Method of predicting phenotypic instability in a cell

A computer-implemented method for predicting phenotypic stability of a cell line, the method comprising:

• generating a plurality of environmental response fingerprints by generating an environmental response fingerprint for the cell line at a plurality of different time points in a cell culture assay over an assay period, wherein each environmental response fingerprint is generated based on incubation data obtained from each of the plurality of different time points following simultaneous incubation of the cell line for the assay period in a presence of each of three chemical cell stressors, wherein the cell line is incubated with a single chemical cell stressor of the three chemical cell stressors;
• detecting a change in the environmental response fingerprint over the assay period by comparing the plurality of environmental response fingerprints of the cell line generated in the presence of each of the three chemical cell stressors to an environmental response of the cell line incubated in an absence of the three chemical cell stressors, the environmental response of the cells in the absence of the three chemical cell stressors generating a reference environmental response fingerprint;
• predicting the phenotypic stability of the cell line by applying a computational model generated using one or more environmental response fingerprints of the cell line generated in the presence of each of the three chemical cell stressors and from the reference environmental response fingerprint generated in the absence of the three chemical cell stressors having known phenotypic stability or instability, or both;
• and
• outputting, from the computational model, a representation of a level of change in the environmental response fingerprint over the assay period in the presence of each of the three chemical cell stressors as compared to the environmental response fingerprint over the assay period in the absence of each of the three chemical cell stressors, thereby providing an indication of a level of predicted phenotypic instability in the cell line.