NEW YORK (GenomeWeb) – Thermo Fisher Scientific has launched next-generation sequencing-based panels for forensics that it said will complement its PCR and capillary electrophoresis forensics products.
The company launched five targeted panels that are based on the Ion AmpliSeq chemistry and designed to run on either the S5 or S5XL system, utilizing the Ion Chef for library prep, and has designated the entire system Precision ID.
The Precision ID GlobalFiler NGS STR panel analyzes 33 loci, including the FBI's 13 Combined DNA Index System (CODIS) loci. The company has also launched two mitochondrial DNA panels — one comprising the entire mitochondrial genome, the other a targeted panel. In addition, it offers a panel comprised of 124 SNPs that can be used to distinguish individuals with similar STRs or to disentangle mixed samples, and an ancestry panel made up of 165 SNPs with relevant biogeographical ancestry information.
Sheri Olson, Thermo's product manager for case work products, told GenomeWeb that the company is now looking to validate its panels through the Scientific Working Group on DNA Analysis Methods (SWGDAM), a group of around 50 scientists that represent federal, state, and local forensic DNA laboratories in the US and Canada.
Thermo already has a big presence in the traditional PCR and CE sequencing-based forensics market with its GlobalFiler and AmpFLSTR products, many of which the FBI has approved for use by laboratories generating DNA profiles for the US National DNA Index System (NDIS) CODIS database. In addition, it also markets a product to analyze short tandem repeats on the Y chromosome for paternity testing, analyzing samples from sexual assault, and identifying missing persons, among other uses.
Olson said she did not expect the newer NGS products to replace the firm's PCR- and CE-based forensic assays, but rather to complement them. The NGS panels will "specifically target applications that need more information per sample," she said. Many samples are challenging to analyze with PCR and CE due to degradation, insufficient quantity, or contamination, she said, and an NGS panel "lets scientists interrogate samples deeper."
In addition, she said, because the profiles in the CODIS database are all based on STR fragment analysis, it will be quite a while before there is widespread transition to NGS techniques.
One reason the company decided to develop a GlobalFiler NGS panel was to serve as a complement to the GlobalFIler PCR products. The NGS version contains the same primers as the CE product, she said, but also includes "additional information to get a deeper level of mixture interpretation."
Daniele Podini, an associate professor in the department of forensic sciences at George Washington University who has tested the panels, agreed that the data is concordant with conventional methods, but also goes beyond those. "It's very promising," he said. "You're able to obtain a lot more data with the same amount of DNA" and are better able to "deconvolute complex DNA mixtures because of the greater information that you can get."
Conventional DNA forensics for human identification analyzes the fragment sizes of STRs, but NGS-based forensics lets one analyze both the fragment size and also the sequence information, Podini said.
"All the concordance studies we've performed demonstrate that you're getting the same result but with greater resolution," he said.
He noted that he is using the panels for research purposes and not in criminal casework, and that before the Precision ID panels or other NGS-based forensics panels could be used for that purpose, they would need to be validated.
Jack Ballantyne, a professor at the University of Central Florida and associate director of the National Center for Forensic Science, agreed that NGS-based forensics would not immediately replace traditional forensic methods, but over time, he said, forensics would slowly evolve to include NGS. "NGS will revolutionize forensic biology by enabling us to get more information from a single source and mixed samples," he said. "Even today, for certain specialized cases, we can start using it," he said, for instance in samples that are too degraded or mixed to analyze with conventional methods.
He anticipates NGS and CE methods being run in parallel initially, before the NGS methods take over.
Ballantyne has also tested the Precision ID panels and previously tested AmpliSeq panels on the PGM. The main advance, he said, has been the automation. Previously, running an AmpliSeq panel on the PGM was a very lengthy process, requiring nearly an entire day of hands-on time. Incorporating the Ion Chef automates the library prep process and the S5 automates the sequencing, so now there is only about 15 minutes or so of hands-on time, he said.
Illumina launched its own forensic-focused system last year, with SWGDAM validation, which it has dubbed the MiSeq FGx.
Ballantyne has also used that system and said that both work well and produce good results, but he is predominantly using the Precision ID panels on the S5 due to the automation.
In addition, he said, he likes the software component of the Precision ID system because it enables him to easily compare results with those from Thermo's PCR/CE products. Thermo's Converge Forensic Analysis software package was originally designed for its PCR/CE products, and the company is now working on an NGS module for Converge. In the meantime, the company has developed plug-ins for SNP, STR, and mtDNA analysis using the Ion Torrent Suite software.
The tools are set up along with the sequencing run and they let customers view results for all markers in a sample and perform comparisons, as well as export results, according to the company.
Olson said the first application for the Precision ID panels will likely be investigative leads or missing person cases, since those types of applications would not involve the use of the panels in a courtroom and would not provide evidence used as the basis for a conviction.
Podini added that NGS methods could also be used for identifying remains found in mass graves or at the site of a plane crash — where there would be DNA from many samples and it would likely be very degraded, making it difficult to analyze via traditional CE methods.
Ballantyne said that his group is also working with Thermo to develop an RNA-based forensic panel. Such a panel could be used in cases of sexual assault, for instance, where RNA analysis could provide additional information, such as the tissue of origin of the DNA.