As of late July, 1,518 victims had been identified-with 779 of them, or just over half, identified by DNA alone. M-FISys brings together three types of DNA analysis-some standard, some not generally used for identification purposes-for repeated "all-against-all" comparisons among victim and kinship samples. The program constructs "virtual" DNA profiles where actual ones have literally gone up in smoke and permits users to add or subtract sample analyses from the composites as the evidence changes. It can link to other databases, such as those containing descriptions of, say, family relationships or what the victim wore to work the day of the disaster, or the medical examiner's postmortem findings. It can present a snapshot of not just every test done on a sample but of the progression of those tests, as well as the forensic scientists' comments. "M-FISys allows us to do quality checks on the software, on the samples, on the analysis," says Robert C. Shaler, director of the Department of Forensic Biology for New York City. "We can, at a glance, get an idea of what samples we have and what results we have on them so that we can quickly go through and ascertain what else we need to do."

The ability to coordinate disparate data sources is key to M-FISys's success, experts believe. "The DNA part of a mass fatality incident is effectively a very small and narrow part of that incident," says Chris Maguire, a consultant scientist with England's Forensic Science Service who evaluated the New York identification efforts for the British Consul General. "When you have something on the scale of September 11, with some 20,000 body parts, potentially 10,000 relatives, and close to 3,000 victims, the actual logic in all of the comparisons [between body parts, family samples, and personal effects] can get lost in the mass of information. That's where a program like M-FISys is so important."
 
M-FISys brings together three DNA technologies in order to increase the likelihood of identifying remains: short tandem repeat analysis, mitochondrial DNA analysis, and examination of DNA markers called single nucleotide polymorphisms. Short tandem repeat analysis is the most common technique used today in paternity testing and forensic matches, as in the O.J. Simpson case. Just four chemical bases-adenine, thymine, guanine, and cytosine (known as A, T, G, C)-make up the DNA organized into 24 chromosomes in each human cell. The chain of letters stretches some three billion bases long. A short tandem repeat is a brief stretch out of that three billion that repeats over and over again. Because many people may have the same repeat at one particular spot, it's necessary, for a conclusive match, to look at as many locations as possible. For its forensic investigations, the FBI examines 13 distinct regions where those repeats occur, plus a marker that indicates the sex of the person being profiled. M-FISys has upped the number to 15 regions for the Trade Center identifications.