Almost a year after the Sept. 11 tragedy, more than half of the victims at New York's World Trade Center remain unidentified.

While about 49 percent of the nearly 3,000 killed as a result of the terrorist attacks on the twin towers have been identified using forensic techniques including DNA analysis, the effort remains far from complete.

Enter Orchid BioSciences Inc., which was awarded a contract by New York's chief medical examiner to continue the process. Though DNA in more than half of the remains is so damaged or degraded that it has been rendered unidentifiable to date, Orchid will use its single nucleotide polymorphism (SNP) analysis technology to analyze remaining DNA samples. Princeton, N.J.-based Orchid said panels of SNPs, the smallest and most common element of genetic variation between individuals that the firm has used in paternity suits and other identity cases, could help identify additional DNA specimens that have failed previous attempts.

"There has been a great deal of interest in SNPs over the last several years, and there are a whole range of applications that are now emerging as appropriate," Chairman, CEO and President Dale Pfost said, naming forensics as one such area. "Because of the degraded state of the samples thought to have been caused by elevated temperatures that fragmented the DNA, the smaller pieces are left."

He said traditional DNA analysis requires long, intact samples. But much smaller samples of SNPs are available. Each SNP represents a single base difference in the more than 3 billion bases of DNA comprising the human genome.

"The only technique available is to look at SNPs, because they reside in small portions of DNA," Pfost said.

Tissue samples from the World Trade Center will be amplified to create copies of the location of the DNA. The amplified sample is added to a reaction that includes the Orchid's SNP-IT technology, the chemistry for doing SNP scoring. The product is then run through SNPstream UHT, Orchid's hardware system that can work with a panel of SNPs and a large number of samples. It is capable of analyzing more than 800,000 SNPs daily.

"In this case, I think we're using a few dozen markers per sample," Pfost said. "So every three or so wells would be another sample. We compare that with samples collected from domestic situations, such as hair in a comb or a brush."

The project, which has completed pilot-stage validation testing, will take several months.

"And if there's a match, we'll find it if there's DNA to be had," Pfost said, though he added there is not a 100 percent guarantee of identification, since DNA may be completely missing from some samples. "This is a very robust, very reliable technology.

"This is being done in a very orderly and appropriate pace to make sure it's done as carefully as possible."

Orchid has built a forensics business based on its SNP-IT technology. Pfost said the market has developed, in part, because of the cost-effectiveness of DNA testing.

Orchid's Cellmark unit carries out its private forensic DNA analysis through an international network of four forensic testing laboratories - three in the U.S. and one in the UK.

"We see this as a vanguard of a whole new range of forensics tests," he said. "It could be used for solving crime, used in identity cards and actually is a very scalable business."

Cellmark has developed the SNP panels being used for the World Trade Center project based on prior work with The SNP Consortium, a public/private partnership to discover SNPs.

"We have assembled the largest DNA testing company in the world," Pfost said. "We do some three-quarters of a million samples per year for a variety of applications, and forensics happens to be one of those."

Orchid's shares (NASDAQ:ORCH) rose 3 cents on Thursday to close at 98 cents.

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