Nom de Ome: A pseudonym for your genome

How common will genomic pseudonyms be in 25 years? When might a person choose to use a Nom de Ome?

In some sense, the Human Genome Project’s human genome reference sequence has a nom de ome (which is “human genome reference sequence”). This sequence was generated mostly from a tissue sample donated by an anonymous male from Buffalo, NY. This volunteer was likely solicited from a newspaper article that ran in the Buffalo News on March 23, 1997. Here are the opening words from that article:

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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We’ve got access to general population level statistics now, much of it is irrelevant, outdated, or just impossible to use.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)?


"Barcodes of Life…Championed by Professor Paul Hebert at the University of Guelph in Canada, Mark Stoeckle at Rockefeller University, and others, this approach would identify short strands of DNA which uniquely identify a specific species, much like UPC codes on consumer products. Importantly, it would take human judgement completely out of the picture - these researchers envision a system where a field biologist could pick a leaf, clip a tuft of fur, or otherwise collect a small DNA sample from a single organism, put it into an Internet-enabled gene sequencer wirelessly connected to a "Google for Lifeforms", and identify the organism instantaneously." (Thanks to Andrew Zolli over at Z + Partners)


SALVATORE SALAMONE, LSID: An Informatics Lifesaver, Bio-IT World, Jan 12 2004.

The vast array of informatics data available today makes it difficult to automate data access and sharing, which in turn makes it difficult to set up production-quality workflows in the research environment.

The Interoperable Informatics Infrastructure Consortium (I3C) is trying to tackle such issues with a new naming standard and data access protocol called the Life Science Identifier (LSID). At its core, LSID provides a uniform way to name and locate specific pieces of informatics data over the Internet.

…Similar to a URL, LSID uses a uniform resource name (URN) to locate data. The URN contains five parameters…that uniquely identify the data of interest.

…To take advantage of the URN in an informatics application requires two pieces of software: a client piece within an informatics application, and a server piece associated with the actual data.

…With LSID, an organization continues to use its normal routines for generating and storing informatics data. The only thing that changes when using LSID is that there is an alternative access route.

Digital Biology

Today is the last day of the conference Digital Biology: The Emerging Paradigm.  At the webpage, two purposes for the conference are listed:

To demonstrate how computational approaches to biomedical research have yielded breakthroughs that advance the prevention, diagnosis, and treatment of disease

To identify national research needs and opportunities in the computational and quantitative sciences critical to the future of biomedical discovery

A recent article on the meeting appeared in Nature Science Update.  It provides a glimpse of the kind of issues to be addressed in the coming years:

At the moment, it is a struggle to link a patient’s genetic profile with their brain scans and the latest clinical studies. It’s like a primitive PC running incompatible word-processing, e-mail and spreadsheet programs, says Erik Jakobsson of the National Institute of General Medical Sciences, who helped to convene the meeting. "We’re way behind in making it all work together," he says.

Interoperability is a big issue.  The biotech industry launched the Interoperable Informatics Infrastructure Consortium (I3C) in 2001 with the mission to "eliminate barriers to application interoperability, data integration, and knowledge flow."  Although, the extent to which I3C pursues formal standards has emerged as a point of contention for at least one member, Sun Microsystems, who recently left the consortium.

UPDATE: More coverage of the symposium here.

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…

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.

Genomic Data and the FDA

Edward R. Winstead, Genomes and Medicine–Part One, Genome News Network, September 19, 2003.

A brief analysis of how the FDA is dealing with the use of new forms of data, such as microarray data, in regulatory submissions. "The newness is a problem and a challenge. There are no universal standards for analyzing and reporting microarray or other genomic data." 

UPDATE: The FDA recently issued guidance for the submission of pharmacogenomic data.  See the press release here
One notable graf from the press release:

This is FDA’s first step towards integration of this new field into the process of demonstrating that new drugs are safe and effective, and thus the regulatory guidance is intended to facilitate this integration. This guidance is intended to ensure that evolving regulatory policies and study designs are based on the best science; provide public confidence in this new field where scientifically appropriate; facilitate the use of such tests during drug development; and clarify for industry what types of pharmacogenomic data to submit to FDA.

"Using genomic testing to guide drug therapy will constitute a significant shift from the current practice of population-based treatment towards "fine-tuning" individual therapy," said Janet Woodcock, FDA’s Director of the Center for Drug Evaluation and Research.