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Software tackles tough DNA puzzles

A genetic-matching computer program that has helped identify the remains of hundreds of victims of Sept. 11 could be easily set up at other disaster sites to do the same, its developers say.
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One more family was on the verge of getting the news that their loved one, lost in the terror attack on the World Trade Center, had been identified on the basis of DNA matching. There was a 99 percent confidence level that lab workers had the right person. Looking back, Howard Cash says it’s a good thing that genetic detectives shoot for 99-point-nine percent confidence — because otherwise they could have made the ultimate mistake.

The case demonstrated how exacting genetic analysis had to be in order to cope with the aftermath of the Sept. 11 attack, said Cash, founder and president of Gene Codes Corp. Cash’s company developed genetic database software just weeks after the tragedy to keep track of the millions of bits of genetic data derived to match up 20,000 individual remains with 14,000 samples provided by mourning relatives and friends.

It was up to New York City’s Office of the Chief Medical Examiner to determine when a match was close enough to notify the family. The 99 percent case looked promising, but it didn’t quite reach the medical examiner’s 99.9 percent standard — and so the identification was held back, Cash recalled.

“It turned out that the first identification was wrong,” Cash told A different set of remains turned out to provide a closer match, and the original specimen ended up being matched with a different victim of the attack.

“It’s bad enough that somebody died,” he said, “worse not to receive any remains, and worst of all to make a mistake and have to tell the family.”

So far, the DNA identification effort for World Trade Center victims has not made a single mistake, he said. As of Friday, 1,491 of the 2,792 people believed to have died in the attack have been matched up with recovered remains. Out of 19,938 victim samples, 7,098 have been identified, 5,809 on the basis of DNA alone.

“We’re still getting two or three or five new identifications every week by means of some heroic measures and the data analysis,” Cash said. “Certainly, 10 years ago the vast majority would never have been identified.”

Sternest test
The Sept. 11 attacks could well represent one of the sternest tests imaginable for DNA identification techniques. Unlike airline accidents, the casualty list is by no means certain — it’s what forensics experts call an “open” rather than a “closed” population. Managing tens of thousands of specimens is a logistical challenge in itself, and many of the samples may be mere bits of bone or commingled remains.

In the wake of 9/11, forensic agencies and genetic testing firms quickly mobilized to deal with the task, under the aegis of medical examiner’s office. Gene Codes, which has been working with the Armed Forces DNA Identification Laboratory since 1997, was chosen to develop the data-tracking software — and in December 2001 it delivered the first version of a custom-built program called M-FISys (which stands for “Mass Fatality Identification System” and is pronounced like “emphasis”).

Gene Codes’ staff in Ann Arbor, Mich., worked 16-hour days and came into the office every weekend to get M-FISys up and running, Cash said. Almost every week, Cash himself delivers software upgrades to New York — and attends memorial ceremonies for the dead, near the refrigerated trailers where remains are kept. “I’ve gotten to know some of the families,” he said.

The software keeps track of the remains as well as the exemplars — that is, reference samples gleaned from toothbrushes, hairbrushes, tissue donor banks, even unlaundered clothing and cheek swabs taken from relatives.

Cash emphasized that M-FISys is just one of the genetic analysis tools used by investigators.

“As a matter of law, neither we nor the software can actually make an identification,” he said via e-mail. “All we can do is present information to the medical examiners and forensic scientists in a way that allows them to make that determination.”

Bettering the odds
Each new piece of data increases the likelihood of an accurate match. Investigators initially aimed for a “less than a 1 in a million chance that any single match is going to be wrong,” Cash said, and they’ve exceeded that statistical goal.

“Certainly it’s a higher level of precision than what people expect would be involved in court cases,” he said.

By now, all the “easy” cases have been solved — and that means increasingly sophisticated DNA tests have to come into play. Virginia-based Bode Technology Group, the lead forensic lab in the World Trade Center DNA effort, has pioneered the extraction of usable samples from the interiors of burned bone fragments.

The labs started out looking for matches using short tandem repeats, the kind of DNA markers used in paternity tests. Then they added mitochondrial DNA analysis. Now they’re looking at single-nucleotide polymorphisms, or SNPs, which can produce a match with one-fifth of the intact genetic characters required for a paternity test.

Gene Codes’ M-FISys program has to keep track of all those data, as well as more traditional evidence such as medical and dental identifying marks. When it comes to making a match, the DNA trumps the physical evidence. Cash recalls the case of a fallen firefighter who was known to have an unusually shaped vertebra — and to carry a St. Christopher’s medal. Just such a victim was found in the course of the recovery effort.

“It turned out that there was another firefighter who was not related, who turned out to have this 1-in-1,000 bifurcated C3 vertebra, and he had a St. Christopher’s medal,” Cash said. “And it turned out that the DNA caught the potential error.”

Emphasis on future applications
New York City is the main client for M-FISys — as part of a three-year, $10 million contract that Cash expects will end up closer to an actual payout of $4 million or so. But Cash believes the program will have much wider application.

“If a hurricane hits the Philippines, or another major earthquake hits Turkey, we can pick this up and drop it in a municipality,” he said. “We’re already in negotiations with several countries — some because they see themselves under terrorist threat, but others just for missing persons.”

He said some of the technology could be used for more mundane applications as well, such as managing the breeding of endangered species in captivity, or to develop tailored drugs that can be flagged to be used — or avoided — by patients with a particular genetic profile.

“We certainly hope it can be used to add to the criminal databases that are set up now, and the databases for missing-person cases,” Cash said.

As for wider-scale DNA databases, Cash is conscious of the potential ethical pitfalls — but advises that each individual might want to create their own makeshift DNA file, just in case.

“If you kept a Band-Aid in the freezer that you used at some point,” he said, “we could go back to that as an exemplar.”

This report has been updated to clarify the roles played by the Office of the Chief Medical Examiner and Gene Codes in the World Trade Center victim identification effort, and to correct a reference to the probability of misidentification.