decision process regarding treatment plans. Second, a couple of months ago, Skeptical Inquirer published an execrably nihilistic article by Dr. Reynold Spector in Skeptical Inquirer in which he declared personalized medicine to be one of his “seven deadly medical hypotheses,” even though he never actually demonstrated why it is deadly or that it’s even really a hypothesis. Come to think of it, with maybe–and I’m being very generous here–one exception, that pretty much describes all of Dr. Spector’s “seven deadly medical hypotheses”: Each is either not a hypothesis, not deadly, or is neither of the two. Third, this time last week I was attending the American Association for Cancer Research (AACR) meeting in Orlando. I don’t really like Orlando much (if you’re not into Disney and tourist traps, it’s not the greatest town to hang out in for four days), but I do love me some good cancer science. One thing that was immediately apparent to me from the first sessions on Sunday and perusing the educational sessions on Saturday was that currently the primary wave in cancer research is all about harnessing the advances in genomics, proteomics, metabolomics, and systems and computational biology, as well as the technologies such as next generation sequencing (NGS) techniques to understand the biology of each cancer and thereby target therapies more closely to what biological abnormalities drive each cancer. You can get an idea of this from the promotional video the AACR played between its plenary sessions:

Which is actually a fairly good short, optimistic version of my post Why haven’t we cured cancer yet? As I mentioned before, with this year being the 40th anniversary of the National Cancer Act, as December approaches expect a lot of articles and press stories asking that very question, and I’m sure this won’t be the last time I write about this this year.
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Posted in: Basic Science, Cancer, Clinical Trials, Diagnostic tests & procedures, Politics and Regulation

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An ICD Code for the Running Piglets!

… animals are divided into (a) those that belong to the emperor; (b) embalmed ones; (c) those that are trained; (d) suckling pigs; (e) mermaids; (f) fabulous ones; (g) stray dogs; (h) those that are included in this classification; (i) those that tremble as if they were mad; (j) innumerable ones; (k) those drawn with a very fine camel’s-hair brush; (l) etcetera; (m) those that have just broken the flower vase; (n) those that at a distance resemble flies.

— Jorge Luis Borges (1899–1986)1

Not too long ago, I came across a disease taxonomy proposed by a certain East-West Medical Research Institute (EWMRI), that includes the kind of fantastic afflictions — such as “running piglet” disorder — fit for the best Borgesian list.

This obscure institute, located at Kyung Hee University in Seoul, Korea, is one of the 800 WHO Collaborating Centres designated to carry out various activities in support of the Organization’s programs. With the collaboration of China, Japan, Vietnam, Australia, and the US, this center is working to incorporate medieval Asian disease nomenclature to the 11th version of the International Classification of Disease (ICD-11).
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Posted in: Acupuncture, Basic Science, Science and Medicine

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Are you sure you’re allergic to penicillin?

As a pharmacist, when I dispense medication, it’s my responsibility to ensure that the medication is safe and appropriate for the patient. There are numerous checks we go through including verifying the dose, ensuring there are no interactions with other drugs, and verifying the patient has no history of allergy to the product prescribed. Asking about allergies is a mandatory question for every new patient.

Penicillin is one of the oldest antibiotics still in use despite widespread bacterial resistance. Multiple analogs of penicillin have been developed to change its effectiveness, or improve its tolerability. And other classes of antibiotics (e.g., cephalosporins) share some structural features with penicillin. These products are widely used for both routine and serious bacterial infections. Unfortunately, allergies to penicillin are widely reported. Statistically, one in ten of you reading this post will respond that you’re allergic to penicillin. Yet the incidence of anaphylaxis to penicillin is estimated to be only 1 to 5 per 10,000. So why do so many people believe they’re allergic to penicillin? Much of it comes down to how we define “allergy.”

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Posted in: Basic Science

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The NCCAM Strategic Plan 2011-2015: The Good, The Bad, and The Ugly

As hard as it is to believe, it’s been nearly a year since Steve Novella, Kimball Atwood, and I were invited to meet with the director of the National Center for Complementary and Alternative Medicine (NCCAM), Dr. Josephine Briggs. Depending upon the day, sometimes it seems like just yesterday; sometimes it seems like ancient history. For more details, read Steve’s account of our visit, but the CliffsNotes version is that we had a pleasant conversation in which we discussed our objections to how NCCAM funds dubious science and advocacy of complementary and alternative medicine (CAM). When we left the NIH campus, our impression was that Dr. Briggs is well-meaning and dedicated to increasing the scientific rigor of NCCAM studies but doesn’t understand the depths of pseudoscience that constitute much of what passes for CAM. We were also somewhat optimistic that we had at least managed to communicate some of our most pressing practical concerns, chief among which is the anti-vaccine bent of so much of CAM and how we hoped that NCCAM would at least combat some of that on its website.

Looking at the NCCAM website, I see no evidence that there has been any move to combat the anti-vaccine tendencies of CAM by posting pro-vaccination pieces or articles refuting common anti-vaccine misinformation. Of all the topics we discussed, it was clearest that everyone, including Dr. Briggs, agreed that the NCCAM can’t be perceived as supporting anti-vaccine viewpoints, and although it doesn’t explicitly do so, neither does it do much to combat the anti-vaccine viewpoints so ingrained in CAM. As far as I’m concerned, I’m with Kimball in asserting that NCCAM’s silence on the matter is in effect tacit approval of anti-vaccine viewpoints. Be that as it may, not long afterward, Dr. Briggs revealed that she had met with homeopaths around the same time she had met with us, suggesting that we were simply brought in so that she could say she had met with “both sides.” Later, she gave a talk to the 25th Anniversary Convention of the American Association of Naturopathic Physicians (AANP), which is truly a bastion of pseudoscience.

In other words, I couldn’t help but get the sinking feeling that we had been played. Not that we weren’t mildly suspicious when we traveled to Bethesda, but from our perspective we really didn’t have a choice: if we were serious about our mission to promote science-based medicine, Dr. Briggs’ was truly an offer we could not refuse. We had to go. Period. I can’t speak for Steve or Kimball, but I was excited to go as well. Never in my wildest dreams had it occurred to me that the director of NCCAM would even notice what we were writing, much less take it seriously enough to invite us out for a visit. I bring all this up because last week NCCAM did something that might provide an indication of whether it’s changed, whether Dr. Briggs has truly embraced the idea that rigorous science should infuse NCCAM and all that it does, let the chips fall where they may. Last week, NCCAM released its five year strategic plan for 2011 to 2015.

Truly, it’s a case of The Good, The Bad, and The Ugly.
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Posted in: Basic Science, Clinical Trials, Politics and Regulation

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Old drugs, new tricks

What does honey bee colony collapse disorder have to do with a potential new cancer treatment?

They both relate – in a convoluted manner – to an old antibacterial drug called nitroxoline.

True to my devotion as a natural product pharmacologist, I’m proud to say that new life would not have come to nitroxoline had not a fungal natural product called fumagillin been studied as an antiangiogenic anticancer drug – one that inhibits the formation of new blood vessels.

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Posted in: Basic Science, Cancer, History, Pharmaceuticals

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Followup: More Evidence against the XMRV Virus as a Cause of Chronic Fatigue Syndrome

A mouse leukemia retrovirus, xenotropic murine leukemia virus-related virus (XMRV retrovirus), has been under consideration as a possible cause of chronic fatigue syndrome (CFS, and also prostate cancer). In a study published in Science in October 2009, Lombardi et al. found XMRV in 67% of CFS patients and 3.7% of controls. Several subsequent studies in the UK, the Netherlands, and the US — by lead authors Erlwein, van Kuppleveld, Groom , Switzer and Henrich — failed to find XMRV at all.

Now a new study published in Retrovirology by Hue et al. shows that the original positive findings were likely erroneous and due to contamination in the lab. The complete article is available online.

We provide several independent lines of evidence that XMRV detected by sensitive PCR methods in patient samples is the likely result of PCR contamination with mouse DNA and that the described clones of XMRV arose from the tumour cell line 22Rv1, which was probably infected with XMRV during xenografting in mice. We propose that XMRV might not be a genuine human pathogen.

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Posted in: Basic Science

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Of SBM and EBM Redux. Part I: Does EBM Undervalue Basic Science and Overvalue RCTs?

During the most recent kerfuffle about whether or not Evidence-Based Medicine can legitimately claim to be science-based medicine, it became clear to me that a whole, new round of discussion and documentation is necessary. This is frustrating because I’ve already done it several times, most recently less than a year ago. Moreover, I’ve provided a table of links to the whole series at the bottom of each post*…Never mind, here goes, and I hope this will be the last time it is necessary because I’ll try to make this the “go to” series of posts for any future such confusions.

The points made in this series, most of which link to posts in which I originally made them, are in response to arguments from statistician Steve Simon, whose essay, Is there something better than Evidence Based Medicine out there?, was the topic of Dr. Gorski’s rebuttal on Monday of this week, and also from several of the comments following that rebuttal. Mr. Simon has since revised his original essay to an extent, which I’ll take into account. I’ll frame this as a series of assertions by those who doubt that EBM is deficient in the ways that we at SBM have argued, followed in each case by my response.

First, a disclaimer: I don’t mean to gang up on Mr. Simon personally; others hold opinions similar to his, but his essay just happens to be a convenient starting point for this discussion. FWIW, prior to this week I perused a bit of his blog, after having read one of his comments here, and found it to be well written and informative.

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Posted in: Basic Science, Medical Academia, Science and Medicine

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Chronic Fatigue Syndrome: Lots of Speculation

Humans love to find patterns in the world. Sometimes patterns exist, sometimes they are imaginary. Sometimes you can see a pattern that may be interesting and ignore its significance. As a resident I used to say that anyone who smokes three packs of cigarettes a day has to be schizophrenic, it was meant more as a joke, when, in fact, it was later discovered that tobacco helps ameliorate the symptoms of schizophrenia. I need to pay more attention.

Part of my job is to look for patterns as a key to the patients diagnosis. Diseases and pathogens tend to (more or less) cause reproducible signs and symptoms and looking for that pattern is often the most helpful clue towards finding the diagnosis. Of course things are never as easy as one would like, as you have to consider whether you are seeing common manifestations of a common disease, uncommon manifestations of a common disease, common manifestations of a uncommon disease and, the hardest, uncommon manifestations of an uncommon disease. When I have a complex or uncertain cause, I explicitly run through that, and other, litanies so I do not miss a unusual diagnosis.

Chronic Fatigue Syndrome (CFS) has, at least to my way of thinking, two patterns. I see the occasional CFS patient in clinic and, I hope, pay attention to their disease patterns. I keep in mind I may be seeing a pattern that does not exist, but looking for disease patterns is what doctors are trained to do.

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Posted in: Basic Science, Science and Medicine

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Fields, Alternative Medicine, and Physics

In 1996 the American Physical Society, responding to a request from the National Research Council, was asked to examine the potential health hazards of power lines. One of the concerns was that electromagnetic background fields of 2 milligauss might cause cancer (for comparison the earth’s magnetic field is 500 milligauss and fields generated by human physiological processes are hundreds of thousands of times less than 2 milligauss). Monitors of outdoor exposure for children to wear were marketed to parents. “Some city regulations sought to constrain B fields to less than 2 milligauss”. The report, which was a comprehensive study of the alleged dangers, included both molecular and epidemiologic studies and found that no adverse health effects could be attributed to these low fields.

One of the conclusions emphasized that physical calculations rule out carcinogenic effects because at physiological temperatures thermal noise fields in human cells are larger than the background fields from power lines.1, 2 Thus the political agenda, concerned with fear of carcinogenic mechanisms arising from low level magnetic fields, lost credibility. However, about 10 years later claims for health effects from mattress pads equipped with small magnets were marketed. A study of this was funded by National Institute of Health’s Center for Complementary and Alternative Medicine and claims for their benefits were published in alternative medicine journals.3

Some of the rationale for the claims were ludicrous. I attended one sales pitch which claimed their mattress magnets were better because they incorporated only North Poles. About  the same time, small 300 gauss magnets, began to appear on the shelves of drug stores. In 2007 a lawsuit brought by the National Council against Health Fraud against advertisers of these products was successfully settled. I was one of the persons who agreed to appear as an expert witness if needed. The Federal Trade Commission also threatened to prosecute purveyors who claimed healthful benefits for these products.
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Posted in: Basic Science

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NDE Update

Back in 2008 I wrote on Near Death Experiences (NDE’s). I have an interest in this topic as I have frequent exposure to near death; my wife has a predilection for watching Judge Judy. Since 2008 there have been a few studies on the topic of NDEs as researchers try and find evidence that consciousness transcends the brain, if that is what a NDE represents. I have also been ill for most of the last week and have not had the usual time to spend generating typos to drive some readers to distraction. Fortunately, I have a miracle cure that is 100% effective in resolving all my self-limited illnesses: time. It passed and with it the illness. As a result I am about 10 days behind in the commitments in my life, so this will be a shorter than usual post.

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Posted in: Basic Science, Faith Healing & Spirituality

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