The Human Embryonic Kidney 293 cell line and its biotech offspring: a full genome analysis.

The 293 cell line is widely used in cell biology and biotechnology, but how its sequence differs from the human reference genome is unknown. Moreover, the 293 karyotype is heterogenous and, consequently, subclones derived from these cells have a different genomic structure. In our study, we provide a full-genome and transcriptome resource for the 293 line and commonly used derived lines (a.o. 293T, 293S and an N-glycosylation-homogenous 293S variant). We custom-designed easy-to-use visualization and querying tools, down to the individual sequencing reads if so desired, interfacing with human genome annotation data. The sequenced 293 cell lines are made available to the community. Furthermore, we developed genome-resequencing based methods to detect human genome-plasmid/viral-vector sequence breakpoints. Finally, we show that genome resequencing-based detection of copy number alterations allows to identify genomic regions that enable 293 cell survival under particular selective conditions, which is likely widely applicable to studies of human cell biology.