Regulatory agencies increasingly demand detailed characterization of transgenic cell lines or organisms that produce biological products. In order to ensure their safety, the origin and history of the cell line, cellular morphology and growth characteristics, purity of the cell line, and genetic stability should be defined.
The combined use of short and the latest ultra-long read sequencing technology and bioinformatics solutions enables identification of SNP incidence and allows monitoring of genetic stability in time.
CELL LINE CHARACTERIZATON PIPELINE
For long read sequencing technology the extraction of high molecular weight (HMW) DNA is essential. BaseClear can extract HMW DNA from your mammalian production cell line. This HMW DNA is used for long read sequencing on the PromethION sequencing platform from Oxford Nanopore Technologies (ONT). With this technology >25X coverage of the cell line genome sequence is generated. The complete genome sequence of the cell line is de novo assembled and corrected, resulting in an assembly with a sequence accuracy of 99%. Optionally we offer sequencing polishing toward >99.9% using short read Illumina data. The transgene integration site, orientation and copy number are mapped at the single nucleotide level!