Bioinformatics and national service

FRAMINGHAM (09/24/2003) - Two years ago, the nation watched in disbelief as two hijacked planes slammed into the World Trade Center. Author William Langewiesche captured the moment in American Ground: "For an instant, each tower left its imprint in the air, a phantom of pulverized concrete marking a place that then became a memory."

More than 1.6 million tons of steel and debris collapsed into the 10-acre, six-story foundation (the "bathtub") of the World Trade Center, "tied together like steel wool and complicated by the existence of human remains." The remains of 2,792 people, to be exact, many of whom were simply cremated in a cauldron of gasoline and steel that exceeded 2,000ºF.

The recovery effort following Sept. 11 showcased the extraordinary heroism of New York's rescue workers, even if some proved to be humanly fallible. (Langewiesche reported one fire truck buried under the rubble contained piles of neatly stacked and tagged blue jeans.) Recovering the remains was difficult enough, but establishing identities was an unprecedented task.

Only 287 intact bodies were hauled from Ground Zero, compared to some 20,000 tissue samples. Relatives provided 7,681 personal effects of the victims (mainly toothbrushes, but also razors, combs, lip balm, and so on) and 11,641 cheek swabs to allow investigators to find their loved ones. Depending on the quality of the victims' DNA samples, three types of analyses were performed at organizations including Bode Technology, Celera Genomics, Myriad Genetics, and Orchid BioSciences.

But as Melissa Kruse reports in her poignant cover story, the chief medical examiner soon realized that an entirely new software package was required to make unequivocal identifications from the reams of DNA data. The call went to Howard Cash, CEO and founder of Gene Codes, a small bioinformatics company in Ann Arbor, Mich. As Cash noted recently in a meeting abstract, "Software tools had never been considered for a problem of this scale and scope."


DNA fingerprinting was pioneered in the mid-1980s by Sir Alec Jeffreys, professor of genetics at the University of Leicester. His group first applied the technology forensically to solve the rape and murder of two English schoolgirls, exonerating one suspect before leading to the conviction of the true culprit. Jeffreys also positively identified the remains of the Nazi war criminal Josef Mengele.

In perhaps the most famous example of DNA fingerprinting, the remains of Russia's last Tsar, Nicholas II, executed by firing squad with his family in 1918, were positively identified following the exhumation of his brother Georgij Romanov's body from a St. Petersburg cathedral. The exquisite matching of a trace of mitochondrial DNA, showing the same mixture (heteroplasmy) of two bases of DNA at a single position, finally allowed the Russian government to officially lay to rest the remains of the royal family in July 1998.

In the United States, the first execution based on DNA evidence took place in 1988. One year later, the Innocence Project, co-founded by attorneys Barry Scheck and Peter Neufeld, used DNA fingerprinting to exonerate the first of 131 falsely imprisoned inmates. As technology improves, mass DNA identification at disaster sites has become almost routine. The victims of several recent disasters, including the 1998 Swissair crash, were all identified.

But these incidents all paled in comparison to the task facing Cash and Gene Codes. The company suspended development of its perennially popular DNA sequence analysis program Sequencher, which it calls "the perfect universal joint in the bioinformatics pipeline," for two years while working on its mass identification program. As Kruse details, the result, which incorporates Sequencher, was born using extreme programming and rigorous quality control, as well as close cooperation with the Office of the Chief Medical Examiner (OCME) to guide the user interface.

Ghosts in the Machine

Debuting in December 2001, M-FISys (mass fatality identification system), currently in its 68th iteration, sorts thousands of DNA profiles of relatives and victims' remains in search of matches. Even now, Gene Codes staffers are helping to trace new matches on a weekly basis, although the official identification is pronounced by the OCME. Each positive identification is treasured for the closure it might afford another grieving family. Remarkably, more than half of the World Trade Center victims have been identified, and there is hope that the final number may reach 2,000.

Cash has maintained a low profile for the past two years -- his presentation at the 2003 Bio-ITWorld Conference was a rare appearance on the scientific circuit. His team's personal and professional sacrifices in the national service is an inspirational strand of the Sept. 11 recovery effort that we can only applaud. Clearly, the victims' families appreciate their dedication: Only a small number have requested not to be informed should their relative's remains be identified.

M-FISys will be probably be pressed into service after another disaster before long, to identify victims of an earthquake or cyclone. Let us at least hope its use is confined to the devastation wreaked by nature, not mankind.

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