Genetics in MD training

Its well-known that a large number of physicians have a very limited understanding of genetics.  This situation is an artefact of medical education, which historically hasn’t included genetics in the curriculum to any significant degree — with the view that genetics is a specialty for rare diseases.  What is surprising though, is that this continues to be the case:

Industry leaders at a recent conference were unanimous in their conviction that personalized medicine will change the practice of medicine and drug development, but expressed grave concern at the lack of appropriate medical education currently available to bring that paradigm shift to fruition…Bruce Korf (University of Alabama, Birmingham) drummed home the medical education crisis. Fewer than 40 percent of medical schools run a genetics course, he said, and according to a recent survey, only one-third of physicians polled feel trained or competent to discuss genetic information. Medical informatics is a disruptive technology akin to a Tower of Babel. "Why can’t [Google] crawl through medical records?" Korf posed. "Is Wal-Mart - Google the future of medicine?"

FYI for all the bloggers out there, this post was written using Performancing for Firefox.  Highly recommended.


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I2B2 and Health Information Altruists

Informatics for Integrating Biology and the Bedside (I2B2) is a multi-year program that aims to learn about the genetic underpinnings of several common conditions (including asthma, hypertension, and diabetes) by mining the medical records of several million patients in the Partner HealthCare system. 

Using electronic health records for medical research is still in its infancy, but will someday provide a powerful boost to the acceleration of medical discovery.  The ability of Kaiser Permanente to identify that there was a problem with Vioxx
early-on by performing adverse reaction
using the health insurer’s electronic patient data is an illustrative example of how electronic data on a population scale might contribute to consumer health (even in near real-time). 

With projects like I2B2 it may be possible for consumers to contribute to the health of future generations, or even see returns on health in their own lifetimes, with minimal engagement  — compared to pariticipating in a clinical trial for example — as long as they choose to share their personal information.

”If we could use routine clinical care to generate new findings
without having to do multimillion-dollar studies, that would be a true
change in the way medical discovery is done," said Dr. Isaac Kohane, an
associate professor at Harvard Medical School who is one of the
project’s directors. ”We want to use the healthcare system as a living
laboratory…Ultimately…the public will have to decide: Do they want research done this way or not?"

We have reached a point where genotypic data is much less an issue than in the past with the advent of new sequencing technologies and the rapid decline in costs per base pair.  The rapid decline in the cost of sequencing should be celebrated (and nourished further), but the reality is that sequence data alone is far from even good.  To provide real insights that will improve human health, this data needs to be tied to health information, i.e. phenotypic data.  The real bottleneck and financial hurdle now is to get good phenotypic data.  And lots of it for lots of different types of people.

So, the solution is simple right?  Set-up a website, pass out colored ribbons, print t-shirts, host an awareness campaign (marathons, fund-raisers, etc) and just ask consumers to volunteer their personal health information.  It is, after all, for the benefit of human health the world-over.  As a sweetner (as if human health isn’t cause enough), researchers might promise volunteers complete confidentiality and anonymity.  While most people could care less if their height, age, and serum iron levels were, in some form, public knowledge, there are other types of personal health information that can carry stigma (think HIV, STD, OCD) or might compromise the privacy of family members (i.e. genetic information).

There’s the rub.  It is increasingly clear that health information confidentiality and anonymity are promises that researchers will be unable to uphold, even when the information is de-identified.  So, when researchers call for volunteers to submit their personal health history to projects like I2B2, they can’t make guarantees that this information will remain totally private.

Isaac Kohane and colleauge Russ Altman proposed a solution in a recent article in the New England Journal of Medicine: health information altruists.  From the article: 

…large-scale studies of genotype and phenotype should specifically seek out volunteers who are information altruists. The guarantees made to these subjects about the risks of re-identification can then be more realistic. The potential damages can be outlined, but the subjects presumably will elect to take the risk in the hope of helping to address human disease…

In the same paper, the authors outline three steps to make projects like I2B2 more practical:

  1. "rules could be implemented to make it illegal to link health information contained in research databases to other data resources, so as to prevent the inference of individual information outside the scope of the original informed consent…"
  2. "researchers who curate genetic databases should have some protection for their activities, provided that they follow an agreed-on set of operating guidelines…"
  3. "most important, patients should be granted explicit control over the disclosure process.  They should be able to indicate the types of users who can see their data, and they should be able to request lists of those who have seen it…"

The next step is to set-up pilot studies and see just how many people will volunteer provided fewer promises of privacy. 

My take: Tapping all the health information altruists out there is great way — if not the only way — to get started at the moment.  I think there are lots of people to keep projects like I2B2 or the Personal Genome Project busy in the near term.  Informed consent will be somewhat tricky.  For example, we know that James Watson is definitely qualified to make an informed decision about his personal genetic information and he recently declined to learn about his genetic predisposition to Alzheimer’s disease (a la ApoE).  Obviously, many consumers at-large (and many practicing physicians too) have a poor understaning of genetics.  We’re all new to the game for the most part.

Exactly how many people will volunteer?  Hard to tell.  The more the merrier.  Perhaps this will be true not only for the gains that can be had toward human health, but also because with large numbers of participants any misappropriation or abuse of the information (by insurers or employers or corporations) would cause such a backlash that would-be wrongdoers may be deterred.  Of course, the-more-the-merrier argument can go the other way too. 

Its exciting to see projects like this starting to take form.

I2B2 Homepage

Gareth Cook "Harvard project to scan millions of medical files" Boston Globe. July 3, 2005.

Isaac S. Kohane, and Russ B. Altman. "Health-Information Altruists — A Potentially Critical Resource" NEJM 353:2074-2077, Nov 10 2005. (sorry subscribers only)

Church on the Personal Genome Project

George Church of Harvard has an editorial on his Personal Genome Project in the recent issue of Molecular Systems Biology.  Snip:

From my first interaction with Wally Gilbert in 1976, it seemed that a large (but appealing) leap would be to go from his new method for sequencing 30 bp segments to a method to get everyone’s full genome sequenced. Six billion base pairs for six billion people had a nice ring to it. This was still merely a fantasy when we published a paper called ‘Genomic Sequencing’ in 1984 (Church and Gilbert, 1984) and conspired to create a 3 billion dollar HGP later that year (Cook-Deegan, 1989). For the subsequent 16 years, radical technology development (while kept alive in a few ‘back-rooms’) was clearly a minor funding priority relative to ‘production’ sequencing. However, by 2001, the criticisms of the old technology grew and the call for affordable personal genomes became irresistible (Jonietz, 2001). In early 2004, the NIH-NHGRI posted a request for applications, and in October 2004 and August 2005, announced grant awards totaling $70 million for technology leading to human genome sequences for $100 000 in 5 years and $1000 in 10 years ( As if the motivation were not already high enough, at the recent Genome Sequencing & Analysis Conference in Hilton Head (October 18), the prospect of a new X-prize arose to encourage this new Personal Genomics field. (The first X-prize, $10 million for re-usable spacecraft, was awarded in October 4, 2005 and is followed by a $50 million prize for orbiting.) Amid all of this positive reinforcement, some key points were left fuzzy—What exactly is meant by sequencing a human genome? What is the utility of personal genomes? What are the ethical, legal, and social implications (ELSI)? The time has come to sharpen these points up. As we begin to purchase personal genomes, we want to know what we are paying for…

The utility of the first personal genome is analogous to the first fax machine, web page, or computer. Until communities of resources build up, these revolutionary new tools serve mainly the ‘early adopters’. These initial participants are heroes and human guinea-pigs paving the way for potentially increasing utility for the general public…

George Church. The Personal Genome Project. Molecular Systems Biology. Published online: 13 December 2005.


Metcalfe’s Law

PGx Webcast December 12

From the press release:

Hosted by the International Society of Pharmacogenomics, the
Pharmacogenomics E-Symposium will be held live & online on 12
December 2005…

Opening Keynote: Allen Roses, GlaxoSmithKline

Live Presentations and Round table debates on:

-Pharmacogenomics : Delivery to patients and patient acceptance
-Prescribing by ethnicity
-What is the role of pharmacogenomics in our approaches to substance abuse?
-The role of Pharmacogenomics as a laboratory tool in diagnostics and therapeutics
-Toxicogenomics - Is the Problem the Toxin or the Genome?
-Cancer Pharmacogenomics
-Cardiovascular Pharmacogenomics
-Pharmacogenomics of Psychiatry
-Pharmacogenomics of Neurological Disorders
and more.

Closing Keynote: Urs Meyer, Biozentrum, University of Basel

Check out the Pharmacogenomics E-Symposium website.

Holiday Reading List

Here is a list of what I’ll be reading over the holiday:

Adam Hedgecoe. The Politics of Pesonalised Medicine: Pharmacogenetics in the Clinic (Cambridge Studies in Society and the Life Sciences). Cambridge UP, 2004.

  • The first half of the book covers APOE-e4 and the second half Herceptin.
Carlota Perez. Technological Revolutions and Financial Capital: The Dynamics of Bubbles and Golden Ages. Edward Elgar Publishing, 2002.

  • Part of my Web 2.0 preparedness kit.
Dale Shaller. Consumers in Healthcare: The Burden of Choice. California HealthCare Foundation. October 2005.

  • This report by the CHCF has been on the to-read list for months.

Frederick J. Simoons. Plants of Life, Plants of Death. University of Wisconsin Press, 1998.

  • Simoons devotes 150 pages and copious notes in a rigorous analysis of the hypothesis that the Pythagorean ban on fava beans bears some relationship to higher rates of glucose-6-phosphate dehydrogenase deficiency among modern Mediterraneans (known as favism). The author explores whether this hypothesis is merely a whiggish interpretation of history or a classic example of biocultural evolution.


ArtiraiArti Rai. “Open Source” Biology: The Role of Law. Webcast of lecture presented at Duke Law School’s Center for the Study of the Public Domain. (realplayer stream)