Advertisement
A photo inside Battelle laboratories. Battelle presented its findings on the use of next-generation DNA sequencing at the International Symposium for Human Identification last week. (Photo: Courtesy of Battelle)

The future of DNA analysis is next-generation sequencing, also known as massively parallel sequencing. The technology literally adds another dimension by analyzing the fundamental building block of life at a deeper level than ever before—a big-data dive to depths of single alleles.

Battelle and its scientists unveiled the results of the first wide forensic science trials of “NGS” last week at the International Symposium for Human Identification.

Their verdict for the ISHI crowd: the technology proved itself to be reproducible, accurate, and incredibly sensitive. It will be in standard use in the future—and will provide an unprecedented level of detail to solve the most challenging forensic mysteries, they conclude.

“With the sequencing, you’re able to detect additional alleles that you couldn’t see through conventional typing,” said Richard Guerrieri, a research leader of applied genomics at Battelle, who presented the work.

But it’s a matter of time and evolution before it becomes adopted in crime labs nationwide, Guerrieri told Forensic Magazine this week. It remains too expensive and time-consuming to effectively replace all the traditional (and already rigorous) DNA analysis out there currently, said Guerrieri.

NGS allows millions of DNA fragments from even minute samples to be strung together at the same time, instead of the one-at-a-time methods of the past, which are still the established standard in crime labs internationally.

The Battelle tests, the most stringent trials of the technology yet, were helmed by the company at their Columbus, Ohio facility, and included eight more institutions: the Armed Forces DNA Identification Laboratory, which also has next-gen capabilities already online; the FBI Laboratory and the California Department of Justice, both of which are currently in the process of validating their own systems; and other laboratories including the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives, the Harris County Institute of Forensic Sciences in Texas, the National Institute of Standards and Technology, the New York Office of the Chief Medical Examiner, and North Carolina State University.

A scientist working in a Battelle lab. Battelle presented its findings on the use of next-generation DNA sequencing at the International Symposium for Human Identification last week. (Photo: Courtesy of Battelle)

They tested the viability of next-gen technology on routine and challenging samples alike, as compared with the STR-based traditional technologies that are currently in use in most laboratories. Different workflows involved ForenSeq by Illumina, ThermoFisher Scientific’s IonTorrent, and a combination of Promega, Illumina and Battelle tools.

The samples involved standard swabs of DNA, blood samples from the aftermath of explosions, two-person mixtures from degraded sources, swabs from fingerprints on electrical tape and even skeletal remains from World War II and the Korean War, among other kinds of samples.

All the laboratories and the different workflows were consistent and accurate, and there were no incorrect detections of DNA down to the level of single alleles. There was more information than ever before, as well. For instance, the Korean War humerus bone yielded seven loci to conventional STR typing—but the NGS determined at least 21 markers, plus other distinct characteristics, including Y-STRs and SNPs.

“The study was to try to assess the technical readiness of this technology—we put it through the hoops, through all of these different validation studies, and the technology was solid in all those areas,” said Guerrieri. “It meets the rigors of what a forensic lab would put it through, to show it’s valid and reliable.”

The formal results will be published in forensic journals in the near future, Guerrieri said.

The level of detail means selected, special cases—like those old bones from wars decades earlier—could be cracked by markers that weren’t even detectable before, Guerrieri explained.

“It has great power for dealing with unidentified human remains, decomposed samples that are very challenging—something maybe from a mass disaster,” Guerrieri said.

But the limitations currently would prevent it from being the sole DNA method at a busy crime laboratory, he added. For instance, DNA cases needing a profile as quickly as possible could be done overnight, getting 20 CODIS markers in six to eight hours. By comparison, the NGS systems produce 10 times the data—200 markers—but it takes at least 24 hours to get all that information together.

That data set is also so large, it will require some special storage space. From lab to lab, that will depend on cloud storage, or bigger servers than ever before, he added.

The kits are already also much more expensive than the standard kits used in standard applications, he added.

But AFDIL and Battelle are already doing work with the NGS tools, and making breakthroughs in cases, Guerrieri said. The Ohio Bureau of Criminal Investigation, which had been working cooperatively with Battelle, has plans to be completely online with NGS by March. (The validation work at the state crime laboratory was accepted for publication by the journal Forensic Science International this week, Gerrieri reported).  The FBI and California DOJ area also working toward getting their NGS tools operational.

“Everyone’s looking for how they’re going to apply it—what kind of cases,” he said.

A lab worker swabs a mobile device at Battelle labs. Battelle presented its findings on the use of next-generation DNA sequencing at the International Symposium for Human Identification last week. (Photo: Courtesy of Battelle)

Sensitivity is not an issue—the cost will come down, and the technology will gradually be added to forensic laboratories across the U.S., Guerrieri predicted. The technology will gradually be added to STR identification—but won’t immediately replace the traditional typing methods, he added.

“The hurdles are already being overcome,” he said. “It’s all coming together.”

Farther down the road is the use of the NGS system for phenotyping, the use of the genetic markers to predict appearance, race, and other traits. Such technology (through SNPs) is currently being used for investigative leads by some agencies.

NGS capacity at the national level could be coming soon. Just days before ISHI, the FBI was presented with a submission to incorporate NGS sequencing into the NDIS and CODIS databases.

The Battelle report seemed to be widely accepted by the forensic community. Matt Gabriel, a product manager of human identification at Thermo Fisher Scientific, told Forensic Magazine by email that the analysis indicates how promising the NGS upside is.

"As a community, we are only scratching the surface of what NGS can offer forensic laboratories," Gabriel said. "NGS in forensics will continue to evolve over the next few years before the widespread adoption occurs.

"Battelle did a fine job coordinating experimental testing across multiple sites and vender platforms in their study," Gabriel added.

Advertisement
Advertisement