What's Really In The Box? Characterizing AAV Encapsidated Nucleic Acid Sequences Using NGS

Due to the nature of AAV particle production, non-targeted sequences may be packaged along with the gene of interest. Even in an optimized system, these non-target nucleic acids could constitute between 1-2% or greater of the entire nucleic acid payload. It is crucial to properly characterize these non-targeted sequences that may be enclosed within the vector, as this is vital for ensuring the safety profile of the end product.

Next-generation sequencing (NGS) offers a more comprehensive insight into the complete range of encapsidated sequences within AAV particles. Here, we discuss the characterization of several representative AAV molecules using NGS, including the sequencing process, bioinformatic analysis, and representative results.