HuGE Book

New book published by OUP:

Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease, 2004. Editors: M. Khoury, J. Little, and W. Burke.

From the Preface:

In this book, we show how the epidemiologic approach will play an important role in the continuum from gene discovery to the development and applications of genetic tests. We call this continuum human genome epidemiology  (or HuGE) to denote an evolving field of inquiry that uses systematic applications of epidemiologic methods to assess the impact of human genetic variation on health and disease.

The table of contents with links to selected chapters can be found here.

Genomic Medicine

This week’s Science has a special feature on genomic medicine (for subscribers only).

Eliot Marshall’s article "First Check My Genome, Doctor" briefly discusses trends related to the development of DNA diagnostics.  A person’s genetic allotment may help doctors determine the effectiveness of drugs, including the severity of side effects. 

For example, recent evidence indicates that DNA diagnostics may be useful for predicting whether patients will respond favorably to anti-depressants.

A handful of companies are in the process of developing such diagnostics.  The article mentions several:   

Roche Molecular Diagnostics
AmpliChip CYP450
(press release)

Signature Genetics

Genaissance Pharmaceuticals



More on International Standards for Genetic Data

I blogged last week that UNESCO was set to release their International Declaration on Human Genetic Data, and they have

GenomeWeb reports on the declaration here.

Relevant excerpts from the declaration:

…It is ethically imperative that human genetic data
and human proteomic data be collected, processed, used and stored on
the basis of transparent and ethically acceptable procedures…

…Human genetic data, human proteomic data and biological samples
linked to an identifiable person should not be disclosed or made
accessible to third parties, in particular, employers, insurance
companies, educational institutions and the family, except for an
important public interest reason in cases restrictively provided for by
domestic law that is consistent with the international law of human
rights or where the prior, free, informed and express consent of the
person concerned has been obtained provided that such consent is in
accordance with domestic law and the international law of human rights.
The privacy of an individual participating in a study using human
genetic data, proteomic data or biological samples should be protected
and the data should be treated as confidential…

…Human genetic data, human proteomic data and the biological
samples collected for one of the purposes set out in Article 5 should
not be used for a different purpose that is incompatible with the
original consent, unless the prior, free, informed and express consent
of the person concerned is obtained according to the provisions of
Article 8(a) or unless the proposed use, decided by domestic law,
corresponds to an important public interest reason and is consistent
with the international law of human rights. If the person concerned
lacks the capacity to consent, the provisions of Article 8(b) and (c)
should apply mutatis mutandis…

…States should regulate, in accordance with their domestic law and
international agreements, the cross-border flow of human genetic data,
human proteomic data and biological samples, so as to foster
international medical and scientific cooperation and ensure fair access
to this data. Such a system should seek to ensure that the receiving
party provides adequate protection in accordance with the principles
set out in this Declaration…

Formulating EHR Standards

Key Capabilities of an Electronic Health Record System: Letter Report. National Acadamies Press, 2003.

This report provides 8 core functionalities for electronic health records as formulated by the Institute of Medicine (IOM) for use by Health Level 7 (HL7) in creating industry-wide standards.
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Patent Application #20030104470

Patent Application #20030104470 reads:

"The present invention relates to electronic medical records having polymorphisms data, an electronic library of these electronic medical records, and systems and methods for managing genetic information. For example, the present invention provides system and methods for collecting, storing, and retrieving patient-specific genetic information from one or more electronic databases."

The assignee name is Third Wave Technologies, Inc.

Microarrays at PLOS Biology Journal

In recognition of the inaugural issue of PLOS Biology, an open-access journal:

Greg Gibson, Microarray Analysis: Genome-scale hypothesis scanning. PLOS Biology 1(1). (FREE to read!)

Here is a nifty flash animation explaining how microarray’s work.

For daily updates on open access, please see Peter Suber’s extensive blog: Open Access News.


EMR Protections

Lets imagine that in ten years from now there is a genome sequencer in every medical doctor’s office.  The price of whole-genome sequencing has plummeted to $500 with the development of new technology.  Since $500 is in the range of other, often less effective diagnostic tests, it is the policy of your insurance company to shell out for this simple procedure.  As part of your regular physical exam, your doctor not only listens to your heart & lungs, takes your blood pressure, maybe draws some blood, but also takes a swab from the inside of your cheek and sequences your genome from those cells.  In an hour or so, all three billion nucleotides of your genome are automatically attached to your electronic medical record (EMR), which is standard fare for doctors in the future (not enough shelf space to do otherwise: your genome alone would fill approx. 200 volumes at 1000 pages each).  In addition to your genome, your EMR contains your complete medical history: every cavity, every medication ever prescribed, every stitch.

A repository (i.e. a database) located somewhere, perhaps at the office of the company which developed the EMR application or the office of a company specializing in genetic data storage (or possibly as part of a nation-wide, centralized project), houses your EMR along with the EMRs of millions of other people. 

The information contained in your EMR may contain information that
you would not want your boss or health insurance company to know, it is
conceivable that you may not want to know some of the information
yourself, especially since genetic sequence data can be predictive
(then again maybe an advanced diagnosis will allow for better disease

What kind of legal protections do you and your EMR have? Who can
legally look at this information and what actions can they legally take
from such knowledge? Can you get fired (or not hired)? Or dropped by
your insurance company (or not accepted to begin with)? Can a medical
researcher use the information in your EMR to aid in the discovery of
disease etiology (which may help you or others in the future)?

Maybe you live in Germany
and during a mandated medical exam to become a teacher, your doctor
identifies you as a candidate for a debilitating degenerative disease.
As a consequence of this information, your employer does not hire you
for future fear of having a less productive and more expensive employee
due to illness.

Or maybe you are an epidemiologist trying to unravel a complicated
disease that strikes a small population with criminal severity. Some
evidence suggests the disease is a genetic disorder. Other evidence
suggests the disease appears in some individuals after taking a widely
prescribed drug. Luckily, the indications of the disease are well
characterized. With the information contained in millions of EMRs, it
is hoped the cause of the disease can finally be discerned.

Or maybe you are a policymaker
today trying to determine what level of protection to afford persons
divulging medical information. What kind of recommendation does one
make? Personal medical records create possibilities of damaging
livelihoods if mishandled by either allowing access to those likely to
abuse it or not allowing access to those which desire to make good use
of it.

International Standards for Genetic Data

UNESCO’s International Bioethics Commission (IBC) will be making a declaration about international standards for the collection, processing, storage, and use of genetic data.

Senate passes Genetics Information Nondiscrimination Act

On Tuesday, the Senate unanimously passed the Genetic Information Nondiscrimination Act of 2003 (S. 1053).  It was approved by the Senate Committee on Health, Education, Labor, and Pensions in May.  The bill now goes to the House for consideration.

Helen Dewar, Senate Backs Safeguards for Genetic Data, Washington Post, October 15, 2003

Kate Dalke, Genetic Nondiscrimination Bill Passes U.S. Senate, Genome News Network.

Ira Carnahan, Gene Policy, Forbes, October 22, 2003.

Office of Legislative Policy and Analysis has a brief summary of genetic discrimination legislation (yet to be updated at the time of this post).


Read more

China to regulate stamp licking?

Human genetic resources outflow under tighter control, Xinhuanet, October 9, 2003.

This (somewhat spotty) news report notes that “the Chinese Ministry of Health and State Administration of Quality Supervision, Inspection and Quarantine” issued a statement that would require “organizations or individuals [to] apply to authorities for a permit to take, mail or transport human genetic materials out of China.”

Are we to assume that there will be no more licking of stamps without a permit in China? The answer isn’t obvious. There are often enough cells on the back of licked stamps and envelopes to extract DNA evidence for forensic investigation. Such tactics were used to aid in the prosecution of suspects involved with the 1993 World Trade Center bombings, one person licked the stamp and another licked the envelope of a letter sent to the NYT claiming responsibility for the act. In an excellent chapter contesting the arguments for genetic exceptionalism, Thomas Murray notes that while the largest tissue bank may well be “in the hands of the Publisher’s Clearinghouse” the motivation and resources to actually extract information from microscopic samples (and return address labels) just isn’t.

It is interesting to conjecture about the motivations behind
China’s maneuver. Like whether this embargo is intended to protect
Chinese citizens from genetic discrimination abroad (?), or whether
this embargo is aimed to protect something else (e.g. profits that
would come from the development of drugs targeted for diseases that
have a high incidence in the large Chinese population)?

UPDATE: The timing of China’s regulatory maneuver suggests it
could have been prompted by UNESCO’s International Declaration of Human
Genetic Data (see here or my post above). The key excerpt:

…States should regulate, in accordance with their domestic law and international agreements,
the cross-border flow of human genetic data, human proteomic data and biological samples, so as to
foster international medical and scientific cooperation and ensure fair access to this data. Such a
system should seek to ensure that the receiving party provides adequate protection in accordance
with the principles set out in this Declaration…

I am curious to know more about the procedure of obtaining a permit
in China to send genetic samples abroad. Presumably, the review process
would examine the circumstances under which Chinese citizen X is
sending the sample, including any contracts between the citizen and the
receiving party. Any information send me email.

Robert Kneller, Ownership of Inventions
Derived from Natural Products and Human Tissues, and Sharing of
Benefits from the Commercialization of such Inventions
. Presented at a symposium entitled “Rethinking International Intellectual Property.” (pdf)

According to this article, the story begins back in 1997 when
“senior Chinese geneticists expressed concern that if foreign
laboratories analyze Chinese tissue samples, discoveries related to
these samples would likely be patented and commercialized by
foreigners, and China would not share in the commercial benefits.” By
June 1998, China issued Interim Measures for the Administration of Human Genetic Resources (text can be found here).
This decree established the Human Genetics Resources Administration of
China (HGRAC), which would oversee all activities related to the
collection and export of human genetic data. How many countries are
attempting to regulate cross-border flows of DNA, I wonder?

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