AFDIL gets the SNP: A New Era in DNA Technology

Story by Staff Sgt. Deven Schultz

Armed Forces Medical Examiner System

DOVER AIR FORCE BASE, Del. – As if being a world leader in understanding and utilizing DNA wasn’t a high-enough achievement, the Department of Defense (DoD) DNA Operations division within the Armed Forces Medical Examiner System (AFMES) has set the bar to a whole new level.

For the record, as someone who graduated High School and didn’t think twice about ever attending college, I have a deep appreciation for those who have committed themselves to earning a degree, or four, and used it for the betterment of our world. The specially trained scientists within the Armed Forces DNA Identification Laboratory (AFDIL) perform what some would call miracles, on a daily basis.

“The DNA our staff work with is typically heavily broken down from years of exposure to the outside world and preservation techniques used in years past,” says Dr. Tim McMahon, Director, DoD DNA Operations. “Traditional methods of identifying remains via DNA just don’t work for what we need. It is typically described as worse than 40,000-year-old neanderthal DNA.”

Instead of throwing in the towel, and giving up, the staff at AFDIL have developed and used several different methods to assist in the identification of unknown service members from past conflicts. That’s where the AFDIL Emerging Technologies (ETS) team comes into play.

“In ETS, we utilize scientists from the many different sections of AFDIL to analyze the processes we currently use and find better, more efficient ways to accomplish them,” explains Courtney Cavagnino, Research Scientist, ETS. “It is our goal to incorporate scientists from the applicable sections into validations to assist with completing lab work and sample analyses. Ultimately, this also serves to ease the transition of a new method into casework.”

For a bit of context, Single Nucleotide Polymorphism (SNP) capture is the newest development – one that is poised to change the game forever. SNP capture builds upon the mitochondrial genome (mtG) Next-Generation Sequencing (NGS) and hybridization capture methods validated in 2016. In 2015, knowing that traditional nuclear short tandem repeat methods would not work on samples requiring mtG NGS methods, AFDIL worked with the DoD Small Business Innovation Research program and Defense Rapid Innovation group, and submitted a public proposal.

The proposal was to develop a large SNP panel and the analytical software for nuclear DNA testing of highly degraded or chemically treated samples. Parabon NanoLabs was competitively selected and awarded the contract. Over the next six years, Parabon, working with AFDIL, created the Parabon Fx analytical software package, providing a way to develop the SNP capture and kinship analysis workflow. The SNP capture methods use nuclear DNA markers that allow for extended kinship prediction with DNA from a family reference sample (FRS) donor whose DNA samples are stored at the AFDIL.

The validation, led by ETS, kicked off in 2022 with a team of seven analysts from the Past Accounting Section. Their time was dedicated to completing the necessary lab work and analyses to meet the validation requirements. Additional contributions were made by the Family Reference Sample – Laboratory Automation section, who prepared the reference samples and the casework administration and evidence manager who anonymized these samples. Following years of hard work, and overcoming unforeseen challenges, the validation summary was signed off in December of 2024.

“We needed to account for variability across different relationships and geographic ancestries. This required finding and testing many samples that also represented the range we encounter in our casework,” says Jacqueline Tyler Thomas, Research Associate, ETS. “When laboratory processing did not work as anticipated, troubleshooting experiments were needed to figure out why. When DNA analysis results were unexpected, we dug into the complexities of the analysis software to find the cause and tested updates.”

The SNP capture and extended kinship prediction methods were validated according to forensic accreditation standards for DNA identification, with statistical support that is incredibly stronger than any current crime laboratory DNA tests can provide.

“Our SNP capture and extended kinship methods result in a DNA statistic that is required for the medical examiner to identify the remains of one of our fallen military heroes,” describes Dr. Charla Marshall, Deputy Director of DNA Operations. “What we are doing is different from forensic investigative genetic genealogy (FIGG) that is often talked about in the news. FIGG can provide an investigative lead to a distant relative of an unknown. But FIGG can’t provide a statistically supported SNP identification like we can using our internal family reference DNA database.”

According to Megan Poffenberger, Supervisory DNA Analyst, Past Accounting Section, “The SNP capture process can be accomplished in as little as two weeks from extraction to data analysis. Data for the first four sets of bone samples were reported at the end of January and FRS data are now being utilized for kinship prediction.”

“Overall, it took us a decade and a dozen staff to finally get to this point and it feels amazing to finally put it to use,” proudly exclaims Dr. Kim Andreaggi, Chief, ETS. “We’re so incredibly thankful for the countless hours that were directly and indirectly contributed to this project by our team, we couldn’t have done it without them.”

At the end of the day, time is of the essence as families wait for answers. By bringing this new SNP capture method online, AFDIL can support expeditious DNA identifications using our existing FRS DNA database. This will enable the Defense POW/MIA Accounting Agency to consistently reach its goal of 200 identifications per year.

“When people think of DoD DNA Operations, they probably see countless lab benches and expensive robots performing tasks on a daily basis,” says Dr. McMahon. “What they don’t see are the creative and gifted minds of the staff using them. As I like to say, ‘these young heroes come here to AFMES a number and leave with a name’, and the process of giving them that name back is only going to get better as long as DoD DNA Operations and its staff continue pursuing this mission while remaining a global leader in forensic DNA analysis.”