Using DNA Forensics to Identify Sept 11 Victims
DNA forensics has played a critical role in identifying the victims from the September 11, 2001, terrorist attacks as we approach the second anniversary of this devastating event.
Published September 1, 2003
By Beth Hanson
Academy Contributor

As its second anniversary approaches, Bob Shaler resurrects the indelible memory of the morning of September 11, 2001. Shaler, director of Forensic Biology in New York City’s Office of Chief Medical Examiner (OCME), quickly realized his office was going to be engaged in a monumental undertaking, he recalls. Early estimates put the number of dead at 20,000; it was thought the possible human remains could number 500,000.
It’s now believed the World Trade Center attacks claimed 2,792 lives, a fraction of that first day’s estimate. Of this total, just over half – or 1,508 people – had been identified by the OCME as of late June this year. To match names with bone fragments and tissue, forensic scientists have scrutinized the 20,000 or so human remains that searchers ultimately collected, testing some of them up to six times for usable DNA. Unfortunately, the extreme heat and moisture inside the mountain of debris presented a highly hostile environment to DNA. “They cause it to fall apart,” Shaler notes.
The first batch of identifications was easy. But Shaler says the remains his forensic team has been working with for the past year or so have yielded very little information about their origins, as analysts encounter more degraded, shorter sections of DNA. To address the problem, Shaler has been working with forensic scientists at cooperating government agencies, private companies and a group of special advisors – the World Trade Center Kinship and Data Analysis Panel (KADAP) – to map out a new strategy to make identifications from these minute scraps of DNA.
“Miniplexes”
Techniques the OCME has adopted include “miniplexes,” which look at the 13 standard short tandem repeat (STR) loci used by forensic crime labs, but allow analysis of more degraded segments of DNA, as well as analysis of single nucleotide polymorphisms (SNPs), and of mitochondrial DNA (mtDNA), which has been used to identify human remains for several years. In the process, the OCME is serving as a kind of proving ground for these techniques in forensics.
“There’s no question that the new techniques developed for the World Trade Center will find their way into the mainstream forensic arena,” says Jack Ballantyne, associate director of research at the National Center for Forensic Science, a program of the National Institute of Justice. “They are an enhancement of our tool kit and will extend our ability to obtain results.”
Until the past few years, such an undertaking would have been technologically impossible, and those who died would have remained unidentified and in a kind of mass grave. The millions of dollars already spent on the identification process reflect “the really compelling need for victims and families to have some closure,” says Sarah Hart, director of the National Institute of Justice, the research arm of the Department of Justice. “We were seeing the agony of families on a mass scale here, but throughout the country families go through this all the time when someone disappears. This technology is extremely important,” she says.
Getting the DNA
For 11 months following the World Trade Center collapse searchers combed through the 1.8 million tons of steel, aluminum, concrete, glass, wood and other debris, collecting anything – down to the size of a thumbnail – that resembled a human remain. The OCME’s forensic anthropologist, Amy Mundorff, then examined each piece to determine whether it was human, and whether pieces found together could belong to the same person.
Forensic scientists at the OCME, New York State Police, and the private companies contracted by the OCME have since worked to extract as much DNA as possible from these remains. Over time, “we’ve had to adjust and redesign the extraction techniques,” says Shaler.
The majority of the remains are bones, and “bone analysis is difficult and tedious,” he says. “Because of the low levels of DNA present, the likelihood of DNA degradation, and the potential presence of PCR inhibitors, bone can be one of the more challenging forensic samples to work with.”
Mitchell Holland, a former lab chief at the Armed Forces DNA Identification Laboratory who is currently lab director at Bode Technologies, agrees: “Bone samples are the bottleneck in DNA analysis.” Bode is analyzing all the bone collected from the World Trade Center, and has reengineered the process using a drill, rather than the usual grinding cup, to remove fine shavings for DNA extraction.
Holland says this change has helped speed the procedure enormously. In addition, he says, Bode has developed a method to extract DNA from bone “using a different combination of reagents, which recovers more DNA and removes more of the bone matrix components such as calcium, which inhibits PCR analysis.”
Creating DNA Profiles
“If we get some results, we may go back and resample,” says Shaler. “If a piece of bone is charred, we may try to find a piece that is not so badly charred. We’re feeling our way as we go with this.”
In an attempt to create a DNA profile from each remain, the forensic scientists made a first pass using the traditional STR test. “We realized early on that a high percentage of the remains would not yield usable STR results,” Shaler recalls. “When we finished testing all the samples, 61 percent didn’t give us enough information to make an identification. The remains were losing the higher weight loci, and we were getting pieces that were more like 100- to 200-base-pairs long.”
So Shaler turned to a modified STR test developed by John Butler, head of the Human Identity group at the National Institute of Standards and Technology, and further refined for the World Trade Center remains by Bode. This method uses smaller probes, and can provide results from shorter, more degraded pieces of DNA. These “miniplexes” are designed to focus on the STR loci that are most likely to drop out as DNA decomposes, pieces with a higher molecular weight that contain between 70 to 200 base pairs. “The first day that we used this test, we made five new identifications,” Shaler says.
The Smallest Mutation on the DNA Molecule
SNPs, until now a tool mainly for medical and agricultural analyses, may also soon yield results. SNPs tests enable scientists to look at the smallest mutation on the DNA molecule – a change in a single base pair. Orchid Biosciences has devised a test for remains from the World Trade Center that looks at pieces of DNA that are 50- to 85-base-pairs long. “We look at 71 loci,” says Shaler, “and we need to match 40 to make an identification.”
The OCME recently concluded its validation phase for SNPs, and the New York State Department of Health is now in the process of certifying Orchid’s lab to do the work. In its trials of this process, the OCME found that in the 35 percent of the samples that gave usable STR results from three or fewer loci, they were able to detect more than 51 SNPs. “I know we’ll get new identifications when we start using SNPs,” Shaler asserts. “I just don’t know how many.”
Mitochondrial DNA is abundant in human cells and is hardier than nuclear DNA, so there’s more of it to analyze, and it’s providing information about the bones and tissue found in the rubble. But in analyzing the World Trade Center remains, “mtDNA analysis is a supplemental method because mtDNA is not a unique identifier,” says Terry Melton, president of Mitotyping Technologies and a member of a group convened by the KADAP to look into the uses of mtDNA. “In this process mtDNA can increase the ability to make a statistical match, and in any one case it could tip the scales” and help make a conclusive identification, she says.
Making Matches
Mitochondrial DNA is helping the forensic team group remains into the families that they could belong to, Shaler notes, and may prove even more useful as new techniques to analyze this genome become available.
Once the OCME has gathered data from the different tests for each remain, staff members attempt to find a match. This is done by comparing the results to the DNA collected from the thousands of toothbrushes, razors, hairbrushes, and other personal items provided by relatives of the victims, as well as from several thousand cheek swabs received from relatives. Gene Codes in Ann Arbor, Michigan, tailored a software application called the Mass Fatality Identification System (M-FISys) specifically for this purpose.
For the past several years, crime labs have contributed DNA evidence from crime scenes and DNA from convicted felons to a national database and searching mechanism called CODIS (Combined DNA Index System). Law enforcement agencies have been able to compare DNA evidence against the database of profiles from convicted felons, for example, and make other searches through CODIS. So “we had the ability to compare a single DNA sample against a large database of samples to look for a match,” says Shaler, “but until 9/11 no one had needed software to compare all against all” – data from all the remains against data from all the razors, toothbrushes and cheek swabs.
“At the beginning our priority was to reduce the haystack, so we figured out how to collapse the data from multiple remains belonging to one person into a single data set,” says Howard Cash, Gene Codes president. Cash continues to fly to New York weekly, bringing updates to the software and adding attributes, such as details about the exact location at the on site where each remain was recovered.
Future DNA Forensics
M-FISys may be useful for other grim endeavors. Gene Codes plans to give the software to the International Commission on Missing Persons, which is at work in the former Yugoslavia, where as many as 40,000 people are missing and believed buried in many different locations. Cash says other countries have inquired about systems similar to M-FISys for missing persons case work and for disaster preparedness.
Using a combination of the analysis techniques described above, and others that may be in the pipeline, Shaler expects his office to continue working to make identifications from the World Trade Center remains for another year or two.
Whether they prove useful for this process or not, many new forensic tools are in development. Holland says research in this field is “heating up,” with people working on ways to get results from a variety of biological materials and from evidence that’s been degraded by exposure to all kinds of environmental insults.
New approaches to DNA evidence include techniques that could repair DNA damaged by environmental conditions such as UV light, says Ballantyne, using one or more of the DNA repair enzymes found in nature. Another approach analyzes DNA evidence from a crime scene to determine physical traits of the suspect, such as hair color or age. “We call this approach the ‘genetic eyewitness’,” he says.
While no one wants to believe another tragedy such as occurred two years ago is likely, Shaler urges other forensic labs to get ready. “I hear a lot of my colleagues say that the World Trade Center was a one-time thing, but that’s faulty thinking,” he says. “Forensics labs should look at what we’ve done and prepare themselves.”
Also read: Saving Lives in the Aftermath of Sept 11 Attack and Annals of the New York Academy of Sciences, Vol 758