Resolving vector insertion sites and cell line characterization: insights from PRINT

Accurately mapping transgene insertion sites is essential for understanding specificity, integrity, and potential genomic impact in cell line characterization and gene therapy R&D. However, repetitive and highly complex regions such as ribosomal DNA can be difficult to resolve using short-read sequencing approaches, particularly when insertion events, methylation patterns, and whole-transgene structure need to be assessed together.

In this webinar, Kyle Burbach (Addition Therapeutics) will present data from platform development and pre-clinical work using PRINT, a site-specific transgene integration platform. The talk will highlight the use of Oxford Nanopore long-read sequencing to investigate insertion specificity in primary human hepatocytes, characterize rDNA methylation, assess transgene integrity, and apply sensitive alignment strategies for accurate detection of integration events.

The presentation also includes a brief overview of nanopore sequencing, and discusses how Oxford Nanopore platforms can support vector insertion site analysis using approaches such as whole-genome sequencing and adaptive sampling.

You will learn:

• Why rDNA genomics presents unique challenges for insertion site analysis, including repetitive sequence structure, duplicated regions, and methylation complexity.
• How whole-molecule, long-read sequencing can help characterize transgene insertion specificity, methylation status, and transgene integrity in complex genomic contexts.
• How Oxford Nanopore sequencing platforms, including whole-genome and adaptive sampling approaches, can be applied alongside sensitive alignment strategies to support vector insertion site analysis.