Digital Detection; ECBC Researchers Explore Pathogen Detection through Open Source Website
CCDC Chemical Biological Center Public Affairs | July 7th, 2016
Edgewood Chemical Biological Center (ECBC) researchers have developed a means for DoD labs across the globe to quickly obtain a genomic analysis of unknown biological samples.
A team of researchers at ECBC have developed a means for Department of Defense (DoD) 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 stateside lab.
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, and ECBC has partnered with the United States Army Medical Research Institute for Infectious Diseases (USAMRIID) and Walter Reed Army Institute of Research (WRAIR) to make genomic analysis more accessible through the development of a website called Pathosphere.org.
Currently, if samples of suspected biological weapons material cannot be matched to known biological agents, the United States and partner nations may consider using genomics to characterize the suspected samples. Unfortunately, the pathogen experts who perform this work are located 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. Pathosphere has been deployed as a freely available resource and is used in OCONUS 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. ECBC, USAMRIID, and WRAIR along with Columbia University put its resources into creating a collaborative 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,” said Andy Kilianski, Ph.D. one of the collaborators on the project. “We are bringing that infrastructure to anyone who wants to do remote data analysis. And now we’ve made it publically available.
How it Works
Pathosphere takes the best-of-breed analysis from ECBC, USAMRIID, and WRAIR and makes these tools available to the global DoD labs via the internet. The DoD lab will upload the data sequence of an unknown biological sample to Pathosphere.org website (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 has the ability to put together an accurate report of what the pathogen is, and that report is emailed directly back to the user.
Putting the Pathosphere to Practice
Pathosphere.org is more than just a good idea – it works. ECBC demonstrated this by creating spiked pathogens within a common sample, and sequenced them with three different sequencing platforms, and then submitted these datasets to Pathosphere website to determine if the site could correctly identify the pathogens present. The results generated by Pathosphere matched the results scientists produced on-site, demonstrating that Pathosphere 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.
Pathosphere.org is already supporting a number of critical projects, and ECBC scientists would like to continue to increase the abilities of the Pathosphere. The ECBC team published their findings from their work thus far in BMC Bioinformatics. Since publication, there has been a spike in new Pathosphere.org users, including scientists within the Department of Defense and outside users from partner nations like Israel and other countries.