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European Forensics Labs to Study Viability of Large-scale SNP Analysis

SAN FRANCISCO, Sept. 5 - The European Commission plans to spend 1.4 million on a three-year study this fall to evaluate and develop SNP-based forensic technologies, according to the study's coordinator.


The move may signal an interest among European forensic specialists to gradually move away from traditional technologies, which can be costly and display distinct limitations.


Peter Schneider, the SNP project's coordinator and a professor of forensic genetics at the University of Mainz, in Germany, says the research will take place at academic forensic labs at the University of Santiago de Compostela in Galicia, Spain; the University of Copenhagen, in Denmark; the Royal London School of Medicine; and the University of Mainz, in Germany.


Project researchers will choose between 50 and 100 SNPs that can be used to identify DNA samples from a variety of ethnic groups throughout the world, and will evaluate a number of high-throughput technologies that can analyze those SNPs in order to identify criminals and human remains, says Schneider.


Researchers at the labs will evaluate MALDI-TOF technology such as those distributed by Applied Biosystems and Sequenom, conventional spotting microarrays such as Affymetrix arrays, and electronically activated microarrays such as Nanogen products.


Schneider says the equipment has already been bought, but not from the 1.4 million expected from the EC. The dispersal of that money, which will support researchers and consumables, remained to be finalized by the EC.

SNP screen

Because between 100 and 200 fewer base pairs are needed for SNP analysis than for STRs, SNPs can be used to identify significantly smaller forensic samples. This advantage, said Schneider, can be useful when trying to identify highly degraded DNA, or when very little DNA exists.

Recently, in fact, the New York City medical examiner's office turned to Orchid Biosciences' SNP technology to help it identify victims of the World Trade Center terrorist attack in cases where more traditional DNA analysis was unsuccessful.


Cost may also play a role in swaying popular opinion to SNPs from STRs. "DNA is turning out to be such a pivotal tool; people want to use it more and more," says Ron Sosnowski, senior director of molecular biology at Nanogen. "[But] doing STR is expensive. SNPs are cheaper."


SNP-based forensic analysis may be cheaper than traditional methods, but a challenge inherent with the technology is making it work on a high-throughput scale. As Schneider says, researchers must first pinpoint the right combination of SNPs before an ID can be deemed accurate--no small feat considering the estimated 1.5 million SNPs in the human genome.


Applying the technology to criminal forensics presents even more challenges. Disparate law-enforcement agencies would have to adopt SNP-based methodology for there to be a uniform and universally searchable database.


"The question is 'Is SNP typing appropriate and can it be used for forensics?'" says Schneider. "And can it be made efficient high throughput?"


Assuming SNPs are found to be more efficient and less costly than the STR way  in forensic genome analysis, proponents of the technology will likely encounter obstacles if they try to unseat an established technology.


Around the world today, STR technology "is the gold standard in what most law-enforcement agencies use in DNA-forensic testing," according to Meri Bozzini, product manager for human identification at ABI.


"In the forensics community, once a database is established"--like the Federal Bureau of Investigation's STR-based Combined DNA Index System--"it takes something a huge order of magnitude better to displace it," she says.


Schneider agrees with Bozzini. "One of the difficulties when you have a good system is you don't want to change," he says. "CODIS and European systems are good."


Despite this, the EC study over the next three years will try to find out if it makes sense to change all DNA databases from an STR standard to a SNP standard, Schneider says. Meantime, in Schneider's eyes SNPs remain a niche approach to be brought in when STR fails.


Adds ABI's Bozzini: "We don't see the forensic community abandoning [STR] technology in the next five to 10 years. We see SNPs as being supplemental to STRs" in that time. But if a SNP panel "becomes recommended, we will develop instruments to do those analyses."

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