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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The Incidentalome

A very important paper was published last week in JAMA.  The punch line is this: Once the new high throughput diagnostic testing technologies — like massive SNP panels — are widely deployed there will be a significant spike in both true-positive and false-positive results.  The implications of this fact are deep and wide.

If you’ve got access to JAMA, check it out.  Otherwise, I’ll summarize the important parts the paper later this week. 

Isaac Kohane, Daniel Masys, and Russ Altman. "The Incidentalome: A Threat to Genomic Medicine" JAMA 296(2): 212-215. July 12, 2006. (sorry subscribers only)

Private Little Revolutions

Best sentence I read today:

"The doctor-patient relationship hinges on informed consent, but the FDA says only a doctor may do some of the informing."

Peter Huber is referring specifically to the informing that is done via diagnostic testing such as pregnancy testing, HIV testing, genetic testing, and innumerable other blood/urine/tissue testing.  Diagnostic testing is a means of extracting and communicating information about personal biology.  Diagnostics are informational devices. 

Some believe there are forms of your personal biological information that you should NOT have access to, or at least access should be complicated to achieve.  AND if you do manage to get access, this information should only be dispensed in a professional setting (i.e. a clinic).  Huber’s thesis:

"Diagnostic technology is on a collision course with the FDA.  A dipstick (or something much like one) is coming to diagnose just about anything: infectious disease, disease caused by your own cells gone haywire or the threat of disease caused by imperfect genes…If the FDA will allow it…"

Some diagnostic tests, like the pregnancy test, have successfully passed through the regulatory gauntlet, and have become, in limited circumstances, common fixtures of drug store shelves, internet commerce, and even home use.

While difficult to imagine, pregnancy testing was once only allowed through a physician.  Today nearly one-third of all U.S. women have taken a home pregnancy test.  In the early part of the 20th century, there were technological barriers to home pregnancy testing — diagnosing pregnancy involved injecting rabbits with a woman’s urine, i.e. the Rabbit Test.  By the late 1970s, once the technology to diagnose pregnancy had been improved and simplified, a different kind of barrier arose: social barriers.  As historian Sarah Leavitt  has recently documented, Consumer Reports in 1978 was no fan of the home pregnancy test:

…the need for an early pregnancy test was seen as evidence of promiscuity. A state health official told the magazine: “there is no reason for a woman in Maryland to buy a kit such as the EPT unless she doesn’t want to be seen at the health department.”  The suggestion that only immoral women with something to hide would need a home test kit led the magazine to conclude that “even if it is used correctly, the EPT appears to be a needless purchase” for its readers.  The editors recommended that women visit their doctor or a clinic to get results instead—but women found ways around these strictures and increasingly demanded access to private, personal, informed, and nonjudgmental health care, of which the pregnancy test was a part.

Consumer Reports has since changed its tune of course.  Twenty years after its original article, inuendos of the immoral nature of home testing had been dropped (they had follow-up articles in 1996 and 2003).

Lynch_clearblueeasy

Caption: Did you know that David Lynch directed an
advertisement for the home preganancy test Clear Blue Easy?

Sarah Leavitt beautifully summarizes the impact of the home pregnancy test:

Women in this generation who take home pregnancy tests are able to know something about themselves and their futures in a time frame that was simply not possible for their grandmothers, or even their mothers.  The kit modified the network of actors involved in diagnosing pregnancy, taking the event from the doctor’s office to the home. It has also modified the time frame of pregnancy by reconfiguring the original discovery. Its revolutionary status, therefore, is small but personal, removing the moment of pregnancy diagnosis from the institutional gaze of the doctor to the private gaze of the pregnant (or not-pregnant) woman herself. It is an example of the way in which the women’s health movement worked to recapture women’s control over much information related to pregnancy.

If Peter Huber’s thesis is correct, there is a similar need for "private little revolutions" in other aspects of health care, a need to recapture control over other forms of personal biological information.

Peter Huber. The Patient’s Right to Know. Forbes.  07.24.06

Sarah A. Leavitt "A Private Little Revolution": The Home Pregnancy Test in American Culture. Bulletin of the History of Medicine 80.2 (2006) 317-345. (sorry subscribers only)

CHECK OUT Sarah Leavitt’s exhibit: "A Thin Blue Line: A History of the Pregnancy Test Kit"

For more on DAT, see Bruce Friedman’s post and the links within.

OTC Cancer Testing

I’m sure OTC diagnostics, whether it be for HIV or cancer is not for everyone — but this doesn’t mean, I believe, that no one should be able to have access to such tests.  This week’s MIT Tech review covers developments in cancer diagnostics that promise to make quick, easy, inexpensive cancer detection a reality:

According to [Charles] Lieber, the device, which uses nanowires to detect
telltale cancer proteins, could lead to inexpensive and highly-accurate
tests — people could even buy them in a local drugstore and perform
the testing themselves. "We can take a very small amount of blood and
with a very simple filtration step get an answer within five minutes,"
Lieber says, adding that the device has "a sensitivity a thousand times
better" than in a lab.


Kevin Bullis, Drugstore Cancer Tests, MIT Tech Review. Oct 31 2005.

Charles Lieber’s Homepage at Harvard University.

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.

 

Roche AmpliChip Video

Roche has posted a video describing their Amplichip CYP450 test, a DNA microarray that can identify 2D6 and 2C19 gene variants.

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.

Genetic Screening and Life Insurance

Quest Diagnostics recently acquired LabOne, which puts them in the position to get involved in genetic screening of life insurance applicants.  A recent quote from the CFO of Quest (via Medscape):

"Gene-based testing allows you to do predisposition testing, and I don’t know that there’s a lot of that done today on the life insurance side, but certainly that’s an opportunity as we go forward because it gives you a better profile of the individual’s risk," said company Chief Financial Officer Robert Hagemann.

What does this mean for life insurance and those seeking it?  I don’t have the answers to this question at the moment, but the best source of information that I’m aware of on this subject is a recent book edited by Mark Rothstein (who also edited a collection of papers on genetics and privacy).

Mark Rothstein (editor). Genetics and Life Insurance : Medical Underwriting and Social Policy. MIT Press, 2004.

Continuous Health Monitoring: The Ring Sensor

This month’s MIT Technology Review has a brief mention of a "ring sensor" device being developed by Harry Asada and Phillip Shaltis.  Have a look at the prototype here.  A medical patient wears this ring and it monitors various vital signs such as heart rate, temp, and blood-oxygen concentration.  The device is also wireless enabled, so the data can be sent to another device such as your computer.  Couple this with a toilet that can perform a urinalysis, such as the Glycosuria Checker WELL-U II by Toto, and one can begin to see the front edge of continuous health monitoring.

Hood on Predictive Medicine

"My prediction is we will have predictive medicine in the next 10 to 15 years," said Hood, co-founder and president of the Institute for Systems Biology (ISB). "There are really two dimensions to this. First, if we can do your genome, we’ll look at your genes and write up your probabilistic health history.

"Second, the blood is a wonderful window that gives you a view of how environmental perturbations interacted upon the individual. I think in 7 to 10 years, we’ll be able to use microfluidic approaches and have a little handheld device that takes a small droplet of blood from your thumb and analyzes 10,000 elements in it, and then be able to distinguish between health and disease."

John Russell, Lee Hood Highlights MIT Meeting, Bio-IT World. Feb 19 2004.

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