Quantification of residual CHO host cell DNA in biotherapeutics in-process samples using KingFisher Flex system

Biopharmaceuticals such as monoclonal antibodies and recombinant proteins represent a major class of therapies used in oncology and immunodeficiency diseases. These products are commonly produced in mammalian systems, particularly Chinese Hamster Ovary (CHO) cells, and residual host cell DNA may remain despite purification steps. Because such impurities can induce severe side effects for patients related to oncogenicity and immunogenicity, regulatory agencies require strict control and quantification of residual DNA. Quantitative real-time PCR (qPCR) is widely recognised for its sensitivity and precision in this context.

This application note presents an approach combining PrepSEQ/resDNASEQ kits with the KingFisher Flex system to improve extraction efficiency and analytical performance. The full technical note is available for download.

KEY HIGHLIGHTS OF THE METHOD

• Quantification of residual CHO DNA using qPCR with the resDNASEQ kit following automated or manual extraction
• Semi-automated extraction with KingFisher Flex enables processing of up to 96 samples in less than 2 hours
• Improved sensitivity with a lower limit of quantification (0.1 pg/test vs 0.5 pg/test for manual extraction)
• Robust performance meeting acceptance criteria for accuracy (50–150%) and precision (CV ≤ 20–25%) across tested matrices
• Confirmed linearity across a range of 0.1 to 100 pg/test (R² ≥ 0.98)
• Specific detection of CHO DNA without interference from human DNA (tested at 10,000 pg/test)

HOW THIS SUPPORTS YOUR BIOPHARMACEUTICAL ANALYTICAL PROGRAMME?

This approach provides a reliable framework for monitoring residual DNA throughout bioprocess development and manufacturing. By combining sensitive qPCR detection with automated sample preparation, it addresses key analytical and operational challenges.

• Enhances sensitivity for low-level DNA detection, supporting regulatory expectations
• Improves reproducibility and precision compared to manual extraction methods
• Enables high-throughput processing, reducing turnaround time for large sample sets
• Minimises operator intervention, lowering the risk of variability, errors and contamination
• Expands quantification capabilities across a broader range of concentrations
• Facilitates robust method validation in line with ICH Q2 (R1) guidelines

Overall, the method supports consistent and reliable monitoring of residual DNA across complex bioprocess matrices.

Typical applications

• Analysis of in-process samples across multiple purification steps (e.g. bulk harvest, protein A eluates, chromatography steps)
• Quantification of residual DNA in Drug Substance samples
• Monitoring DNA removal efficiency during purification workflows