NEW YORK (GenomeWeb) – Battelle has released software called ExactID that it claims is the first commercially available product to provide forensics laboratories with the exploratory capabilities that they will need to analyze next-generation sequence data when the technology becomes the normative tool for extracting information from biological clues in criminal investigations.
ExactID was developed by researchers in an applied genomics group that is part of Battelle's national security division, one of four areas in which the non-profit research and development organization operates. The software identifies the 24 standard genetic markers that law enforcement uses to match suspects to samples. But, more importantly, it can help forensic labs analyze the more detailed genetic information that next-generation sequencing instruments make available and make more precise predictions about characteristics such as physical appearance, ancestry, clinical traits, and familial relationships, Brian Young, a geneticist and technology initiatives leader at Battelle, explained to BioInform.
Young and his colleagues began working on ExactID in 2013. They believe that they have created a unique solution for the market that strikes the right balance between precision and speed. "What we've developed is a signal processor" that is "able to extract the genetic markers out of fastQ files, faster than any other alternative," the majority of which are from academia, Young said. One benchmark, he mentioned, is that the software can process a 100 megabyte fastq file in less than 30 seconds on a standard laptop.
Battelle will demonstrate the capabilities of its patented system next week at the International Symposium on Human Identification conference in Phoenix, Ariz. Following the conference, Battelle will launch a three-month beta, during which a number of pre-selected and unnamed participants will generate NGS data and use it to put the software through its paces. It is also currently negotiating a commercialization plan with an unnamed partner, Young said. Additional details are not being disclosed at present, but Battelle has said that the solution will be both affordable and accessible to law enforcement at all levels.
Separately, Battelle has received a federal grant — it's not disclosing the exact amount at this time — to work with several federal and state laboratories to explore the use of NGS as a forensic technology. Under the auspices of the grant, they will test the entire sequencing process from DNA extraction through to analysis using tools like ExactID, Young said.
The catalyst for this particular study is the recognition of "tremendous applications" for NGS in human identity and forensics, particularly as a more precise alternative to the status quo for generating genetic profiles, Young told BioInform. However, before the technology can be accepted by the larger investigative community and moved into routine use, it needs to be vetted and tested, Young said, and "we are right at the beginning of that process for adaptation within the industry."
Currently, forensics labs rely on the well-established capillary electrophoresis methodology to build genetic profiles from biological samples. Specifically, they use the method to analyze DNA fragments that have been amplified by polymerase chain reactions, and look for 23 polymorphic short tandem repeats (STRs). This is the gold standard for DNA profiling because the exact pattern of alleles varies from person to person, making it very unlikely that two people, with the exception of identical twins, will having the exact same profile. They also look for amelogenin, a gene which because it appears differently on the X and Y chromosomes is used to determine sex.
The ideal scenario would be to sequence the amplified DNA fragments because that would provide far more information than capillary electrophoresis can, Young said. Sequencing would make it possible to figure out not only how many repeats a given individual has but also to look at more alleles per locus and explore the differences between the alleles at the sequence level. And that’s important because it would help labs differentiate between individuals with similar profiles, he said. For example, two individuals can have identically sized alleles at a locus, say 10 repeats long, but the alleles themselves have different sequences, so having access to sequence-level information would make the identification process that much more precise, he said.
Furthermore, sequencing would make it possible to explore other genetic markers useful for investigative purposes that cannot be "exploited" by the mainstream fragment analysis technology, Young noted. That includes SNPs for "externally visible characteristics," such as hair color, eye color, skin tone, and also markers that indicate biogeographic ancestry and ethnicity, he said.
It's not clear how long it will take for the community to accept NGS as the standard for forensic testing, but when that day comes, Battelle intends to have its freshly minted software tested and in line with the apposite approval standards for use in such settings.
It also is the first commercial application to come out of the organization's efforts to use NGS-based technologies — which began in 2010 — although Battelle has developed other solutions that are owned and used by the US government.
Battelle believes that technology that underlies ExactID can be used in other contexts such as microbial analysis and medical diagnostics as well, and it intends to pursue applications for its system in those markets in future. In microbial analysis, for instance, the software could be used to analyze metagenomics samples quickly and simply, Young said. Battelle is looking at moving into that particular space as early as next year.