Cell Line Characterization 2.0:
Implementation of Sequence Variant Analysis
via RNA-seq and Future Perspectives

Benjamin Lindner, Senior Data Scientist, Boehringer Ingelheim

The genetic characterization of CHO production cell lines is a crucial requirement for the production of therapeutic biologics. Current gold standards are quite classical molecular biological methods e.g. Sanger sequencing. Here, we present RNA-seq as an alternative to Sanger sequencing to confirm the transgene’s transcript sequence. We demonstrate that RNA-seq provides superior sensitivity for mutation detection as well as high specificity, repeatability and robustness. Further, it streamlines the laboratory workflow and is scalable up to 96 samples per batch. It also offers the possibility of unsupervised automatic bioinformatic analysis reducing the uncertainty of personal evaluation of Sanger sequences. In addition, RNA-seq could potentially be used to screen for clones with high transgene expression or to identify transcriptionally unstable clones. Future applications may comprise the identification of problematic transcripts affecting CHO stability, product quality and platform fit as well as single cell sequencing to assess the cellular heterogeneity of CHO clones early on.