Fig. 3

Comparison of processes based on karyotyping of mitotic chromosome spreads and ddPCR chromosome counting. Panel a details the method including chromosome spreads that we used for karyotyping by chromosome counting of ES cell lines. Note that the ES cell amplification phase spans several culture passages, including intensive preparation and evaluation of samples. The overall length of the process covered a period of 3 weeks for each sample. Panel b details the alternative process based on the novel ddPCR method introduced in this article as implemented at MRC Harwell. Note the shortened cell culture period, less intensive wet laboratory time (PCR-based), a faster readout of copy numbers from raw data with an overall process time of less than 1 week for each sample. For operational reasons, the ddPCR screen is implemented at a later passage at ICS. A key aspect of the workflow is that the DNA extraction is performed from an ES cell passage number close to that at which the cells are injected