DNA analyst Lalani Palmer prepares her lab space inside the Armed Forces Medical Examiner System (AFMES) facilities at Dover Air Force Base. The Armed Forces DNA Identification Laboratory provides scientific consultation, research and education services in the field of forensic DNA analysis to the Department of Defense (DoD) and other agencies. (Delaware State News/Dave Chambers)
DOVER — For some, having one last chance to see the body of a deceased family member can be consoling, especially if that loved one dies overseas, thousands of miles from home.
Just having identified remains can be helpful to some mourners.
But many Americans who died during wars have never been identified. A plane shot down in combat might leave behind only small, scattered remains of bone, rendering identification impossible with traditional methods.
The Department of Defense is working to change that.
Much of the work falls to a facility at Dover Air Force Base that many base personnel don’t even know exists.
The DoD DNA Registry, part of the only federal medical examiner’s office, analyzes DNA to help the military identify deceased servicemen and servicewomen.
Containing the Armed Forces DNA Identification Laboratory, it hosts scientists who use advanced tools and techniques to break down DNA.
From there, they carefully compare it to an in-house database in hope of finding a relative of the deceased and ultimately making a positive identification.
A daily snapshot
It’s Wednesday around noon, and a scientist is hard at work carefully sanding a bone fragment. After the bone is clean, it will be broken down and dissolved so the DNA can be collected.
The process calls to mind “Jurassic Park,” but the results are drastically different. More pertinently, this is not fiction.
“A lot of these bones had been out in the environment for the past 60-plus years, and so we want to sand that dirt and outside contaminants off,” explained Dr. Tim McMahon, the deputy director of forensic services.
The bone dates back to one of three foreign conflicts increasingly known to Americans only through history textbooks: World War II, the Korean War and the Vietnam War.
In this case, the scientist, Leilani Palmer, uses a small piece cut out from a cylindrical piece of bone. Lab analysts do not need much bone to do their work — just a piece a few millimeters in size.
As incredible as it may sound, she is preparing to duplicate the DNA.
“We put chemicals in there, we put DNA, and over X number of cycles it exponentially doubles, so if I have one copy of DNA, the second cycle I’ve got two, four, eight, 16 and so on,” Dr. McMahon said. “So we copy the DNA.”
Before Ms. Palmer can do that, though, she must extract the DNA. That’s accomplished by grinding the bone into a fine power and then dissolving it with chemicals. Once the bone is dissolved, the DNA can be collected and replicated.
Replication is a process that involves running the DNA through a thermocycler, or polymerase chain reaction machine, at different temperatures. It’s measured in cycles, with each cycle consisting of three different steps.
DNA is first heated at 94 degrees for 30 seconds, then between 58-62 degrees for 30 seconds and then at 72 degrees for 30-60 seconds. The individual processes are known as denaturation, annealing and extension, respectively.
Depending on what the scientists are aiming for, anywhere from 28-42 cycles can be done.
“What they’re doing is they are mimicking what’s done in your body in a tube, so they’re adding chemicals that will allow the DNA to be copied in a mechanism that’s similar to what’s occurring within your own body,” Dr. McMahon said.
The mission
Since 1991, the registry has been working to analyze DNA. It has been in its current location in Dover for three years, after moving from Rockville, Maryland, due to base realignment.
Although Dr. McMahon is responsible for overseeing the day-to-day operations of the lab, he’s not a member of the military. The DNA Registry has about 132 outside contractors and five military personnel who handle the three missions the lab is tasked with: present-day, database and past accounting.
Those in the present-day section work on identifying remains of men and women killed in the wars in Afghanistan and Iraq, as well as in natural disasters, training accidents and airline crashes.
The database division focuses on keeping the instruments working smoothly and overseeing the long list of potential family members.
The past division, the DNA Registry’s largest, is dedicated to older remains. On occasion, its scientists have looked at DNA that dates back more than a century, such as when they helped identify two Confederate soldiers who died when their submarine, the Hunley, sank during the Civil War.
Technicians assist analysts in the processing, a practice Dr. McMahon compares to an “assembly line.”
While the lab helps in making possible identifications, another component of the Department of Defense actually makes the decision. That’s the responsibility of the Defense Prisoner of War/Missing in Action Accounting Agency (DPAA). Located in Hawaii, the DPAA’s medical examiner makes the final call.
A quick look at the DPAA’s website shows three military members have been identified this month: one from Vietnam, one from Korea and one from World War II.
The DNA Registry officially supports the DPAA, with both agencies falling under the Department of Defense.
The registry is part of the larger Armed Forces Medical Examiner System, which also consists of the Office of the Armed Forces Medical Examiner and the Division of Forensic Toxicology.
The DPAA sets the priorities for the lab, determining what remains are examined and when.
Though some may wonder why remains of men and women killed half a century ago have yet to be identified, the process of DNA testing is still relatively new. It began around 1988, according to Dr. McMahon, and the Department of Defense registry is only 24 years old.
Excavations are also still ongoing. The DPAA recently conducted a recovery effort for remains from eight members of the Army who died in a plane crash in the Himalayan Mountains 71 years ago. Excavators spent 35 days on the mountain, unearthing bones more than 10,000 feet up on the mountain.
Identifying different types
Since 1992, the Department of Defense has been gathering DNA from living family members of military personnel whose remains have not yet been labeled.
The procedure for collecting DNA from a living, breathing human is a good deal simpler than extracting it from bones. In fact, just a simple cheek swab will do.
Once added to the database, the specimens are stored at the lab in a controlled environment. In total, more than 20,000 samples are kept there.
It’s that DNA from family members that allows matches to be made.
After the extraction and replication, technicians can search for a comparison. In that step, they have three different procedures they can use: Y-STR, mitochondrial and autosomal.
Y-STR looks at Y chromosomes, which are present only in males.
“In order to be male you’ll have one X chromosome and one Y chromosome,” said Suzanne Shunn, a DNA analyst. “In female you’ll have two Xs.”
In other words, every man has the same Y chromosome as his father, who has the same Y chromosome as his father, and so on. The STR refers to a type of DNA.
Mitochondrial DNA, in contrast, is passed down through females.
“Your autosomal DNA is the DNA usually when people say DNA that that’s what they’re thinking of, in the nucleus of your cell, where you get half of it from your mom and half of it from your dad,” Ms. Shunn said.
The most helpful comparison for identification is direct relatives, or nuclear family: siblings, parents or children. Because of direct descent, DNA from a parent or child is the best to use for analysis.
All three methods are used to provide for more potential details, especially when only DNA from distant relatives is available.
The same set of DNA is assigned to two different lab workers.
To eliminate potential biases, the DNA submitted is part of a blind examination: Scientists know where the sample came from but virtually nothing more about it.
If both bits of DNA are matched to the same deceased servicemember, the information can be submitted to the DPAA for judgment.
“So we write ‘believed to be’ reports, “Ms. Shunn said. “Since we’re not the ones identifying, we say that it’s believed to be this individual, and in that report we will show the sequence that we got from the bone or tooth sample.
“And then, also the sequences of the references that it was compared to and also the statistical analysis that says how strong the comparison is.
“And those statistical analysis, the more information we have, the better the statistics are. So if we just have mito, it’s not as strong. If we have mito and Y, it gets better. And if we have autosomals, where we can compare to a close relative like a brother or a daughter or son, then the statistics usually get even stronger.”
In the event two samples do not match up, others will be examined until two sets match with a reference.
Dr. McMahon emphasized the DNA Registry’s task is different from criminal laboratories, which are tasked with identifying a suspect out of millions or even billions of people. Scientists working at the base deal with “closed populations,” making the process simpler.
Citing the example of a downed military plane with 10 crew members aboard, he said scientists can compare mitochondrial DNA and sometimes match references and DNA through process of elimination. While autosomal DNA is more definitive, it is not always needed due to the smaller group of potential individuals the lab is seeking to identify.
“We always tell the families that even if it’s not their loved one that we’re comparing to, that their DNA is really helpful to exclude, that most of the time what we’re doing is excluding everybody else that we know it can’t be those people,” Ms. Shunn said.
Challenges and advances
Some DNA extraction and analysis can more difficult, depending on how well the remains were preserved. Bones left exposed to the elements for decades can be hard to extract DNA from, as can bodies embalmed under certain older techniques.
Fortunately for all involved, the lab is on the cutting edge of new methods, constantly working to innovate and stay ahead of ever-changing technology and practices. What’s revolutionary today will be obsolete within a few years.
“Toward that end, in the first part of 2016, we will be the first forensic lab in the United States utilizing a next-generation sequencing method, and that method was developed in-house to attack very, very degraded samples,” Dr. McMahon said.
To help stay ahead of the curve, a support section consisting of six scientists works to develop new technology.
In one of the registry’s current projects, scientists are working to identify hundreds of service members killed during the attack on Pearl Harbor in December 1941.
The USS Oklahoma was sunk during the battle, killing 429 crew members and Marines onboard the ship.
In June, the Department of Defense began disinterring graves in an effort to identify the 388 service members from the Oklahoma who had never been labeled.
Ms. Shunn is responsible for collecting the results. So far, the lab has received about 1,300 separate bones.
“The individuals have been comingled, so it’s not like one grave is one person,” she said, explaining the fragmented nature of the remains makes the overall process much more complex.
While the registry handles about 350 samples at any one time, there’s not a backlog like the kind sometimes seen in criminal labs.
Dr. McMahon credits that to the teamwork both between the lab and other Department of Defense agencies and between scientists within the mission.
“I know for a fact that if we report out no results, I can say that there’s no lab in the world that will get a result from that sample,” he said.