Video Round-up: Esther Dyson on Charlie Rose, Spencer Wells on Colbert, and important video I can’t show you on genetic discrimination

Esther Dyson was interviewed on the Charlie Rose Show this past week. Charlie Rose ends the show by saying to Esther, “I can’t wait to see your genome”. I think this is the first time I’ve ever witnessed this expression being used like this — said with such endearment too! — but I’m sure it won’t be the last. (A google search for this phrase shows zero results at the time this post was written.)

The first twenty minutes of the show are mostly about Esther’s involvement in the Personal Genome Project (PGP) [disclosure: I work for the PGP]. The discussion doesn’t stop at genomes or health; the rest of the show ventures into the future of commercial space travel, the internet, cookie monsters, personalized search, AI and more. Esther never ceases to inform and inspire me, and challenge the way I think. I’m so glad she is among the folks that will be pioneering personal genomics for the rest of us via the PGP. Check it out:

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Richter Scale and Your Genomic Portfolio

The field of personal genomics needs a richter scale. This scale would provide a mechanism for giving each new genomic association a score, maybe from 1-10, based on some criteria such as penentrance, actionability, and validity. Existing genetic tests should be scored as well. Commercially available tests might have additional criteria, like whether there is an FDA-approved test or whether the test is reimbursed.

The higher the score the “better” the association or test. A low score might indicate that the association is very likely just “noise” regardless of the fact that it was all over your morning newspaper.

This scale will be very handy once you have a copy of your own genome. Let’s be honest, if you’re sipping on your morning cup of coffee, reading the paper, and see an article about a newly discovered “gene for alzheimer’s” or “snp for sudden stroke”…you’re going to be compelled to run over to your computer to see if your genome possesses that genetic variant. Without a good way to quickly judge the relevance of the news article, journalistic sensationalism may have you running over to your computer several times a day. That doesn’t sound like a very good use of time, does it?

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Hodosh to lead Archon X-Prize for Genomics

The Archon X Prize for Genomics has appointed Marc Hodosh to lead the $10 million competition. Hodosh is an entrepreneur and tech geek who recently chaired a robotics competition for segway inventor Dean Kamen.The Archon X Prize will be awarded to the first group that can “build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.” In other words, the winner must be able to sequence 100 human genomes in 10 days for a $1 million.

The X Prize Foundation has published a video describing the competition, check it out:

So far three teams have registered to compete, including VisiGen Biotechnologies, 454 Life Sciences, and the Foundation for Applied Molecular Evolution.Here are the competition guidelines (PDF).Want to compete? Register here (PDF).

Video: Virtual Genomic Counseling vs. Face-to-Face

The PBS television station KQED in San Francisco recently aired a very thoughtful segment comparing online genomic counseling through DNA Direct to traditional face-to-face counseling via UCSF.  Check it out:


KQED, Genetic Testing through the Web. Feb 20, 2007.
Full discolure: I am employed by DNA Direct.

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
epidemiology
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)

In a Home Near You Soon: DIY Tests for Nearly Everything?

More and more do-it-yourself (DIY) medical tests are coming down the pike.  This week A DIY home HIV test will be reviewed by the FDA’s Blood Products Advisory Committee, they are expected to give guidance on potential OTC status for the OraQuick Advance test on November 3.  The manufacturer, Orasure Technology, currently sells the kits to clinics and doctors for less than $20 each.

This past week, scientists from the Morgagni-Pierantoni Hospital in Forli, Italy published a paper in JAMA demonstrating efficacy of a urine test for bladder cancer.

Maria Aurora Sanchini et al. "Relevance of Urine Telomerase in the Diagnosis of Bladder Cancer" JAMA Vol. 294 No. 16, October 26, 2005.

Bernard M. Branson, MD. "Home Sample Collection Tests for HIV Infection" JAMA. 1998; 280:1699-1701.

 

Leroy Hood on the Future

Leroy Hood, tireless generator of good quotes (among other things):

My prediction is that within 10 years, we will have a predictive medicine that will have two separate components.

No. 1, it will have the ability to sequence every human’s genome for
less than $1,000. We will be able to make predictive health histories for each individual from the varying genes that come from that
sequencing.

Perhaps a better term than predictive health histories is
health futures.  Is it me, or does having health sandwiched between predictive and history feel claustrophobic?

No. 2, we will have a little hand-held nanotechnology device that
will prick your finger and make a thousand measurements and by
wireless, send that to a server. It will analyze all your past records.

It will say, "Nothing’s changed. You’re fine. Do it again in six
months." Or it will say, "Go see your oncologist or go see your
rheumatologist" or whoever might be appropriate.  Your physician would get an e-mail, too.

There’s more from Leroy:

Take into account that your genome and mine differ by 6 million
nucleotides…

We have to treat you differently than we treat me and everybody
else. How we create an era of highly personalized medicine will depend
entirely on new diagnostic, therapeutic and ultimately, these
preventive techniques.

What we’ll do is feed your genome sequence into a grid network of
computers that will do many different kinds of analyses simultaneously.
You’ll get a summary sheet that says here are the things and here are
the probabilities that you’ll likely have to worry about in the future…

Oh yeah, and this is good too..

It takes five years for people to get anything. The first few times
they hear it, they can think of a thousand reasons why it’s wrong.
Then, after they’ve heard it a few more times, it starts to sound more
logical.

If you’re a missionary, you’ve got to be patient with your
congregation. We are at the very beginning stages of thinking about
this.

Read the whole piece in the SeattlePI.

Event: Future of PHI Liquidity

How do we improve personal health information liquidity?  An upcoming event hosted by Esther Dyson will explore this and related topics.

PHI liquidity is a good term, in the conference description it is defined as:

"the ability of that information to move around, relatively friction-free, to where it is most useful and relevant"

A really exciting topic.  Much of medical progress depends on our ability to aggregate and plumb health information.  The possibilities that are available when this information is all hooked together becomes really interesting…and not just for scientists, epidemiologists, drug-makers, physicians, (oh yeah and insurers), but also for regular information consumers.

We’ve got access to general population level statistics now, much of it is irrelevant, outdated, or just impossible to use.  Information is always more interesting when it is about you.  This remains true at a population level too.  Imagine being able to view real-time, population-level health information filtered by your personal health record, including such things as age, pharamaceutical regimen, location, genotype, medical history, family history, weight, diet, etc. 

How do ensure privacy is maintained?  How do ensure people have an incentive to share their information (other than not giving them a choice)?

Francis Collins on Personalized Medicine

So, what’s in it for me? That question probably crossed many minds five years ago following the news that scientists had successfully assembled the first draft of the human genome — the genetic blueprint of a human being. The answer for most of us was ”not much."

What a difference five years can make. Today, we are witnessing a
revolution in the understanding of health and disease, spurred on by
the sequencing of the human genome and the subsequent creation of a map
of human genetic variation. And, like most historic movements, this
revolution has been given a name: personalized medicine.

Francis S. Collins. Personalized medicine: A new approach to staying well. July 17, 2005

Healthcare Unbound

In a 2002 Forrester research brief, Michael Barrett et al. defined Healthcare Unbound as: "Technology in, on, and around the body that free care from formal institutions."  Just as the technology boom in the 20th century centralized the delivery of medical care to specialized facilities, technology in the 21st century, the authors argue, will unbind healthcare delivery from the institutional setting.

Technology enthusiasts and early adopters alike will find that a tantalizing agenda (in pdf) is set for an upcoming conference (like tomorrow) in Cambridge, Mass bearing this catchy Forrester phrase.  The subject of the conference is, as one would expect, the unbinding of healthcare from the institutional setting or "…the convergence of the consumer and healthcare technologies."

How about the summary of Robin A. Felder’s keynote address:

“HEALTHCARE IN THE FUTURE–PASSIVE SMART HOUSE MONITORING COUPLED WITH GENETIC AND PROTEOMIC PROFILING FOR DISEASE DETECTION AND MANAGEMENT
Genetic single nucleotide polymorphisms (SNPs) can be used to predict monogenic diseases. Recently, the use of SNP panels have proven useful for predicting complex diseases such as hypertension (elevated blood pressure).  Once a positive predictive value has been obtained, continuous monitoring of quality of life and physiologic parameters in the home can be useful in detecting the earliest onset of disease. We have developed a genetic panel for screening for the propensity for hypertension as well as passive monitoring technology for elders in their home in order to demonstrate the utility of this new health care delivery paradigm.”

Robin Felder is Professor of Pathology, University of Virginia Health Sciences Center & Director of the Medical Automation Research Center (MARC).


Here is the citation for the Forrester brief I mentioned above:
Michael J. Barrett, Bradford J. Holmes, Sara E. McAulay. "Healthcare Unbound." Forrester.  Dec 17 2002. Available online (with free registration) here.

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