Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern <i>In Silico</i> Approaches
John SantaLucia, Shanmuga Sozhamannan, Jason Gans, Jeffrey W. Koehler, Ricky Soong, Nancy J. Lin, Gary Xie, Victoria A. Olson, Kristian M. Roth, Linda Beck
Abstract
We describe the use of in silico approaches to improve the process of molecular assay development and reduce time and cost by utilizing available databases of whole genome pathogen sequences combined with modern bioinformatics and physical modeling tools. Well-characterized assays are needed for accurately detecting pathogens in environmental and patient samples and also for evaluation of the efficacy of a medical countermeasure that may be administered to patients. The polymerase chain reaction (PCR) remains the gold standard for pathogen detection due to the simplicity of its instrumentation, low cost of reagents, and outstanding limit of detection (LOD), sensitivity, and specificity. However, creation of such PCR assays often involves iterations of design, preliminary testing, and thorough validation with clinical isolates and testing in relevant matrices, which can be time consuming, costly, and result