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Battelle, Forensic Labs to Put NGS Technology through Its Paces for Human Identification

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NEW YORK (GenomeWeb) – With $825,000 in grant funding from the National Institute of Justice, researchers at Battelle Memorial Institute, in collaboration with seven forensic laboratories across the US, are embarking on a 19-month feasibility and validation study of next-generation sequencing technology for forensic applications.

The goal of the project funded under the grant, which Battelle announced last week, is "to objectively guide the use and eventual adoption of next-generation sequencing in the broader DNA forensics community," according to the abstract.

Over the last 25 years or so, forensic DNA analysis has become a widespread and well-accepted tool for law enforcement and the criminal justice system, but the technology used – short tandem repeat typing by capillary electrophoresis – has not changed much, according to Richard Guerrieri, who is the research leader for applied genomics at Battelle.

"The introduction of next-generation sequencing really changes the game," Guerrieri told In Sequence. "It addresses the limitations of this legacy system while expanding the level of information that can be gained investigatively."

But up until now, NGS technology has only been adopted by a few forensic laboratories for certain applications and "has not been used to anywhere near the level of the current capillary electrophoresis," which measures DNA fragment size, he said.

Importantly, NGS is backward compatible with CE-based STR profiles, meaning that NGS sequence data generated for STRs can be used to search against STR profile databases, such as the FBI's National DNA Index System, NDIS, which is part of the Combined DNA Index System, CODIS, and contains more than 13 million DNA profiles.

However, in addition to fragment length information, NGS also delivers sequence information for the STRs, "which adds a whole additional element of discrimination," Guerrieri said.

Next-gen sequencing can also generate SNP marker sets from other loci, in chromosomal as well as mitochondrial DNA, providing additional information about gender, physical appearance, ancestry, and family relationships.

Another possible advantage of NGS is its ability to discern DNA from several individuals in the same sample, which cannot be done with current tools.

Finally, because it can glean information from smaller DNA regions than STR analysis, NGS might be better suited for analyzing DNA from degraded samples, such as decomposed bodies or skeletal remains, which are common in missing person cases.

But, like any new technology to be used in forensics, NGS will have to go through "a battery of quality assurance testing to show that it's reliable, reproducible, and has the merits for sensitivity of detection, among other validation criteria," Guerrieri said. "We will begin to assess those points and hopefully lay a strategic roadmap that forensic labs will be able to follow."

Besides Battelle, the study, which will commence in January, will involve the Armed Forces DNA Identification laboratory at the Dover Air Force Base in Delaware as well as labs at the Bureau of Alcohol, Tobacco, Firearms, and Explosives in Washington, DC; the California Department of Justice in Sacramento; the Harris County Institute of Forensic Sciences in Houston; the National Institute of Standards and Technology in Gaithersburg, Md.; Pennsylvania State University; and the Philadelphia Police Department.

During the first phase of the study, the researchers will define key requirements and performance evaluation criteria for NGS systems and test commercially available amplification kits, sequencing platforms, and bioinformatics software tools.

They will sequence standard reference material DNA samples that have been previously characterized; actual forensic samples will not be part of the study.

The samples will be analyzed on several NGS platforms, such as the Illumina MiSeq Forensic Genomics, or FGx, an adaption of the MiSeq for forensic use that Illumina announced earlier this year but has not yet launched, and Thermo Fisher Scientific's Ion PGM.

The study will also test commercially available STR, SNP, Y-STR, and mitochondrial DNA reagent kits and will analyze the data using Battelle's proprietary bioinformatics software, including its recently released ExactID software for NGS data, as well as NGS platform-specific software.

Guerrieri said the list of sequencing platforms to be tested has not yet been finalized. While the goal is to establish their performance, the study is not intended to be a bake-off between different products.

The second phase of the project, directed by Battelle, will test NGS technology in a series of studies across the different laboratories. The goal is to demonstrate whether the same answer can be obtained by multiple labs; to establish the sensitivity of the technology with decreasing amounts of DNA; to see whether the groups can detect and discern mixtures of DNA in different ratios; and to show how reproducibly the same sample can be analyzed several times.

Results of the studies are expected by July 2016 and will be presented at conferences, published in peer-reviewed journals, and be used as part of training forums and webinars for forensic practitioners, Guerrieri said.

But even after the completion of the evaluation and validation studies, it might still be some time before NGS will overtake CE technology completely for forensic applications.

"There are still strategic decisions that will have to be made with regard to how to phase a technology, and I would fully expect that there will be a co-existence of next-generation sequencing with current technology for several years," he said. "I don't see this as any replacement in the near future at all."

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