A project funded by the European Union will soon begin evaluating SNP-based tools as a potential supplement to the short-tandem repeat technology that has become the core of European forensic labs.
The European Commission gave the green light to the project, SNPforID, in November and pledged €1.4 million in funding over three years, according to coordinator Peter Schneider. One month later the project was initiated, and participants met in Stromberg, Germany, last week to set goals for the first year.
The research will take place at forensic labs at the University of Santiago de Compostela in Galicia, Spain; the University of Copenhagen, Denmark; the Royal London School of Medicine; and the University of Mainz, Germany.
While the participating groups are already active in SNP research, study coordination will move into high gear over the next few weeks, said Schneider. Regular meetings will take place every six months to assess progress and adjust the direction of research.
The next meeting is tentatively scheduled to take place in Brussels, Belgium, and an EU representative will likely participate. Initial research results of the effort will be presented in September at the 20th Congress of the International Society for Forensic Genetics, in Arcachon, France.
The labs will also partner with private companies on aspects of the project. “We will try to establish closer contacts to companies who are active in SNP research, and will try to integrate these into our research efforts,” said Schneider, who is also a professor of forensic genetics at the University of Mainz. “We will invite company representatives to our meetings and, based on mutual interest, collaborate on specific areas of the projects. This may include technology as well as SNP-locus selection.”
Schneider declined to disclose the names of companies the project was contacting.
Choose your weapon
The interest in SNPs stems from the fact that 100-200 fewer base pairs are needed for SNP analysis than for STR-based detection, enabling the identification of substantially smaller forensic samples. This advantage, said Schneider, can be useful when trying to identify highly degraded DNA, or when very little DNA exists. [For example, The New York City medical examiner’s office, faced with highly degraded DNA material at Ground Zero, turned to SNP-based tools made by Orchid Cellmark last August to help them identify remains.]
Cost may also play a role in swaying popular opinion to SNPs from STRs, the gold standard in much of the world. “DNA is turning out to be such a pivotal tool; people want to use it more and more,” said Ron Sosnowski, senior director of molecular biology at Nanogen. “[But] doing STR is expensive. SNPs are cheaper.”
SNPforID researchers will choose between 50 and 100 SNPs that can be used to identify DNA samples from a variety of ethnic groups around the world. The aim, said Schneider, is to evaluate a number of high-throughput technologies that can analyze those SNPs and identify criminals and human remains.
Working at their academic labs, project researchers will evaluate MALDI-TOF technology, like the kind distributed by Applied Biosystems and Sequenom; conventional spotting microarrays, like those made by Affymetrix; and electronically activated arrays, like the one manufactured by Nanogen.
Schneider said equipment has already been bought with cash from equipment budgets at individual research centers; the €1.4 million, in fact, will be used to support researchers and consumables rather than equipment.
Though SNP-based forensic analysis may be cheaper than some traditional methods, a challenge with the technology is making it work on a high-throughput scale. As Schneider said, 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.
While it is widely known that SNPs are generally cheaper than STRs, it is not known by how much. According to Schneider, the European market for STR tools is “substantial” when one considers it costs $.30 to identify a single DNA sample using the technology, and that the UK alone has more than 2 million samples in its forensic database — a figure that grows by as much as 100,000 samples each year. Germany, a late-comer to the forensics database game, currently holds around 250,000 samples.
Applying SNP technology to criminal forensics presents even more challenges: Disparate law-enforcement agencies would have to adopt SNP-based methodology before a uniform and universally searchable database can be created.
“The question is, ‘Is SNP typing appropriate, and can it be used for forensics?’” said Schneider. “’And can it be made efficient [and] high throughput?’”
Assuming SNPs are found to be more efficient and less costly than STRs in forensic genomic analysis, proponents of the technology may still encounter obstacles if they try to unseat an established technology. Around the world, 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 said.
In Europe, Schneider said, since reliance on STRs among forensic specialists is universal it will take at least three years before SNP-based tools gain a foothold there. “One of the difficulties when you have a good system is you don’t want to change,” he said. “CODIS and European systems are good.”
Despite this, the EC study over the next three years will research whether it makes sense to switch all DNA databases from an STR standard to a SNP standard. 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, she said. “But if a SNP panel “becomes recommended, we will develop instruments to do those analyses.”