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.

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