One-Fifth of Human Genes Belong to the “Patome”

A new study reveals that 4382 of 23,688 human genes in NCBI are patented.  The authors of the study actually mapped the patents to their location on the chromosomes using computational techniques familiar to bioinformaticists (cool graphic in the paper shows chromosome 20 with IP righs mapped to it).

While most patented genes have only one IP claim on them, some genes have many claims.  The two most highly patented genes were found to be  BMP7, an osteogenic factor, and CDKN2A, a tumor suppressor gene.  The sequences of these two genes were claimed in more than 20 patents each. 

This research appears to be part of a larger examination on the impact of gene patents on innovation.  The authors of the paper summarize two sides of the intellectual property debate as follows:

Critics [of gene patents]…suggest that overly broad patents might block follow-on research… Alternatively, gene IP rights may become highly fragmented and cause an anticommons effect, imposing high costs on future innovators and underuse of genomic resources…Both situations, critics argue, would increase the costs of genetic diagnostics, slow the development of new medicines, stifle academic research, and discourage investment in downstream R&D…

In contrast, the classic argument in support of gene patenting is that strong IP protection provides incentives crucial to downstream investment…and the disclosure of inventions. Patents are also regarded as the cornerstone of vibrant markets for ideas…and central to the biotech boom of the 1980s and 1990s…

Kyle Jensen and Fiona Murray. "Intellectual Property Landscape of the Human Genome" Science 14 October 2005; 310: 239-240 (sorry subscribers only) Update: See here!

Stefan Lovgren. "One-Fifth of Human Genes Have Been Patented, Study Reveals." National Geographic News. October 13, 2005

Fiona Murray’s homepage

Read more

NPR Piece on Genetics

Robert Siegel and Joe Palca. "DNA: The Machinery Behind Human Beings" NPR All Things Considered. October 10, 2005. Listen to Part One, Listen to Part Two.

IBMs Pledges to Protect Genetic Privacy of Workforce

Developing story from the New York Times:

I.B.M., the world’s largest technology company by revenue, is promising not to use genetic information in hiring or in determining eligibility for its health care or benefits plans. Genetics policy specialists and privacy rights groups say that the I.B.M. pledge to its more than 300,000 employees worldwide appears to be the first such move by a major corporation.

Steve Lohr. "I.B.M. to Put Genetic Data of Workers Off Limits" October 10, 2005

Update: Over at IBMs excellent collaborative blog on the future of healthcare, HealthNex, IBM’s Chief Privacy Officer Harriet Pearson introduces the genetic privacy policy and says "I hope the fortuitous coincidence of these public events [Eddy Curry case, IBM's policy, etc] — and many
more that will certainly arise in the weeks, months and years ahead –
will promote the kind of discussion around the future importance of
genetic security and privacy that our policy initiative today was
intended to generate."

Update2:  Amy Barrett. "IBM’s Smart Stance on Genetic Testing" OCTOBER 11, 2005

Modifier Genes vs. Susceptibility Genes

The identification of gene modifiers may improve our ability to understand differences in the severity of disease.  Having such information may help guide decisions about therapy, for both patients and doctors.  The outcomes of a search for gene modifiers for cystic fibrosis are described by one of the authors:

"There are likely a number of gene modifiers in CF and other diseases, and this current paper describes one of the first robust examples," [Michael] Knowles said. "Some CF patients may do worse because of ’severe inflammation’ genes, whereas others may do worse because of differences in mucus genes. Still others might because of their growth and metabolism genes, etc… Thus, therapy might need to be targeted to a particular area or areas in individual patients. This is important not only for CF, but for other lung diseases as well because gene modifiers we discover in CF will be seen in other diseases, and there are already examples of that."

An editorial accompanying the article in the New England Journal of Medicine describes how modifier genes are different from susceptibility genes:

"Susceptibility genes and modifier genes are two biologic phenomena that few clinicians should ignore in the genome era. Susceptibility genes, which are genes with functional variants that affect the causes of disease, are routinely being identified for simple mendelian diseases and, more recently, for common genetic disorders. Modifier genes are distinct from susceptibility genes, in that they are genetic variants that affect the clinical manifestation of disease (as opposed to liability)…The identification of gene modifiers and their interactions in cystic fibrosis and other diseases has only just begun."

Christina K. Haston and Thomas J. Hudson. "Finding Genetic Modifiers of Cystic Fibrosis" NEJM 353(14)1509-1511. October 6, 2005. (sorry subscribers only)

Drumm et al. "Genetic Modifiers of Lung Disease in Cystic Fibrosis" NEJM 353(14)1443-1453. October 6, 2005. (sorry subscribers only)

Eddy Curry and a genetic test for Hypertrophic Cardiomyopathy

Apparently the Knicks have picked-up Eddy Curry from the Bulls, bringing to a close (for now) a story that appeared to be heading toward a dramatic conclusion: a career being determined by the result of a genetic test.

Here is an outline of the story:  Eddy Curry has had some heart problems recently.  Doctors disagree about the diagnosis.  It has been suggested that he may have Hypertrophic Cardiomyopathy (HCM), a serious and potentially fatal heart condition.  Vigorous exercise, like playing basketball, can be fatal for people with HCM.  Several athletes with HCM have died while playing professional sports in recent memory.  One doc told the Bulls that there is a genetic test for HCM.  This past week, amid contract negotiations the Bulls request that Eddy Curry submit to a genetic test for HCM.  Eddy Curry refused.

The main issues here are: (1) Should an employer be able to demand that an employee take a genetic test (and share the results)? (2) Should employers be able to make employment decisions based on genetic information?  (Editor: Answers aren’t necessarily straightforward by the way, demonstrated by the sheer variety of reactions to the Eddy Curry case.  This is an excellent opportunity to work through the issues.)

AP, Bulls Ship Curry to Knicks, New York Times. Oct 3 2005.

Laura Spinney. Heart-stopping action. Nature. 04 August 2004.

Henry T. Greely, Banning Genetic Discrimination, NEJM September 1, 2005.

P. A. Schulte, Geoffrey Lomax. "Genetic Testing of Railroad Track Workers with Carpal Tunnel" Human Genome Epidemiology. Chapter 29.

Freakonomics: Dog Doo DNA

The two authors that freakishly took the dismal science to the top of the bestseller lists with Freakonomics turn their attention this week to dog doo and DNA:

Twenty-five hundred tons. That’s how much manure was produced every day by the 200,000 horses that moved people and goods around New York City in the late 19th century…Like so many seemingly overwhelming problems, this one was resolved, quite painlessly, by technology. The electric streetcar and then the automobile led to the disappearance of the horses, and with them went their dung.

Most of the animal dung produced in today’s New York comes from our dogs…With horses, the solution was simply to eliminate them.  Might there be away to get rid of dog poop without getting rid of the dogs?  Here’s an idea: DNA sampling…

The authors put some numbers to an idea which has been kicked around this past year by several city officials in Europe.  They estimate it would cost NYC about $30 million to get into the dog doo DNA business.  Excellent read.

STEPHEN J. DUBNER and STEVEN D. LEVITT. "Dog-Waste Management: The DNA of Dog Dirt" New York Time Magazine. October 2, 2005.


Free Short Courses in Statistical Genetics

Several years of streaming video lectures on statisical genetics at the University of Alabama, Birmingham.  The courses range from basic genetics to bayesian methods.  Thanks UAB. 

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