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On September 26, 2001, Howard Cash got a phone call that changed his life. On the other end of the line was the Office of the Chief Medical Examiner of the City of New York. Could Cash-the founder of Gene Codes, a bioinformatics company recognized for a DNA-sequencing program called Sequencher-build the software necessary to manage and identify the remains of the 2,792 missing victims of the September 11 attacks on the World Trade Center? Existing identification tools were inadequate for the task: The scope of the project was mind-bogglingly large, and the remains to be identified had been pulverized and commingled by the falling towers and burning jet fuel. Ultimately, 19,937 separate remains were found, with some victims recovered in as many as 200 pieces.

Using $2 million in profits to hire 11 new people and double his office space, Cash sprang into action. He started a wholly owned subsidiary called Gene Codes Forensics to develop a new breed of identification software: M-FISys (pronounced “emphasis”), an acronym for Mass-Fatality Identification System. (The subsidiary would protect the parent company against potential lawsuits should any victim not be identified.) The day the medical examiner’s office first turned on the software, December 13, 2001, 55 new matches that ultimately resulted in identifications were made. Says Cash, “There was such a mountain of information, there wasn’t a way to sift through it and find the matches until that first day. Suddenly, there were these loved ones’ remains waiting to be sent home.”

Before M-FISys, the New York medical examiner’s office was attempting to make DNA identifications using an FBI program called CoDIS (or Combined DNA Index System), which is generally used to identify felons based on the DNA found at crime scenes, along with Charles Brenner’s longstanding DNA-VIEW and Benoit Leclair’s Mass Disaster Kinship Analysis Program. But by mid-December, CoDIS, which was designed to compare a single sample to a large database of DNA profiles, had identified just 203 remains representing 105 people. Information-everything from DNA analysis of victims’ remains and their personal effects, as well as of relatives’ cheek swabs, to dental records and fingerprints-was being stored in 22 different databases as varied as FileMaker Pro and Oracle. As of June 2003, the medical examiner’s office had collected 7,681 personal items, including toothbrushes, razors, and hairbrushes, and 11,641 cheek swabs from some 7,166 relatives.

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