Thursday, July 26, 2007

Informed consent, exploitation and "Developing a SNP panel for forensic identification of individuals"

Conflicts of interest and ethical blindness to how others may perceive one's actions can take many forms in biomedical science. Here's an example a bit off the beaten path:

I am troubled by an article "Developing a SNP panel for forensic identification of individuals" by Kenneth K. Kidd, Andrew J. Pakstis et al in the Journal Forensic Science International: Forensic Sci Int. 2006 Dec 1;164(1):20-32, PubMed link here.

The abstract of the article states:

Single nucleotide polymorphisms (SNPs) are likely in the near future to have a fundamental role in forensics in both human identification and description. However, considerable research is necessary to establish adequate scientific foundations for these applications. In the case of identification, because allele frequencies can vary greatly among populations, the population genetics of match probabilities is a critical issue. Some SNPs, however, show little allele frequency variation among populations while remaining highly informative. We describe here both an efficient strategy for identifying and characterizing such SNPs, and test that strategy on a broad representation of world populations. Markers with high heterozygosity and little frequency variation among African American, European American, and East Asian populations are selected for additional screening on seven populations that provide a sampling of genetic variation from the world's major geographical regions. Those with little allele frequency variation on the seven populations are then screened on a total of 40 populations (~2100 individuals) and the most promising retained ...

What is troubling is the apparent use of human DNA samples for the purpose of validating if DNA SNP's can be used for forensic "identification" purposes. It is unclear if and how informed consent was obtained from the individuals who contributed the DNA samples for such non-medical purposes as "forensic identification", if these issues were even considered, and how such a study passed an IRB (the lead authors are at Yale School of Medicine):

For our initial identification of likely candidates, we have used the Applied Biosystems catalog database of SNPs for which there are pre-designed, synthesized, and pre-tested TaqMan assays. We chose this source because it provides off-the-shelf assays that are guaranteed to work with no effort on our part to design and optimize an assay. Our objective is to identify appropriate SNPs; subsequently others could determine the appropriate typing methods for forensic applications of the set of markers identified. From Applied Biosystems we obtained the frequencies for those TaqMan markers that had allele frequency data on four populations (African Americans, European Americans, Chinese, and Japanese). These markers were then rank ordered by both average heterozygosity and minimal difference in allele frequency among the four populations. We then test markers with average heterozygosity >0.45 and Fst <0.01.>

For the initial screen we have selected a total of 371 individuals from seven populations in order to sample genetic variation from all major geographical regions: European Americans (92), Biaka (66), Hausa (39), Ibo (48), Cambodians (25), Taiwanese Chinese (49), and Maya (52). These and the other populations studied are listed in Table 1 along with the unique identifiers (UIDs) in ALFRED, the ALLELE FREQUENCY Database (, for the descriptions of the populations and samples.

The second screening of the best of the markers from the initial screen consisted of samples from an additional 33 populations (Table 1). Thus, markers making it through the second screen will have been typed on ~2100 individuals from 40 populations. By geographic region the number of samples are: Africa (including African Americans) (459), Southwest Asia (211), Europe (558), Northwest Asia (90), East Asia (345), Northeast Asia/Siberia (51), Pacific Islands (60), North America (105), and South America (191).

This are not trivial issues. As I wrote at earlier posts "New book: Analysis of the Commodification & Ownership of Life" and "Academic abuses in biomedicine vs. Indigenous Peoples: The Genographic Project", indigenous populations around the world have had quite an unpopular view of human genome projects, causing the Human Genome Diversity Project to wither on the vine. That project became known by the indigenous peoples that it purported to study as the “vampire” project. Their fear was, and is, misuse of genetic materials without consent. Some of those issues are relevant to use of DNA samples to perfect a "forensic" identification capability essentially based on ethnic ("population") origins. We've been there before:

In 1995, the National Research Council (NRC) issued its recommendations on the Human Genome Diversity Project (HGDP). While the NRC endorsed the concept of diversity research, it criticized the HGDP's procedure, claiming that the HGDP had too many ethical lapses and problems. The NRC report suggested several alternatives such as doing sampling anonymously (i.e. sampling genetic data without tying it to specific racial groups).

... A number of the principal collaborators with the HGDP have been involved in the privately-funded Genographic Project launched in April 2005 with similar aims.

Potential problems


One major concern with the research project has been the potential for racism in certain countries resulting from HGDP data. Some have speculated that when governments are armed with genetic data linked to certain racial groups, they could feel the need to deny people rights based on this data. For example, countries could define races purely in genetic terms and deny a certain person right(s) based on their lack of conformity to a certain race's "genetic model."

The ETC Group (formerly RAFI) has been a major critic of the HGDP citing issues of racism and stigmatization that could occur should the HGDP be completed.

Biological weapons

Another concern with the HGDP has been the threat of racially targeted biological weapons from the project. Since the project will identify genes that tend to conform to specific racial groups, many have theorized that groups could create biological weapons that could target specific racial groups. Should the HGDP uncover specific diseases that tend to affect certain races, it is conceivable that groups could develop a biological weapon that targets certain disease and killing that specific racial group only. While most have called these ideas ridiculous, many concede that such weapons are theoretically possible and could have a dire impact.

To these concerns I might add a concern about "eugenic profiling" that attempts to characterize the genome of, say, criminals, or followers of 'undesirable' political ideologies.

A friend studying these issues mentioned to me that many samples used in this new paper's study may have been taken from an HGDP DNA collection in Europe, despite the fact many indigenous groups totally opposed the HGDP project for just that type of reason - i.e., concern about problematic secondary use of samples!

A new book entitled "Pacific Genes & Life Patents" has been written on these issues and is freely available at the link below:

For several years, indigenous groups have taken issue with scientists studying their DNA. When National Geographic began collecting DNA samples for The Genographic Project , the Maori of New Zealand along with Alaska natives feared that DNA evidence would invalidate their history and break family ties. Aroha Mead and Dr. Steven Ratuva have put together a volume of essays, entitled Pacific Genes & Life Patents , that examine how Pacific Indigenous communities have been affected by genetic research and products, and patents on life forms. The book is available for free online from the following website: (Publications), (Latest Publications).

The editors and authors of
Pacific Genes & Life Patents present articles, case studies, and other information which show that “outsiders” are predominantly interested in harvesting genetic information for profit without any regard for Pacific cultural values and norms.

In the "Developing a SNP panel for forensic identification of individuals" article, it appears a new excuse has been found for gathering DNA worldwide that seems of little medical value, but possibly of great commercial value in developing profitable forensic tools:

The narrow range in the distribution of the average match probability across populations validates the low Fst strategy for identifying SNPs for use in forensic human identification. While Fst depends on the specific set of populations studied, it is clear that a global set of DNA samples can be used to screen for markers with globally uniform Fst values.

It's quite convenient that there's now a Human Genographic Project, a "five-year effort to understand the human journey—where we came from and how we got to where we live today. This unprecedented effort will map humanity's genetic journey through the ages." Is that all the project has planned, or are there numerous "side research" projects that will be enabled through this seemingly innocuous and sweeping collection of DNA, such as genetic forensics with potential for misappropriation, misinterpretation and misuse?

Just to further cause concern to indigenous peoples, there's this in Kidd's SNP forensics paper:

It is also noteworthy that the populations with the largest average probability of identity (and the highest frequency for the most common genotype) tend to be the more genetically isolated populations (Mbuti, Samaritans, Komi Zyriane, Taiwanese aboriginals, Nasioi) and the Native American groups . This is not unexpected. The isolated populations have undergone more genetic drift and tend to have less variation than the less isolated and historically larger populations. The Native American groups are known to be diverse [16], possibly because of historical reproductive barriers between tribes. We would expect the Fst values to increase as more such populations are studied for these markers. However, the much more relevant factors--the frequency of the most common genotype and the average probability of identity--are not likely to greatly exceed the ranges seen for the 40 populations that we have studied.

Finally, I should mention in the interest of full disclosure that I'd had an ethcial run-in a decade ago with the lead author of this article. Those events are documented here and here and occurred over a computer program I authored as part of a project to try to help improve care of children in certain Middle Eastern countries with a high rate of consanguinity, and thus experiencing very common and severe birth defects. Ironically, my little act of attempted Judeo Islamic reconciliation was treated with disdain by my own (ostensibly) Christian colleague.

Regarding the defunct Human Genome Diversity Project, Kidd had this to say:

Yale geneticist Kenneth Kidd, one of the project's founders, says he has never fully understood what went wrong. "There was a huge amount of misunderstanding." At the time, scientists were starting to take out patents on human genes. "Indigenous populations say you're out to steal our unique genes, patent them, and make lots of money."

I imagine it would indeed be hard to understand what might have gone wrong - why indigenous peoples might "misunderstand" your intentions - when you see no problems with misappropriating the intellectual property of your own colleagues.

Perhaps in the current paper on forensic identification by SNP, informed consent was obtained at some time in one form or another; perhaps the IRB review of this research was entirely proper. However, the paper raises questions in that regard.

-- SS

Addendum: Peripherally related in the scientific sense but perhaps closely related in the ethical and ideological sense, I've just discovered via a recent newspaper that Yale has some additional problems of late regarding property: "Peru demands return of Machu Picchu treasures by Yale", Miami Herald, July 25, 2007, by Tyler Bridges (now a Peruvian resident). Yale apparently went so far as to interpret the laws of a foreign nation, which is, of course, Yale's right as a sovereign entity, the People's Republic of Yale, it would seem:

Key documents include a 1912 Peruvian decree stating that Peru reserved the right to request the objects' return, and a 1916 letter that [Yale professor/explorer Bingham] wrote to the National Geographic Society about the artifacts from the 1914-15 expedition. ''Now they do not belong to us, but to the Peruvian government, who allowed us to take them out of the country on condition that they be returned in 18 months,'' Bingham wrote. Yale officials have said that Peruvian law in force in 1912 does not require the university to return objects from Bingham's expedition that year.

(Is it irony that parts of this upcoming movie are being filmed at Yale?)

It is also not surprising to this author that a federal investigation into Yale University’s management of research grants was initiated in 2006 by NIH, DoD and NSF, among others. FBI agents apparently sought out professors in their homes and vacation spots at night, which would seem to indicate rather serious problems (details are in this Powerpoint presentation).

Why is it that the intersections of "unusual genetics research" and universities like Yale make me uneasy?

-- SS