NGS Bioinformatics Pipelines For Enhanced Viral Vector QC And Analytics

By Mohine Alam, Brian Baier, Francesca Bennett, Siobhan Clerkin, Michal Fleszar, Sherin Parokkaran Johny, Weiheng Su, Vaughan Leydon

Gene therapy relies on viral vectors such as AAV and Lentivirus to deliver therapeutic payloads, making rigorous quality control essential for patient safety and treatment efficacy. Next-generation sequencing (NGS) has become a cornerstone for assessing vector integrity, and advanced bioinformatics pipelines now elevate this process. These pipelines provide comprehensive QC by analyzing mapping rates, coverage profiles, and read length distributions to confirm genome structure and detect anomalies. They identify mispackaged plasmid or host DNA, truncated genomes, empty capsids, and sequencing artifacts, while also profiling residual contaminants in detail.

For lentiviral vectors, specialized workflows predict RNA splice donor and acceptor sites, uncovering unexpected splicing patterns that could impact transgene expression. Modular configurations allow alignment to multiple references and custom contaminant detection, ensuring flexibility for diverse applications. By combining robust sequencing with tailored analytics, these pipelines deliver actionable insights that support the development of safe, potent, and consistent viral vectors—critical for advancing gene therapy and related research.