Evaluating Bioinformatics Pipelines for NGS-Based Biosafety Analysis of Viral Vaccine Crude Harvest
March 20, 2023
Next-generation sequencing (NGS) is immensely valuable for the rapid, comprehensive, and unbiased identification of adventitious agents introduced during vaccine and advanced therapy medicinal product development and manufacturing.
NGS-based assays have several key advantages compared to traditional assays used for identifying biological contamination and assessing product quality, however, the successful generation of clear insights from NGS data depends heavily on the computational algorithms used for data processing and analysis. Here, we provide an overview of the most important metrics to consider when developing a bioinformatics pipeline for NGS-based adventitious agent detection. We use raw data from the available assay optimization studies of Sanofi Pasteur, where a viral vaccine crude harvest was spiked with 22 viruses  to assess the effects of multiple analysis decisions and identify best practices. We demonstrate how full control over bioinformatics pipelines and visibility of NGS data outputs offered by Genedata Selector®, the end-to-end platform, contributes to adventitious agent detection of increased sensitivity and specificity.
. Charlebois, R. L. et al. Sensitivity and breadth of detection of high-throughput sequencing for adventitious virus detection. npj Vaccines 5, 1–8 (2020)