CHO_cell_line_sequencing_and_assembly

Chinese hamster ovary (CHO) cells are widely used both in research and in the manufacture of most of the biopharmaceuticals currently on the market. They were first described in 1957 by Theodore Puck who isolated them from animals obtained from Dr. George Yerganian's laboratory at the Boston Cancer Research Foundation. Since then, CHO cells have been a cell line of choice in advanced manufacturing of therapeutic antibodies and other proteins because of their rapid growth and high protein production. They have become the mammalian equivalent of E. coli in research and biotechnology today, most notably when long-term, stable gene expression and high yields of proteins are required. While biotherapeutics is rapidly expanding and manufacturing processes are constantly evolving and improving, the CHO cells used in these processes have changed little in the past 50 years. Current gene editing technologies (CRISPR/Cas9, rAAV and zinc finger nucleases) offer the opportunity to engineer mammalian cell lines and create new vectors for research and biomanufacturing. However, in order to enable this work to take place, a reliable reference genome is required to develop targeting strategies with current editing technologies. In 2012, the BGI published a draft genome for the chinese hamster using illumina sequencing and optical mapping. However this genome sequence has many gaps as it was primarily assembled from short illumina sequencing reads. In this project, we are proposing to collaborate with Horizon Discovery (Cambridge, UK) to use a combination of second and third generation sequencing technologies, optical mapping, and karyotyping to generate a high quality draft genome sequence for the CHO glutamine synthetase knockout cell line (using the knowledge and expertise gained at Sanger from the de novo assembly of 16 mouse genomes). This genome sequence will form the basis for making modifications to improve performance in delivering the next generation of biotherapeutics. This will be the first data of its kind for glutamine synthetase KO version of the cell line and the data will be a valuable tool to enable progress with genome editing technologies. With this data we will learn more about the plasticity of the cell line compared to the original parental population. All of the sequencing data and assembled genome sequence will be released under the standard Sanger open data release and made freely available to the wider scientific community. In the coming years, Horizon Discovery will also release the cell line to key academics to provide a universal platform for research and drive CHO functional genomics forward