Advanced Sequencing Approaches For Comprehensive AAV Vector Characterization

AAV vectors are central to gene therapy delivery, but their complexity presents analytical challenges—especially when it comes to characterizing DNA impurities and structural variants that can impact safety and efficacy. This asset explores how next-generation sequencing (NGS) methods, both short and long read, are being applied to fill gaps left by traditional tools like ddPCR, AUC, and TapeStation. Short read sequencing offers a rapid and cost-effective way to confirm vector identity and detect contaminants, while long read platforms like Oxford Nanopore and PacBio provide deeper insight into truncation patterns, sequence motifs, and capsid packaging profiles.

This also compares sequencing technologies across cost, accuracy, and throughput, and outlines use cases for each within the AAV development pipeline—from early screening to near-final product characterization. Importantly, it highlights how extraction parameters and sequencing strategy can influence data quality and interpretation. For teams working on AAV-based therapies, this resource provides a practical framework for integrating NGS into analytical workflows, enabling more reproducible and scalable vector characterization.

If you're looking to strengthen your AAV analytics strategy or evaluate sequencing platforms for your pipeline, this is a must-read.