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“Precision medicine”: Hope, hype, or both?

The cost to sequence a whole genome has been plummeting impressively since 2007.

The cost to sequence a whole genome has been plummeting impressively since 2007.

I am fortunate to have become a physician in a time of great scientific progress. Back when I was in college and medical school, the thought that we would one day be able to sequence the human genome (and now sequence hundreds of cancer genomes), to measure the expression of every gene in the genome simultaneously on a single “gene chip,” and to assess the relative abundance of every RNA transcript, coding and noncoding (such as microRNAs) simultaneously through next generation sequencing (NGS) techniques was considered, if not science fiction, so far off in the future as to be unlikely to impact medicine in my career. Yet here I am, mid-career, and all of these are a reality. The cost of rapidly sequencing a genome has plummeted. Basically, the first human genome cost nearly $3 billion to sequence, while recent developments in sequencing technology have brought that cost down to the point where the “$1,000 genome” is within sight, if not already here, as illustrated in the graph above published by the National Human Genome Research Institute. Whether the “$1,000 genome” is truly here or not, the price is down to a few thousand dollars. Compare that to the cost of, for instance, the OncoType DX 21-gene assay for estrogen receptor-positive breast cancer, which costs nearly $4,000 and is paid for by insurance because its results can spare many women from even more expensive chemotherapy.

So, ready or not, genomic medicine is here, whether we know enough or not to interpret the results in individual patients and use it to benefit them, so much so that President Obama announced a $215 million plan for research in genomic mapping and precision medicine known as the Precision Medicine Initiative. Meanwhile, the deeply flawed yet popular 21st Century Cures bill, which passed the House of Representatives, bets heavily on genomic research and precision medicine. As I mentioned when I discussed the bill, it’s not so much the genomic medicine funding that is the major flaw in the bill but rather its underlying assumption that encouraging the FDA to decrease the burden of evidence to approve new drugs and devices will magically lead to an explosion in “21st century cures,” the same old antiregulatory wine in a slightly new bottle. Be that as it may, one way or the other, the federal government is poised to spend lots of money on precision medicine.

Because I’m a cancer doctor, and, if there’s one area in medicine in which precision medicine is being hyped the hardest, it’s hard for me not to think that the sea change that is going on in medicine really hit the national consciousness four years ago. That was when Walter Isaacson’s biography of Steve Jobs revealed that after his cancer had recurred as metastatic disease in 2010. Jobs had consulted with research teams at Stanford, Johns Hopkins, and the Broad Institute to have the genome of his cancer and normal tissue sequenced, one of the first twenty people in the world to have this information. At the time (2010-2011), each genome sequence cost $100,000, which Jobs could easily afford. Scientists and oncologists looked at this information and used it to choose various targeted therapies for Jobs throughout the remainder of his life, and Jobs met with all his doctors and researchers from the three institutions working on the DNA from his cancer at the Four Seasons Hotel in Palo Alto to discuss the genetic signatures found in Jobs’ cancer and how best to target them. Jobs’ case, as we now know, was a failure. However much Jobs’ team tried to stay one step ahead of his cancer, the cancer caught up and passed whatever they could do. (more…)

Posted in: Basic Science, Cancer, Clinical Trials, Science and the Media

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ND Confession, Part II: The Accreditation of Naturopathic “Medical” Education

Editors’ note: Britt Marie Hermies of NaturopathicDiaries.com returns to SBM to continue her series on naturopathy from the point of view of someone who has left that profession. If you missed it, the first post was “ND Confession, Part 1: Clinical training inside and out“. She has also contributed “The Wild West: Tales of a Naturopathic Ethical Review Board“.


Prior to renouncing naturopathic medicine and starting NaturopathicDiaries.com, I knew very little about the accreditation of higher education in the United States. I had the impression that accreditation signified that a program or school had the endorsement of the federal government for quality standards. When I first looked into attending naturopathic programs, I remember learning that they are accredited by the U.S. Department of Education.

For me, and I assume for many others, accreditation of naturopathic doctoral programs stood for a medical education of high quality that delivered career prospects similar to those available to primary care physicians who earn an MD or DO. Accreditation also meant I could take out federally-subsidized loans to pay tuition and cover living expenses. Because the $40,000 annual tuition at naturopathic programs was (and still is) comparable to regular medical school, my perception of the validity of naturopathic education at accredited programs made me feel that I was investing in a secure career.

It wasn’t until I graduated from Bastyr University and had been in private practice for several years that I learned the truth about accreditation. Naturopathic programs are accredited by an organization dominated by naturopaths; this authority has been granted to them by the U.S. Department of Education, and they make up their own standards. Leaders in the naturopathic profession can then use the accreditation status of naturopathic programs to convince the public that naturopathic medicine is safe and effective and convince students that they are matriculating into a bonafide medical school.

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Posted in: Naturopathy, Politics and Regulation

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(Dys-)Functional Medicine Comes to Dentistry

Now there is some functional dentistry!

Now there is some functional dentistry!

The great philosopher Deepak Chopra wrote: “I do not believe in meaningless coincidences. I believe every coincidence is a message, a clue about a particular facet of our lives that requires our attention.” So when SBM author extraordinaire Jann Bellamy emailed me last week with an article about so-called “Functional Dentistry” with the comment “Blog fodder?”, I looked it over with interest and then promptly filed it away in my brain along with other things that I might get around to doing but probably won’t. The very next day, Dr. Clay Jones – also an SBM bloggist extraordinaire – asked me if I’d mind pinch-hitting and write a blog post for his upcoming Friday morning time slot while he was away on vacation.

Coincidence?

Personally, I find it more plausible that Jann and Clay secretly conspired to have me write this article in order to lure me into a rage spiral, than the notion that The Universe was sending me a message about a particular facet of my life that required my attention. But we are at Point B now, are we not? Regardless of whether the first domino was pushed by The Universe or by Jann and Clay, I suppose it is now incumbent upon me to share with the SBM readership yet another way where pseudo-scientific practices and deceptive branding and marketing tactics have trickled down from medicine into dentistry.

In this blog post, I will review what Functional Medicine (FM) is, what is wrong about it and what is right about it (yes, there are aspects of FM that are legitimate, if not admirable), and how it has infiltrated (some say contaminated) the field of dentistry. I think you’ll find that, when you pull back the curtains, the reality of FM as a “new and improved” medical/dental paradigm is vastly embellished and overstated, and the Great and Powerful Functional Medicine Oz is really just an old geezer pulling the levers of spin and hyperbole and pushing the buttons of pseudo-science. (more…)

Posted in: Dentistry, Science and Medicine

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Is there a natural treatment for tinnitus?

Ear Tone is a supplement claimed to help tinnitus. Does it work?

Ear Tone is a supplement claimed to help tinnitus. Does it work?

“Why do you bother blogging?” asked a colleague. “You take hours of your personal time to write, and you do it for free. You’re not even getting any citations for all that work.” I admit I found the questions a bit surprising. True, you won’t find SBM posts abstracted in PubMed. But I’m writing for an entirely different audience. I blog for the same reason that I became a pharmacist: to help people use medicines more effectively. Practicing as a pharmacist is one way to do that. In that setting, you’re helping one patient at a time. And seeing how your advice and support can enhance someone’s care is tremendously gratifying.

I see blogging as another form of pharmacy practice, hopefully with similar effects. Yes I do get regular hate mail, and the occasional legal threat, but there’s also gratitude for a post that resonated with someone, or helped them make better decisions about their health. When Google searches don’t give answers, I get questions — too many to answer. Today’s post is based on a request for help from someone seeking advice on natural supplements to treat ringing in their ears. They have tinnitus, and they’re frustrated at the limits of what their physician (and medicine) can do. They sent me an advertisement for a supplement called Ear Tone, a natural health product which is advertised (and approved) to provide tinnitus relief. Can natural supplements do what conventional medicine cannot? (more…)

Posted in: Herbs & Supplements

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An Industry of Worthless Acupuncture Studies

Electro-AcupunctureEven more interesting to me than the question of whether or not acupuncture is effective for any particular symptom is the meta-question of how acupuncture proponents have managed to promote a treatment with systematically terrible scientific data. A new study provides a fresh example of this, which I will discuss below.

I think the behavior of acupuncturists reflects the fact that there are subcultures within science, where each community has its own standards, culture, and typical practices. You see this reflected in how they conduct their research and support their claims. Chiropractors, for example, have what is in my opinion a very unscientific culture. Their treatments are not science-based; science is an afterthought cherry-picked to support what is ultimately their philosophy.

The culture of acupuncture

The world of acupuncture has its own culture as well. Within this world there are special, very permissive rules of science that allow acupuncture to work for almost anything. One trend is to look for anything that happens locally in the skin when you stick a needle into it and then declare that a “mechanism for acupuncture.” The rules of the acupuncture culture also allow for a shifting definition of what acupuncture actually is, allowing the definition to conform to whatever the evidence shows. It’s a neat and subtle trick that allows acupuncture proponents to completely subvert the purpose of science.

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Posted in: Acupuncture

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Taxpayers Fund Scientology Research on Gulf War Veterans

Church_of_Scientology, Fountain Avenue, Los Angeles

The “Hubbard protocol” is Scientology’s religion-based, pseudoscientific “detoxification” treatment used in its Narconon program to treat drug addiction. It was dreamed up by a science fiction writer with no medical training. Now it is being studied as a treatment for veterans suffering from Gulf War illness. Our limited public money for research is being wasted on a study with no scientific merit. Whether or not you consider this a church/state conflict, the study is clearly ill-advised.

The study: $600K worth of sweat

A description of the study is available online in the government’s clinical trials registry. The DOD funded this study to the tune of $633,677. The subjects are veterans with Gulf War illness characterized by persistent memory and concentration problems, headaches, fatigue, and muscle and joint pain. The illness has not been well defined, and its cause has not been determined; but the researchers are working on the assumption that toxins are the cause and that the treatment will relieve symptoms by removing toxins from the body.

The control group will get only “usual care.” The experimental group will get:

A four to six week regimen consisting of daily, supervised, mild-moderate exercise as tolerated for 20 minutes, supervised, intermittent Finnish saunas (at about 140’F) sauna time with breaks and showers, gradually increased as tolerated to approximately 4 hours, dietary supplements including immediate release niacin in gradually increasing doses from 100 mg to a maximum of 5000 mg per day, salt and water, other vitamins, minerals and oils per Hubbard protocol.

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Posted in: Clinical Trials, Religion

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Vaccine Whistleblower: BS Hooker and William Thompson try to talk about epidemiology

Vaccine Whistleblower – a highly edited misrepresentation of the facts

Vaccine Whistleblower” – a highly edited misrepresentation of the facts.

Here we go again with the whole “CDC Whistleblower” thing, this time with a book about the recorded conversations between Brian J. Hooker and William Thompson. Well, not the whole conversations, of course. If they were to release the whole conversations, we might get the truth, and the truth always gets in the way of the antivax crowd. Instead, we get an edited transcript of the conversations between those two in which, according to them and the book’s editors and authors, there is some sort of massive cover-up at all levels of science, government, and public health. What’s the cover-up? As usual, vaccines are evil and whatnot.

I’m not going to review the whole book for you because Dr. Gorski has already done so, and Dorit Reiss has discussed the legal aspects of what is discussed in the book. You can go read his review and/or Prof. Reiss’ analysis and then come back, or stay here and read what I have to say about the failed attempts at epidemiology from both BS Hooker and Thompson.

Let’s start by reviewing BS Hooker’s credentials. He is a bioengineer and chemical engineer, not an epidemiologist, despite what the author of the book wants you to believe:

With the publication of Kevin Barry’s Vaccine Whistleblower: Exposing Autism Research Fraud at the CDC, any claims of credibility for the CDC’s science has collapsed. Barry built his book upon four legally taped conversations between CDC senior vaccine safety scientist Dr. William Thompson and Simpson College professor and epidemiologist, Dr. Brian Hooker.

Later in the book, in the transcript of one of the conversations between BS Hooker and Thompson, BS gets a list of things he needs to do to earn an “honorary” degree in epidemiology. Among those things was to look at some of the earlier studies that Thompson had coauthored. And BS did. He would go on to write a flawed paper that I critiqued here and ended up being retracted, as I told you about here. That paper alone should tell you everything you need to know about BS Hooker’s epidemiological understanding, but the transcripts given to us by his camp in the form of the book really reveal his ignorance.

So let’s go through the calls we have transcripts for and pick at the epidemiological and biostatistical missteps that Thompson suggests for BS Hooker. (more…)

Posted in: Politics and Regulation, Public Health, Vaccines

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Vaccine Whistleblower: An antivaccine “exposé” full of sound and fury, signifying nothing

Life’s but a walking shadow, a poor player
That struts and frets his hour upon the stage
And then is heard no more: it is a tale
Told by an idiot, full of sound and fury,
Signifying nothing.

– Shakespeare’s Macbeth, Act 5, Scene 5

 

"Vaccine Whistleblower"? More like the next Andrew Wakefield in the making.

“Vaccine Whistleblower”? More like the next Andrew Wakefield in the making, albeit a shy, really pissed off Andrew Wakefield.

I don’t review books that often. The reason is simple. My posts for this blog sometimes take as much as a several hours to write (particularly my more “epic” ones that surpass 5,000 words), and I usually don’t have the time to add several more hours to the task by reading an entire book. Also, by the time I’ve read a book I might want to review, weeks—or even months—have often passed, and a review is no longer of much interest to our readers anyway. Fortunately, Harriet does an admirable job of reviewing books for us.

Today, I’m making an exception for a book hot off the presses. The main reason is curiosity, because the book is about a topic that I’ve blogged about three times here and several times more for my not-so-super-secret other blog, and I really wanted to find out more about what was going on. I didn’t expect to find out what really happened, because I knew from the beginning that the book, Vaccine Whistleblower: Exposing Research Fraud at the CDC by an antivaccine lawyer named Kevin Barry, would be highly biased. However, as I found out a few weeks ago, the book promised four complete transcripts of telephone conversations between the “CDC whistleblower,” a Centers for Disease Control and Prevention (CDC) psychologist named William W. Thompson who has been a co-investigator on important CDC studies since the late 1990s.

Given my rather public skepticism about the particulars of Thompson’s story, I was quite surprised when my request to Barry’s publicist for a review copy of Vaccine Whistleblower was enthusiastically answered in the affirmative, thus giving me time to read the e-book before it was released. I also sent a copy of the book to a law professor familiar with the saga, Dorit Reiss, to write a legal perspective (also being published on SBM today) which is why I will say little about this aspect of the book in my discussion. In addition, René Najera has examined the book from a statisticians’ standpoint.
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Posted in: Book & movie reviews, Politics and Regulation, Public Health, Vaccines

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Review of Vaccine Whistleblower: A Legal Perspective 

"Vaccine Whistleblower"? More like the next Andrew Wakefield in the making.

“Vaccine Whistleblower”? More like the next Andrew Wakefield in the making.

This post addresses some legal issues raised in the Vaccine Whistleblower book. The first part explains whistleblower protections and how Dr. Thompson’s allegations fit into them. The second part addresses Dr. Thompson’s suggestion of an independent research agency. The third part explains why the book’s claim that school mandates violate international human rights is incorrect.

A note on the book: Chapters 1 is an executive summary of Chapters 2-5, the interview transcripts; Chapters 6-12 are the author Kevin Barry’s thoughts on what should be done. (Note that Dr. Gorski has also discussed this book from the perspective of the science.)

Prologue: to set the scene

The “Vaccine Whistleblower Book” has four transcripts of telephone conversations between William Thompson and Brian Hooker, recorded between May 1, 2014 and July 28, 2014.

Hooker has elsewhere stated that these conversations were only four of over thirty conversations between Thompson and Hooker. Hooker asserts these conversations began in November, 2013, and that Thompson initiated the conversations. It is not clear if these four recorded conversations were the only ones during that time frame, or what was discussed in the non-recorded conversations.

William Thompson was a co-author on a number of vaccine-safety studies published by the CDC. The most salient one for this discussion is (hereinafter DeStefano 2004):

DeStefano F, Bhasin TK, Thompson WW, Yeargin-Allsopp M, Boyle C. Age at first measles-mumps-rubella vaccination in children with autism and school-matched control subjects: a population-based study in metropolitan Atlanta. Pediatrics. 2004 Feb;113(2):259-66. PMID 14754936

It is not clear why Thompson became concerned enough to reach out in 2013 about a paper that had been published almost a decade previously.

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Posted in: Politics and Regulation, Public Health, Vaccines

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How should we treat DCIS?

How should we treat DCIS?

I’ve written more times than I can remember about the phenomenon of overdiagnosis and the phenomenon that is linked at the hip with it, overtreatment. Overdiagnosis is a problem that arises when large populations of asymptomatic, apparently healthy people are screened for a disease or a condition, the idea being that catching the disease at an earlier stage in its progression will allow for more successful treatment. Two prominent examples include—of course—screening for breast cancer with mammography and screening for prostate cancer with prostate-specific antigen (PSA) testing, and I’ve written about the problem of overdiagnosis with each of them on many occasions. Basically, overdiagnosis occurs when the screening test picks up what we call “preclinical” disease (i.e., disease that hasn’t become symptomatic) that, if left untreated, would never become symptomatic or endanger the health or life of the patient). Although intuitively, it seems to the lay public (and, truth be told, most doctors) that detecting cancer earlier must be inherently better, it turns out that it’s way more complicated than you think. There is a price to be paid for early diagnosis in the form of overtreatment of disease that doesn’t need treatment and for disease that is destined to threaten the life of the patient earlier treatment doesn’t always result in better outcomes. Also, whenever you screen for a condition in asymptomatic people, you will always—always—find much more of it, and the significance of those added diagnoses is not always clear, as a new study in JAMA Oncology shows.

DCIS and mammography: Some background

Before I get to the meat of the study, from my perspective, nowhere is the problem of overdiagnosis and overtreatment in cancer screening as pronounced than in the condition known as ductal carcinoma in situ (DCIS). DCIS is commonly referred to as “stage 0″ breast cancer and is characterized by milk duct cells that appear malignant but remain confined to the milk ducts. In other words, they haven’t invaded the tissue surrounding the ducts. In general, DCIS is treated similarly to breast cancer, with surgical excision, either by mastectomy or breast-conserving surgery, followed by radiation therapy if breast conserving surgery is used. Then, depending on its hormone receptor status, adjuvant treatment consists of blocking estrogen for five years. The rationale for this treatment is the view of DCIS as being a precursor to fully invasive breast cancer and that treating the DCIS will prevent the development of breast cancer. Over the last couple of decades, however, it has become clear that not all DCIS is created equal. Much of it will never progress to breast cancer in the lifetime of the woman (particularly if the woman is older, which means less time for fully malignant transformation to occur). Evidence suggesting this includes studies showing an increase in DCIS incidence by 16-fold since the 1970s, when mammography started to be introduced on a large scale, with little change in the incidence of invasive cancer. Today, 20-25% of mammography-detected breast cancer diagnoses are DCIS; forty years ago, DCIS was an uncommon diagnosis, except associated with an invasive cancer.
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Posted in: Basic Science, Cancer, Clinical Trials, Science and the Media

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