Since the mother of bioinformatics Margaret Oakley Dayhoff first published her comprehensive, computerized collection of protein sequences in 1965, the science has continued to evolve and enhance our understanding of biological data. The Defense Threat Reduction Agency’s Chemical and Biological Technologies Department, in conjunction with MRI Global, is furthering the science by developing rapid detection and analysis laboratory capabilities for our warfighters on the frontlines and in remote locations.
MRI Global developed a simplified, deployable sample-to-sequence workflow and associated bioinformatics tools for the unbiased detection of all human pathogens in clinical and environmental sample matrices. The workflow and tools are designed to be used by minimally trained users for remote analysis of metagenomic samples and provide high confidence detection in less than a day.
MRI Global initially conducted an evaluation of 43 discrete technologies for sample preparation through library preparation, along with sequencing optimization. They also developed and optimized a custom bioinformatics analysis pipeline that was benchmarked against 16 commercial and open-source analysis algorithms. The evaluation and subsequent optimization of the workflow reduced the time from sample-to-answer from 48 hours to less than 24 hours and standardized the workflow for clinical and environmental samples. This greatly simplifies analysis for the end-user and reduces the time from sample-to-answer for faster response time, allowing warfighters to get the results they need quickly.
One of the key strengths of the developed workflow is the Pan-Genomics for Infectious Agents (PanGIA) bioinformatics pipeline. This metagenomic data analysis software provides an unbiased analysis for human pathogen detection using a simple to use graphical user interface that is optimized for the minimally trained user (Figure 1). Results can be obtained in less than 30 minutes. PanGIA does not require an internet connection, instead runs on a portable hard drive, allowing the reference genome database to be updated or tailored for specific users. These key features provide the warfighter with a fast, flexible and easy to use bioinformatics tool ideal for field-forward or remote environments.
PanGIA also integrates a biological select agents and toxin (BSAT) characterization tool which identifies key markers and classifies potential pathogens. These capabilities provide deployed warfighters high confidence detection rapidly, allowing for improved decision making in mission critical settings, and enabling reach-back support.
Customer and end-user engagement has played a key role throughout the development and success of the program, which is currently being transitioned to the Joint Program Executive Office for Chemical Biological Defense for the next stage of development. PanGIA and related sample-to-sequence workflows are one example of DTRA CB providing simple, fast, accurate and high confidence detection tools for warfighters deployed in harsh environments.
DTRA CB POC: Kristen O’Connor; kristen.l.oconnor5.civ@mail.mil MRI Global POC: Kristine Werking; kwerking@mriglobal.org