Publications

Real-Time Automated Pathogen Identification by Enhanced Ribotyping (RAPIER) LDRD Final Report

Bartsch, Michael B.; Bird, Sara W.; Branda, Steven B.; Edwards, Harrison E.; Jayamohan, Harikrishnan J.; Krishnakumar, Raga K.; Patel, Kamlesh P.; Schoeniger, Joseph S.; Sinha, Anupama S.

Funded through the IHNS/E&HS investment area for FY16-18, the RAPIER LDRD sought to evaluate the potential benefits and applicability of the new Oxford MinION nanopore sequencer to pathogen diagnostic applications in biodefense, biosurveillance, and global/public health. The project had four primary objectives: 1) to investigate the performance of the MinION sequencer while building facility with its operation, 2) to develop microfluidic library prep automation facilitating the use of the MinION in field-forward or point-of-care applications, 3) to leverage CRISPR/Cas9 technology to enable targeted identification of bacterial pathogens, and 4) to capitalize on the real- time data output capabilities of the MinION to enable rapid sequence-based diagnostics. While the rapid evolution of the MinION sequencing technology during the course of the project posed a number of challenges and required a reassessment of initial project priorities, it also provided unique opportunities, notably culminating in our development of the RUBRIC real-time selective sequencing software.