DNA Sequencing Technology Identifies Fallen Soldier and Colleague’s Great Uncle

By Christina P. Hooton

Harold Francis Carney, U.S. Navy machinist’s mate 1st class, was among the 429 sailors and marines that perished aboard the USS Oklahoma moored at Ford Island, Pearl Harbor, on that fateful day in December eight decades ago that catapulted the U.S. into World War II. In the years that followed, his remains and those of hundreds of others were determined to be unidentifiable and buried in the National Memorial Cemetery of the Pacific (NMCP), also known as the Punchbowl, in Honolulu, Hawaii. In 2015, many of these remains, including Carney’s, were exhumed by the Defense POW/MIA Accounting Agency (DPAA) and, thanks to advances in science, successfully identified.

Finding a DNA Match

The U.S. Navy first contacted Steve Becker, Carney’s great-nephew, over the summer to find the fallen seaman’s oldest living relative as a DNA reference. “That turned out to be my mom,” said Becker, senior director of Licensing and Commercial Supply for Genetic Sciences and Clinical Next-Generation Sequencing at Thermo Fisher Scientific. His team works with equipment manufacturers and assay developers to integrate Thermo Fisher technologies into their products, which are then used to diagnose a variety of conditions such as cancer, cardiovascular disease, and COVID-19. Indeed, one of their customer’s products was the first used to sequence the SARS-CoV-2 virus in Wuhan.

A trained biologist himself who was keen to learn more about the process of identifying his great uncle Harold, Becker started reading through the official U.S. Navy medical report. He recognized some of the products mentioned and contacted Martin Guillet, vice president and general manager of Human Identification, Thermo Fisher Scientific, to confirm his suspicion. Testing was performed on his great uncle Harold’s remains using various technologies, including the Applied Biosystems™ AmpFLSTR™ MiniFiler™ and Yfiler™ PCR Amplification Kits identified by name, both products of Thermo Fisher Scientific.

Identifying Our Fallen Heroes

Identifying the remains of fallen soldiers is the primary objective of the Armed Forces DNA Identification Laboratory (AFDIL), a division of the Armed Forces Medical Examiner System founded in 1991. Their work encompasses modern conflicts, such as Afghanistan and Iraq, and past wars dating as far back as World War I. Today, both active service members and their family members provide DNA samples in the event that someone goes missing in action.

Identifying service members from past conflicts is much more of a puzzle. Remains exhumed from the Punchbowl had been buried for close to 80 years and were exposed to heat, humidity, and harsh chemicals, elements that lead to challenging DNA analyses.

“These are some of the most challenging forensic samples that exist, short of ancient DNA samples that are used to understand human lineages and migration patterns,” said Matt Gabriel, former AFDIL scientist and senior business manager for Thermo Fisher Scientific. “You have to look at smaller and smaller DNA pieces and try to stitch together the DNA sequence to lead to an identification.”

During his time at AFDIL, Gabriel helped develop a DNA amplification strategy for analyzing the small pieces of DNA extracted from such challenging samples.

Both autosomal short tandem repeat (STR) testing and Y chromosomal STR testing are often used. Still, mitochondrial DNA (mtDNA) testing is AFDIL’s preferred analysis method for identifying missing service members because of the DNA’s maternal inheritance and high copy number per cell. This process starts with extracting the total genomic DNA from the remains and amplifying the mtDNA molecule from that sample. First-generation or Sanger sequencing can then be performed using Applied Biosystems™ BigDyeTM Terminator Cycle Sequencing Kits and Applied Biosystems™ 3500 Series Genetic Analyzers for capillary electrophoresis.

More recently, AFDIL has implemented next-generation sequencing (NGS) and probe capture hybridization methods to analyze the most challenging of AFDIL’s casework samples recovered from past military conflicts. Hybridization capture methods attach DNA or RNA probes with sequences of interest to magnetic beads or a microarray and wash away unwanted DNA. NGS techniques can then be used to process many of these enriched samples to lead to a consensus DNA sequence for the sample.

In Carney’s case, scientists successfully used mtDNA analysis, confirming his specific mtDNA base sequence and comparing it with the DNA of his oldest-living maternal relative, his niece, and Becker’s mother, Patricia Joyce.

“They did a tremendous amount of work to lead to that identification,” said Gabriel. “It’s really a testament to the federal government and all of the scientists who work at AFDIL and CILHI (Central Identification Lab, Hawaii) to be able to do this regularly, year over year. They just keep pushing through and try to bring closure to every family member that has lost a service member.”

According to the DPAA, there are currently over 81,000 missing soldiers from past conflicts.

Honoring Great Uncle Harold

Carney volunteered for the U.S. Navy before the draft at 23 years old during a turbulent time in history. While on leave for Thanksgiving, he stopped to visit his sister in Kansas City and gave his niece, Joyce, a red tricycle before returning to Hawaii in early December 1941.

On November 6, 2021, his remains finally returned home to Benton, Wisconsin, a town with a population of just over 800. In addition to his family members, active-duty honor guards, local veterans groups, and more than 100 members of the community were there to welcome him home with hands on their hearts. American flags lined the streets. He received full military funeral honors and was laid to rest alongside his parents and brother John Carney, who was also stationed in Pearl Harbor and died shortly after returning home from war in an electrical accident.

Joyce spoke on behalf of her uncle’s family, expressing her pride in the Navy and the entire military for showing up in force, remarking that patriotism is alive and well in America.

“The fact that they would go to these lengths to honor a fallen soldier like this today was truly impressive and heartwarming for our family,” said Becker. “I want to thank all of those at Thermo Fisher who served,” he said, recognizing the legacy they share with his great uncle Harold.

Rear Admiral Terry W. Eddinger, CHC, USN, deputy chief of chaplains for Reserve Matters, who traveled from North Carolina to serve as flag officer for the ceremony, said, “It’s quite an honor to do this. We ought to welcome these people home. They left 80 years ago, and to me, it’s about bringing them home and reuniting them with their families. They deserve to be honored and paid respect for their sacrifice.”

December 7, 2021, marks the 80th anniversary of the Pearl Harbor attack and, just in time, a fallen soldier has returned home — thanks to cutting-edge science, and with the thanks of a grateful nation.