Researchers at the U.S. Army Edgewood Chemical Biological Center have developed a means for Department of Defense labs across the globe to quickly obtain a genomic analysis of unknown and potentially hazardous biological samples without incurring the cost and risk of shipping them to a robust lab in the United States.
Genomics is an area within genetics that concerns the sequencing and analysis of the complete set of DNA within a single cell of an organism, said Dr. Andy Kilianski, who worked on the project. ECBC has partnered with the U.S. Army Medical Research Institute for Infectious Diseases and Walter Reed Army Institute of Research to make genomic analysis more accessible by developing a website, pathosphere.org.
Currently, if samples of suspected biological weapons material cannot be matched to known biological agents, the United States and partner nations may use genomics to characterize the suspected samples, Kilianski said. However, the pathogen experts who perform this work are at laboratories such as ECBC, USAMRIID or WRAIR.
Those samples would be collected at the overseas location and sequenced in the United States. The shipment of the sample to the experts and the subsequent analysis require time, money, significant subject matter expert labor hours and the use of on-site hardware and technical support.
The development of Pathosphere removes the need for shipment and on-site analytical support, while still providing customized analysis on genomic datasets, he said. Pathosphere has been deployed as a freely available resource and is used in overseas DoD labs.
ECBC began developing the concept behind Pathosphere in 2009. The idea was expanded by partnering with USAMRIID and WRAIR in response to requests from organizations such as the Defense Threat Reduction Agency Joint Science and Technology Office and the Joint Program Executive Office for Chemical and Biological Defense to find ways to streamline and cut the cost, Kilianski said. ECBC, USAMRIID and WRAIR, along with Columbia University, created a capability that is uniformly available.
“Pathogen detection within complex samples is a computationally expensive process, and doing it on-site requires servers, IT support and software engineers,” Kilianski said. “We are bringing that infrastructure to anyone who wants to do remote data analysis. And now we’ve made it publicly available.”
Pathosphere takes the best-of-breed analysis from ECBC, USAMRIID and WRAIR and makes these tools available to the global DoD labs through the internet. The DoD lab will upload the data sequence of an unknown biological sample to pathosphere.org, which also supports interrupted uploads from data austere environments. The person uploading the data has full control over who sees the sequencing data and results. After analysis time that ranges from a few minutes to a few hours, pathosphere.org is able to put together an accurate report of what the pathogen is, and that report is emailed to the user.
ECBC demonstrated the website by creating spiked pathogens within a common sample and sequenced them with three different sequencing platforms, Kilianski said. The center then submitted these datasets to the website to determine whether the site could correctly identify the pathogens present. The results generated by pathosphere.org matched the results scientists produced on-site to demonstrate the website has the similar capabilities to the currently deployed local NGS analysis tools.
Pathosphere.org also serves as an online community for innovation where scientists can share information and findings with each other. Occasionally, an uploaded sample will require that a subject matter expert is required for further analysis. In these instances pathospere.org can be used to elicit support from the online community fostering collaboration among colleagues across the globe.