Knowing Thyself: Beyond the Human Genome Awaits the Human Microbiome

The fruits of the Human Genome Project (HGP), completed in 2003, have given scientists and researchers unparalleled insight into the structure and function of the human genome and ongoing research — such as the 1,000 Genomes Project and the Personal Genome Project — continue to refine our map of the human genome.  But the human body is home to thriving microbial community where, by some estimates, human cells are outnumbered by microbial cells by a factor of ten to one.

sampling-locationsIn an attempt to gain a more complete understanding of the complexity of human microbial communities, in 2007 the NIH launched the Human Microbiome Project (HMP).  The HMP’s goals include:

Determining whether individuals share a core human microbiome
Understanding whether changes in the human microbiome can be correlated with changes in human health
Developing the new technological and bioinformatic tools needed to support these goals
Addressing the ethical, legal and social implications raised by human microbiome research.

Last week, NIH awarded more than $42 million in grants through the HMP to “expand its exploration of how the trillions of microscopic organisms that live in or on our bodies affect our health.”

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Filed under Direct-to-Consumer Services, Genomic Sequencing, Genomics & Society

“Three Generations of Imbeciles Are Enough”

So wrote Justice Oliver Wendell Holmes, Jr. in Buck v. Bell, a 1927 Supreme court case upholding a Virginia law that authorized the state to surgically sterilize certain “mental defectives” without their consent. The fascinating and disturbing history of the case is covered in a recent USA Today article.

Carrie Buck was a patient in the Virginia State Colony for Epileptics and Feeble-minded. Upon a finding that she was “the probable potential parent of socially inadequate offspring, likewise afflicted, that she may be sexually sterilized without detriment to her general health, and that her welfare and that of society will be promoted by her sterilization,” the Court upheld her involuntary tubal ligation. The Court infamously justified its decision as follows:

We have seen more than once that the public welfare may call upon the best citizens for their lives. It would be strange if it could not call upon those who already sap the strength of the State for these lesser sacrifices, often not felt to be such by those concerned, in order to prevent our being swamped with incompetence. It is better for all the world if, instead of waiting to execute degenerate offspring for crime or to let them starve for their imbecility, society can prevent those who are manifestly unfit from continuing their kind. . . . Three generations of imbeciles are enough.

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Filed under Genomics & Society, Informed Consent

Recap from the Consumer Genetics Show: Illumina Gets Personal in Advance of the Coming Bioinformatics Bottleneck

The first annual Consumer Genetics Show took place last week (June 9-11) in Boston, MA. With much anticipation — and some uncertainty about what to expect from the inaugural event — research, commercial and thought innovators from across the country came together to discuss the present and the future of consumer genetics technologies and services and the research and science that is driving the development of those technologies.

Highlights from the show — which was attended by most of the GLR team — included Francis Collins’s anonymous genome sequencing and Zak Kohane’s discussion of the “Incidentalome.” In addition, the GLR’s own David Clark presented a well-received talk on the Emerging Legal Issues in the Expanding Genomics Space.

But arguably the most newsworthy event of the show came courtesy of Illumina’s  CEO, Jay Flatley, who officially launched Illumina’s personal genome sequencing service. The announcement was covered extensively by Genetic Future, Forbes, GenomeWeb and others, and Illumina has produced its own site — — to explain the service. The short version is this: for $48,000 — just under half of the previous low-water mark of $99,000 established by Knome earlier this year — consumers can purchase a whole-genome sequence and, after consulting with a physician, completing a consent form and confirming their interest after a one-week waiting period, have it delivered to them on their own Apple iMac.

Illumina's personal genome sequencing service

Illumina's personal genome sequencing service

But perhaps the most interesting feature of Illumina’s service is what you don’t get for your $48,000 investment. Although your iMac comes loaded with some 3 billion base pairs representing your genome, Illumina does not provide any data interpretation, relying on third party providers to assist consumers and their doctors with the all-important process of attempting to understand the significance of all of those newly-delivered As, Ts, Cs and Gs.
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Filed under Bioinformatics/IT, Direct-to-Consumer Services, Genomic Sequencing

The ACLU v. Myriad Genetics Suit: Legitimate Challenge or Publicity Stunt?

By now everyone has heard of the ACLU-instigated suit against Myriad’s patents on the breast cancer susceptibility genes BRCA1 and BRCA2 (read: ACLU release; the complaint).  These patents emerged from research at the University of Utah and were assigned to Myriad, a private spinoff.  The broadest product claims cover “an isolated DNA coding for a BRCA1 [or 2] polypeptide [protein], said polypeptide having the amino acid sequence” listed in the patent.  Related patents also challenged in the suit cover methods for screening for genetic mutations.  As a result of these patents, research and diagnostic testing involving BRCA1/2 must be done by or with the approval of Myriad, usually at some cost.

The ACLU has assembled a broad coalition of authoritative and sympathetic plaintiff.  They include medical and scientific organizations, individual researchers and physicians, the women’s health cooperative that publishes Our Bodies, Ourselves, and cancer patients who allege that they need but cannot afford (and cannot get their insurers to pay for) BRCA1/2 testing.  The defendants are Myriad, the U.S. Patent and Trademark Office, and several directors of the University of Utah Research Foundation.

The suit comes against the background of some recent decisions that nibble around the edges of gene patentability. Earlier this year, in In re Kubin, 561 F.3d 1351 (Fed. Cir. 2009), the Federal Circuit affirmed the PTO’s obviousness rejection of a patent on polynucleotides that encode natural killer cell activation proteins (the NK cells help fight infections and cancer).  The holding was that it would have been obvious to try to isolate these nucleotide sequences in light of existing knowledge of the proteins in question and the sequencing methods.  Back in 1995, in In re Deuel, the Federal Circuit had had rejected this “obvious to try” objection to a generally comparable gene patent.  But now the same court took the view that the Deuel had been “discredited” by the Supreme Court’s 2007 obviousness decision, KSR International v. Teleflex.
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Filed under Badges, Genetic Testing/Screening, Myriad Gene Patent Litigation, Patents & IP, Pending Litigation