Next-Generation Sequencing and Omics Technologies for Biotherapeutic Manufacturing Development

Driven by a continuous innovation of experimental and computational methodologies, Next-Generation Sequencing (NGS) and other Omics technologies continue to advance at a rapid pace. These technologies have led to a revolution in biological research and medicine but have applications well beyond those areas. One field in which these technologies have started to make a positive impact is the development of cell lines and bioprocesses for biotherapeutic manufacturing.

At Biogen, we are using NGS to both characterize therapeutic production clones and evaluate manufacturing culture processes, many of which use Chines Hamster Ovary (CHO) cells. One application is an NGS screen of candidate production clones to ensure their biotherapeutic mRNA sequence is free of mutations. For this screen we developed a targeted mRNA sequencing assay that multiplexes samples of multiple clones onto a single sequencer lane. This mutation screen has become a standard part of our cell line development workflow to which it adds quality and rigor on decisions about candidate production clones. Another application uses targeted genome sequencing to characterize integration sites of the biotherapeutic transgene. This integration site assay allows for clone fingerprinting, provides information on genetic stability, and supports efforts for locus specific engineering of transgene integration into the CHO genome. In addition to clone characterization we use NGS (RNA-Seq) to obtain insights into the cell biology of bioprocessing. The genome for CHO is much less resolved than the genome for human or mouse and to set up a robust omics platform around CHO we evaluated several draft CHO genome assemblies and annotations. In addition, we developed a standardized computational pipeline to process CHO RNA-Seq data. This enabled comparing gene expression profiles across our bioprocess which led to the identification of changes related to particular growth stages and transgene expression.

In conclusion we successfully developed and implemented a toolbox of NGS technologies that we continue to refine and expand. These NGS tools provide improvements to our cell line development workflows and generate new insights into our CHO production processes