Mammalian cells employed in biopharmaceutical production undergo a large number of cell divisions from a single cell clone to the reactor. Over time, the cells accumulate somatic mutations resulting in a heterogeneous cell population.  Identification of mutations in the cells is crucial to assess the stability of both the cell lines and the product.  While major mutations can be detected through genome sequencing, variants occurring at a much lower percentage require great depth, which is often attained through transcriptome sequencing.  We established a methodology to identify high confidence variants from Illumina sequencing that excludes the vast majority of putative variants which are likely to be sequencing artifacts.  Some of the variants were verified independently using Sanger sequencing.  This methodology was applied to identify transcript variants in the libraries of Chinese hamster tissues and Chinese Hamster Ovary (CHO) cell lines.  Data were evaluated to estimate the mutation frequency and the risk of such mutation occurring in the product gene over its life cycle.  The analysis presented here will provide a new understanding of cell line and product stability.

Diverse single nucleotide variation in Chinese hamster ovary (CHO) cell lines

245th National Meeting (2013)

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