September 28, 2012

Supreme Court Asked to Review Gene Patent Challenge (Again)

The plaintiffs have filed a petition for certiorari with the Supreme Court in the ongoing gene patent challenge, Association for Molecular Pathology v. U.S. Patent and Trademark Office et al. (AMP v. USPTO). The litigation centers on whether genes and methods for their use qualify as patentable subject matter. The doctrine of patentable subject matter asks whether a patent fits into the kinds of inventions that are eligible for patenting or whether it goes too far and extends into the impermissible categories of "abstract ideas, natural phenomena and laws of nature;" more background here. The Supreme Court had previously been asked to hear the case, but then remanded the case back to the Federal Circuit in view of the Mayo v. Prometheus (a patent to a method of drug treatment) decision that they had just handed down. In their decision this summer, the Federal Circuit upheld the patent claims to genes, rejecting arguments that such patents covered products or laws of nature. In the opinion authored by Judge Lourie, the court relied on the chemical differences between native and isolated DNA to find enough structural differences to confer patent eligibility. In her concurrence, Judge Moore also cited the reliance interests held by existing patentees and the biotechnology industry as a reason for not undoing decades of patenting. The new petition argues that Supreme Court precedent supports their view that the function of a molecule is paramount in the analysis comparing native to isolated; they argue that the isolated gene maintains the functions of native DNA and therefore cannot not be patentable. The petition also advances a First Amendment basis for not patenting genes (the patent interfering with a right to use information) and revives another source of dispute in this case, which is over which parties in this complex coalition of plaintiffs have the standing to sue. We could get a decision on whether the Supreme Court will take the case in the next few months. The Court has not heard a patentable subject matter case that involves molecular genetics since Diamond v. Chakrabarty in 1980. However, that case involved a genetically engineered organism (a bacterium), while this case centers on isolated genetic molecules - the genes.

September 20, 2012

EFF Asks 9th Circuit to Consider ENCODE Research in Haskell v. Harris DNA Database Challenge

The recent release of 30 research papers, collectively describing the results from the ENCODE project, prompted headlines around the country characterizing this as a milestone in genetic research. As a follow-on project to the release of the original Human Genome Project sequence (which focused on the genes), the ENCODE project attempts to identify what the rest of the DNA in our genome – the so-called “junk” – is doing. It’s already known that only about 1% of the human genome actually contains the genes. What are the rest of the 3 billion bases for?  “Junk DNA” was never an accurate or worthy title for it – it simply revealed the state of ignorance about the human genome. Now, the ENCODE consortium reports its further annotation of human DNA – they were able to “assign biochemical functions for 80% of the genome.” They “systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.” This work begins to detail the underlying genetic switching mechanisms that operate behind the scenes in the genome and "regulate" how genes are expressed. No one doubts that nature is likely to have retained much of the DNA in our genome because of its usefulness. However, it's not clear that the ENCODE project, in cataloguing the signals from any biochemical event to describe "function," has yet produced a map with high genetic resolution. The Human Genome project - writ large - continues to unfold. However, the legal system has made use of DNA identification technologies that were developed from current genetic knowlege. If we look for any impact on the uses of DNA sequence information in the law, several consequences of the ENCODE research emerge. First, in using DNA as a forensic tool – relying on individuality in sequence to create a personally distinguishable identifier – criminal (and other) law has come to rely on a consensus use of a set of DNA sites (the STR (short tandem repeat) loci, retained in the FBI CODIS database) that were chosen because they offered variation but minimal biological information. Thus, these DNA sites could be used for forensic comparison while revealing very little about an actual person; that fact minimized any privacy invasion from use of these markers. In theory, they capture genotype differences without revealing critical phenotypic information. It was already known, for example, that some of the STR sites were found in an intragenic region – e.g., CSF1P0 maps to an intron – but these sites were not considered informative for any particular trait or condition. Could these STR sites now now be recharacterized as informative – and could they reveal more about the phenotype of an individual? My colleague, David Kaye, has more thoughts on ENCODE and "junk DNA."  Practically, might the STR loci now be susceptible to a more critical look when a 4th Amendment-based privacy interest in invoked to challenge a government DNA database? 

A key question emerges: does the ENCODE research meaningfully reclassify the STR loci for 4th Amendment purposes? This is not an abstract inquiry; already, the ENCODE data has been invoked in the rehearing of Haskell v. Harris by the 9th Circuit en banc in California. This case is a 4th Amendment challenge to the state’s practice of collecting DNA from arrestees (9th Circuit panel upheld; see earlier story). The Electronic Frontier Foundation, as amicus, has asked the court to reconsider the privacy interest advanced by the challenger in view of the ENCODE findings. A precise ENCODE-derived analysis of the STR loci is not available; the EFF letter simply states that “ENCODE has determined that “junk” DNA plays a critical role in determining a person’s susceptibility to disease and physical traits like height” (citing to the New York Times article on ENCODE) and that it is "highly likely that the genetic markers contained in each Appellant's DNA profile reveal much more information than just his or her identity." That's speculation which lacks any precision with respect to the STR loci that underlie the legal challenge. It’s true that ENCODE has certainly opened the door to a reunderstanding of purpose in much of the human genome (actually, that is its goal); it is not known whether the STR loci, however, are individually tracked to real phenotypic expression, and whether STR loci variations contribute to a more complex DNA profile for an individual than was previously thought. In general, the constitutional analysis now confronts an evolving scientific portrait of the human genome, but at this point, it has not been shown that the precise STR loci at the center of the DNA database challenges have been reconceptualized by ENCODE in a manner that undermines their genetically inert status. What's noteworthy about this period in DNA database litigation is that Haskell v Harris and the recent King v. Maryland (likely to be heard by the Supreme Court) are advancing the constitutional issues of DNA collection from arrestees in the nation's leading courts at a time where the underlying science is more in flux than usual.

September 16, 2012

Relevance of Scientific Research and Instability of Federal Funding

Several items regarding the federal funding of life science research are worth noting because they illustrate the tensions over how the government funds science and what the public may or may not receive in the form of benefit. As a general matter, the federal government allocates approximately 10% of its discretionary funding to research and development, a percentage that has declined from about 25% in the mid-1990's. One point of contention in science funding debates is that the government funds useless research that appears to have no link to human improvement. That charge resonates with some of the parameters of basic research in molecular biology, where by definition, scientists have used seemingly obscure organisms as models (e.g., fuitfly, yeast, nematode, fish) for studying molecular processes, and the argument for such research has been that such work reveals universal biological processes that apply to humans. Now, in recognition of the fact that wild-card research observations could have great relevance for human benefit (including health), a Golden Goose Award has been established by a coalition of universities, think tanks, and businesseses for the purpose of “highlighting examples of seemingly obscure studies that have led to major breakthroughs and resulted in significant societal impact.” In a ceremony this week, one of the awards was for the research on the green fluorescent protein from jellyfish - which first explained why some jellyfish glow - but then the isolation of the gene allowed it to be used as a portable flashlight attached to genetic switching molecules, providing a means to track how gene expression occurs in any cell; such a technique has been used in HIV and cancer research. Other awards this week recognized analogous work in radiation physics and material science. So that is all to the good, but such efforts occur against real funding instability for federal science research. In a related but unfortunate linkage, the ongoing federal budget politics have produced a sequestration deal that ended the budget standoff last August but then embedded automatic cuts in federal spending that occur in January 2013. There's no progress in Washington on avoiding such an outcome. As a result, the current projection is for an 8.2 percent cut in federal science funding, with a specific loss of at least $2.5 billion for NIH alone. That would (and already has) greatly impact existing grant programs and plans for upcoming research in biomedicine; e.g., see a Mayo Clinic analysis. All of this is worth remembering as the political season produces a lot of verbiage regarding the criticality of American science, but a peek behind the words reveals mathematical truths that will undermine how much research can get done.

September 9, 2012

Science and the Election: Questions for Obama and Romney

Science and technology policy has been recognized as an integral component of the Presidential election cycle for the past several elections. The organization  has managed to place a set of science policy questions before the presidential candidates in 2008 and again this year; President Obama and Governor Romney have answered the questions here. It’s clear that the major political parties, based on ideological and process preferences, differ on how the (federal) government should be involved in the operation of American science operates and in how its emerging technologies should be regulated by government. One policy lever is fiscal: the decision to authorize spending on “big science” (e.g., space exploration or the Human Genome Project) or to calibrate annual funding levels for the major federal research agencies (in the case of life sciences, the National Institutes of Health and the National Science Foundation are closely watched). Those decisions are on the input side. On the output side, what happens to the technologies produced with the help of federal monies?  Here are such critical issues of regulation as those governing genetically engineered food and crops, genetic testing, nanotechnologies, and stem cell research. Although Obama and Romney provide general remarks to the set of general question, there is an absence of any details regarding some critical and pressing issues in the biotech-related life sciences:, e.g., authorization of (embryonic) stem cell research, labeling of genetically engineered (GE) food, or how the government manages dual-use research and disclosure with bioterrorist potential  For example, the 2008 questionnaire specifically asked about genetics research and embryonic stem cell research. Obama's policies are evident from his record (e.g., yes to embryonic stem cell research, no to regulation or mandatory labeling of GE food). The current set of questions did not require either candidate to be specific on those issues. In general, with respect to the formation of government policy for the life sciences, the president has an Office of Science and Technology Policy (since 1976), and the last several presidents have created their own bioethics-related advisory panels (Obama's is here) to study current controversies. Despite that, this election-year project to focus the (major) presidential candidates on the role of science in today’s government portfolio is useful, but more explicit questioning on the actual issues confronting regulatory agencies and legislatures would place the very real policy differences between the candidates in sharper focus.

September 3, 2012

European Court: PGD Ban Violates Reproductive Human Rights

The use of genetics in reproductive decisions has a long pedigree, as prospective parents consider their genetic background when considering whether children will be born free from disease. As molecular genetics enters medicine, a technique known as preimplantation genetic diagnosis (PGD) has been available for couples at high risk of giving birth to offspring with genetic disease (e.g., two parents that are carriers for the recessive cystic fibrosis). By using in vitro fertilization with genetic screening, PGD offers the possibility of selecting an embryo without disease for implantation. This technique is used in the U.S. as a modality in the general field of assisted reproductive technologies (ARTs), which are largely unregulated by the government here, although subject to professional norms (e.g., American Society for Reproductive Medicine). This past week, the European Court of Human Rights ruled that Italian Law 40 forbidding the use of PGD violated the human rights of a couple that sought to use the technique because of their risk in birthing a second CF child. The law was a violation of Article 8 (right to respect for private and family life) of the European Convention on Human Rights. By analogy to U.S. law, the challenge was a familiar type of assertion for reproductive autonomy against the interference of the state. Italy was ordered to pay damages to the challenging couple. The court noted the "inconsistency of the Italian legal system" - prohibiting the preemptive and avoidant approach of PGD while simultaneously allowing abortion to terminate pregnancy. While the opinion by the ECHR is advisory and does not repeal the law, the ruling will increase pressure on Italy (and possibly Austria and Switzerland, which have similar laws) to reconsider the ban on this ART. Earlier this year, the EHCR ruled that Ireland's abortion ban violated the human rights of a pregnant woman with cancer who could not access abortion services despite her pregnancy-related health risk.