Analytical assessment of clonal derivation of eukaryotic/CHO cell populations

Cell populations that are exclusively composed by descendants from a defined single parental progenitor are referred to as monoclonal, or more correctly as derived cell population. Clonal derivation of cell lines used in the manufacturing of recombinant biologics is a regulatory requirement that aims to ensure a robust process and consistent quality throughout the life cycle of a product. Clonal derivation of cell lines is usually ensured by the process (e.g. two subsequent rounds of limiting dilution). Here we present an approach to analytically assess the probability of clonal derivation of existing cell populations. Using target locus amplification (TLA) followed by next generation sequencing (NGS), unique genetic features can be identified, for example the integration site of the plasmid in the host cell genome or plasmid-plasmid junctions of the plasmids used for expression of recombinant biologics. Whereas a direct assessment of clonal derivation using TLA/NGS data is challenging due to limitations in specificity, confirmed clonally derived populations generated from the cell line population can be analyzed by qPCR for the presence of the unique genetic features identified by TLA/NGS. In the present study, a statistical analysis allowed the demonstration that two independently generated CHO cell lines were clonally derived with an upper 95% confidence interval limit of a potentially present contaminating population of 1.3%.