NEW YORK (GenomeWeb) – Parabon NanoLabs was recently awarded a two-year contract for an undisclosed amount with the US Department of Defense to develop software for forensic DNA analysis.
The software, called Keystone, will be able to coordinate data collection, storage, and analysis from a variety of different forensic analysis instruments, addressing a need for interoperability in molecular forensics.
Parabon is a DNA technology company that develops products and services for next-generation therapeutic and forensic analysis, including its Essemblix Drug Development Platform and Snapshot DNA Phenotyping Service. The company is staffed by scientists and technologists with expertise ranging from bioinformatics and chemistry to computer science and pharmacology.
"Keystone is a plugin architecture, a platform if you will, to allow for a variety of [tools] to be managed under a common software structure," Parabon CEO Steven Armentrout told GenomeWeb.
Armentrout said that the software will ultimately function a little bit like a smartphone. It will be able to support a variety of plugins, like a smartphone can support a variety of apps. "It's a fairly fundamental departure from [Windows] CE-based [software]," he added.
Bruce Budowle's lab in the Institute of Advanced Genetics (IAG) at the University of North Texas Health Science Center is a subcontractor on the project. Budowle and his lab have already developed a plugin for short tandem repeat (STR) allele identification that has been dubbed STRait Razor. The plugin detects STRs using a method similar to capillary electrophoresis, enabling a user to generate a custom locus list to sort out targets of interest.
The most recent version of the application, STRait Razor v2.0, was released in 2014 and is currently available for download on the UNTHSC website to help researchers identify STRs in raw data generated by massively parallel sequencing.
"The analytical tools developed by the forensic research community for next-generation DNA analysis are not designed to interoperate, and they require considerable expertise," Budowle said in a statement. Keystone will integrate these tools under a common software, which will streamline raw DNA data storage and analysis, he added.
One of things that Budowle will be consulting with Parabon on will be hammering out the application program interface (API). The company plans to use the API that they develop to make contracts for individual applications that would operate under Keystone, Armentrout said.
After Parabon sets up the basic Keystone infrastructure, it can develop more plugins, such as STRait Razor, to tackle different types of forensics data. For example, the company may develop an application to process raw mass spectrometry data or to pick out other genetic variations in raw next-generation sequencing data.
Armentrout said that it is reasonable to expect that the project will be completed within the two-year contract period, but it's possible that it could be sooner depending on how the development process evolves. Once Keystone is commercially available, Parabon plans to market it directly to forensics laboratories, he added.
Other Parabon projects
This project is the latest of Parabon's endeavors to tackle various niches in the genetic research market. One of its more recent projects, a DNA phenotyping service called Snapshot, received a grant from the National Geographic Society Expedition Council last year. The grant funded a blind evaluation study of the Snapshot service.
Snapshot predicts ancestry and physical appearance using a combination of data mining software and SNP analysis technology that translates select biomarkers from a DNA sample, Armentrout said.
The project was developed over a five-year period and to date it's been used very broadly within the law enforcement community. "A lot of the police forces have gone public with our composites," Armentrout said. To date it has been used across 75 law enforcement agencies in 10 countries, and has become a routine part of the business that the company provides, he added.
In addition, since the company's inception in 2008 it has invested a great deal of its research efforts in DNA nanotechnology, which has resulted in its Essemblix platform. The company uses the platform to offer molecule design services to its customers. The basic idea is to use DNA as a "construction substrate" to build custom molecules, which can be particularly useful for drug and therapy development, Armentrout said.
For example, Parabon received funding from the US DoD in 2011 to develop synthetic vaccines— created purely through chemical synthesis to avoid the risk associated with live vaccine. The first target pathogen the company is working on is Ricin, a toxin naturally found in castor beans.
"We are used to thinking of [DNA] as a beautiful helix," Armentrout said. "[But] you can get DNA to weave [itself into different shapes]" which offers interesting opportunities in therapeutics development, he added.