Application of Targeted Sequence Capture (TSC) for Genetic Characterization of Antibody Producing Cell Lines

Genetic stability is an important attribute of biotherapeutic production cells, and as such, regulatory agencies require that production cell lines exhibit genetic comparability throughout the entire manufacturing process when applying for a commercial license. Cell line selection typically occurs well before good manufacturing process (GMP) cell banks are available for genetic characterization, so it is important to develop tools for assessing genetic stability during early cell line development (CLD) that can reduce the risk of nominating a genetically unstable cell line for a commercial process. Herein, we describe the development of next-generation sequencing (NGS)-based methods and novel bioinformatic analyses to assess the genetic stability of cell lines. A targeted sequence capture (TSC) pipeline was applied to 82 clonally derived antibody-producing CHO cell lines to characterize genomic transgene sequence identity, genome integration sites, integrated vector sequence integrity, and copy number estimation for the development cell lines. The NGS data provided an early determination of genetic stability that was subsequently found comparable to traditional genetic characterization methods when GMP cell banks were available. These data demonstrate the utility of NGS to establish genetic stability early in the biotherapeutic manufacturing lifecycle and as a suitable method for genetic characterization.