Integration site analysis in engineered T cell therapies: what we measure, what we miss, and what regulators expect

The safety assessment of genome-engineered cell therapies relies on accurate characterization of vector integration sites, clonal dynamics, and genomic integrity. In CAR-T cell products, integration site analysis (ISA) underpins evaluation of insertional mutagenesis risk, clonal selection, and long-term safety. However, no single assay resolves all relevant dimensions of integration behavior. This article reviews contemporary ISA methodologies through three practical questions: where vectors integrate, how large individual clones become, and which complex genomic events may be missed by standard workflows. We examine the strengths and limitations of restriction-based, fragmentation-based, and unique molecular identifier (UMI)-enabled short-read approaches for population-level mapping and clonal quantification, alongside emerging long-read and orthogonal methods that resolve structural complexity. Emphasis is placed on quantitative biases, structural blind spots, and regulatory interpretation rather than exhaustive method comparison. We propose a layered analytical framework that integrates complementary technologies to support regulatory-grade genomic safety assessment in CAR-T and other engineered T cell therapies.