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Reconciling ENCODE and CODIS

DNA image From tmkeesey use of DNA in forensics is powerful yet subject to uncertainties. Jennifer Wagner, JD, PhD, a Research Associate at the Center for the Integration of Genetic Healthcare Technologies at the University of Pennsylvania (Penn CIGHT), and Sara Katsanis, MS, an Associate in Research at the Duke Institute for Genome Sciences & Policy at Duke University (Duke IGSP) conducted an exhaustive search of the literature and genome databases to put forensic markers used in the Combined DNA Index System (CODIS) into a context of current understanding of the human genome. Their findings are available in an early online issue of the Journal of Forensic Sciences (“Characterization of the Standard and Recommended CODIS Markers”) and a Letter (“Out with the ‘Junk DNA’ phrase”).

CODIS is a DNA database funded by the FBI. It stores DNA profiles created by crime labs and is searchable to aid in identifying suspects in crimes. The database is comprised of DNA profiles that are indicative of a person's individual DNA, enough to infer identity but not a person’s traits and conditions. The profiles consist of sequences of variable DNA repeats, most notably ones called “short tandem repeats” or, simply, “STRs.”

Recently we have seen a tsunami of coverage of dozens of papers in major scientific journals describing a ten-year project to decipher the non-coding portions of the human genome. This well-orchestrated release of scientific reports came out the same week the Journal of Forensic Sciences paper appeared online. Wagner and Katsanis explain how their work relates to this news.

Earlier this month a series of publications related to ENCODE (Encyclopedia of DNA Elements) caused a surge in the use of the phrase “junk DNA” in the press (for example, in the New York Times and USA Today) and created an academic ruckus (for example, Nature and The Register) over whether the project signaled a significant change from what we previously knew about the genome. Indeed, understanding the elements of the human genome has far-reaching implications for both medical and law enforcement applications. The ways in which non-scientists conceptualize the human genome are bound to have a serious effect on the ways our society integrates genomic technologies and information into our lives.

For example, the way the genome has been conceptualized in legal contexts is of tremendous importance and may affect many of our lives. Across the United States there are numerous cases challenging the constitutionality of statutes that integrate DNA profiles (namely, the CODIS profiles often called “DNA fingerprints”) into the routine booking procedures upon arrest.[i] At the heart of these cases is whether a CODIS profile provides law enforcement with only identification information or, in the alternative, with information about an individual’s physical appearance or health conditions.

A review of recent court opinions[ii] suggests there is significant confusion about our current understanding of the genome, particularly in light of the emerging knowledge of regulatory functions of non-protein-coding regions of the genome (knowledge which, contrary to much coverage of ENCODE, did not just emerge this month but has been developing slowly since the 1970s and more rapidly since the 1990s). Is it possible to develop a panel of forensic markers that provides only identification information?

Motivated to provide clarity for the legal profession, we explored the human genome and scoured the available literature and databases for evidence that the DNA markers used by CODIS have any function. We found that, while the markers often lie within genome regions and genes associated with disease states or genome function, there was no evidence that the markers’ “short tandem repeat” genotypes are predictive of human traits.

The recent ENCODE publications, rather than undermining our findings, support the notion that much of the genome has “association” with varying genome function, including the regions containing the CODIS markers. The ENCODE research makes no reference to the potential importance of short tandem repeats within functional genome elements, which would implicate CODIS markers.

Clearly, the release of the ENCODE data demonstrates that our understanding of non-coding regions of the human genome are evolving. The recent papers reveal that much of the genome has function outside of protein production. Similarly, our review of CODIS markers found many of them to lie within regulatory elements and even genes. However, there remains no evidence that repeat-length genotypes at these markers correlate with actual gene function or genome regulation.

It is unfortunate that so much of the coverage of ENCODE has focused on the “junk DNA” catch phrase, which really wasn't accepted by the scientific community as a fair or accurate conceptualization of the genome. Non-scientists now are faced with trying to understand what this all means, and this phrase only causes confusion and misconceptions. To reduce the significance of ENCODE as simply having “debunked the junk DNA theory” is a disservice to the researchers involved and a distraction from the ENCODE project’s contributions to the advancement of a more nuanced and holistic understanding of human heredity and development.

We worry that the headlines associated with the ENCODE publications carry foreseeable risks of signaling to non-scientists in the legal profession who are trying to make sense of the information decipherable from CODIS profiles that our understanding of these markers is fundamentally altered from that of just a week ago. That is just not the case.

We are hopeful that how the forensic, scientific and legal communities think about genome “function” and “associations” will become more nuanced to include genotypes so that policy discussions regarding law enforcement use of DNA markers and constitutional privacy rights afforded by the Fourth Amendment can be appropriately placed on whether any of the CODIS genotypes have measurable positive (or negative) predictive value for any known human traits.   

[i] For further discussion, see, for example, Jennifer Wagner, “Minnesota the latest to weigh in on DNA Fingerprinting of Arrestees,” Genomics Law Report, 2/22/12; Jennifer Wagner, “Courts in Unsettled Territory turn to the Map Available: United States v. Mitchell,” Genomics Law Report, 4/2/12; Henry Greely, “The Supreme Court and Mandatory DNA Collection of Arrestees: Stay Tuned,” Center for Law and the Biosciences Stanford Law School, 7/22/12; and David H. Kaye, “The Constitutionality of DNA Collection Before Conviction: An Updated Scorecard,” Double Helix Law, 9/7/12

[ii] For example, State v. Abernathy, No. 3599-9-11 (Vt. Super. Ct. June 1, 2012); People v. Buza, San Francisco Co. Super. Ct. SCN 207818, First App. Dist. Ct. of App. CA, August 4, 2011) citing Haskell v. Brown, 677 F. Supp. 2d 1187, 1190 (N.D. Cal. 2009); and United States v. Mitchell, 652 F.3d 387 (3rd Cir. (PA) 2011) dissenting opinion citing United States v. Kriesel, 379 F.3d 941, 947 (9th Cir. 2007).

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