Host Residual DNA Research Articles

Method validation of Q-PCR detection of host residual DNA in antibody drug based on protein A magnetic beads

The residual DNA derived from host cells in antibody drugs have potential safety risks. In this paper, the antibody in the test sample was removed by magnetic bead separation method, and the residual DNA were quantitatively determined by Q-PCR method. The residual DNA in the sample was analyzed according to the standard curve. We validated the species specificity, accuracy, precision, quantitative restrictions, reproducibility of this method. The results showed the linearrange was of 1 × 10−1～1 × 102 pg/μL and the curve linear was good, this method can specifically detect CHO cell DNA. Compared with the method of extracting residual DNA by magnetic beads, the method has the advantages of simplicity, rapidity and low cost, and can be used for quantitative determination of the residual host cell DNA in antibody drugs producted by CHO cells.

A Direct Droplet Digital PCR Method for <i>E. coli</i> Host Residual DNA Quantification

Injectable drugs manufactured in E. coli must be tested for host residual DNA (hr DNA) impurity in ensuring drug purity and safety. Because of low allowable hr DNA as impurity, highly sensitive methods are needed. Droplet digital PCR (ddPCR) is a new method where the reaction is partitioned into about 20,000 nanoliter-sized droplets and each droplet acts as individual PCR reaction. After completion of end-point PCR, droplets are analyzed for fluorescence and categorized as positive or negative and DNA quantified using Poisson statistics. Here we describe development of a direct E. coli hr DNA dd PCR method where the drug is directly added to the ddPCR reaction. We show that the ddPCR method has acceptable precision and high accuracy, works with different biologic drugs, and compared to qPCR shows higher tolerance of drug matrices. The method does not require DNA extraction or standard curves for quantification of hr DNA in unknown samples.

A Droplet Digital PCR Method for CHO Host Residual DNA Quantification in Biologic Drugs

The Chinese Hamster Ovary (CHO) cells are the preferred host for manufacturing therapeutic biomolecules in the biopharmaceutical industry. Host residual DNA (hrDNA) is an impurity and needs to be monitored in the purified drug to ensure purity and safety. Currently, real-time quantitative PCR (qPCR) based methods are widely employed for quantification of hrDNA, however, digital PCR technology promises higher assay sensitivity and precision. Here, we report a method where the protein drug is digested with a protease, the protease is denatured and the CHO primers and fluorescent-tagged probe from Bio-Rad Laboratories, Inc. and droplet digital PCR (ddPCR) mix are added to the reaction and nanoliter-sized droplets are generated. The droplets are then subjected to end-point PCR followed by analysis for fluorescence. Compared to qPCR, the ddPCR method shows increased sensitivity, with high precision and accuracy of determination. Additionally, the method eliminates DNA extraction step and the requirement of DNA standards in routine sample testing. The method was successfully applied to hrDNA quantification in several biologic drugs under development at Merck.

A direct droplet digital PCR method for quantification of residual DNA in protein drugs produced in yeast cells

Yeast cells, in particular Pichia pastoris, are the host cell of choice for manufacturing several protein therapeutic agents in the biopharmaceutical industry. Host cell DNA is an impurity of such manufacturing process and the residual DNA after the purification process of the drug must be monitored to ensure drug purity and safety. Currently, real-time PCR (qPCR) based methods are widely employed for quantification of host residual DNA. At the same time the digital PCR technology is coming into prominence with promise of higher sensitivity. Here we report a method where the protein drug is directly added to the droplet digital PCR (ddPCR) reaction including yeast-specific primers and fluorescent-tagged probe and nanoliter-sized droplets are generated. The droplets are then subjected to PCR followed by analysis for fluorescence. This Pichia residual DNA direct ddPCR method for yeast can be used to test higher amount of drug compared to the corresponding qPCR method thereby increasing sensitivity, retaining high precision and accuracy and has a wide linear range of determination. The method has been successfully tested with three batches of a recombinant human IgG1-Fc-based drug (RP-1) and with commercially available human insulin, both manufactured in yeast cells. This method simplifies the residual DNA quantification protocol by eliminating DNA extraction or protease digestion and eliminates use of DNA standards in day-to-day running of the method.

A direct qPCR method for residual DNA quantification in monoclonal antibody drugs produced in CHO cells

Chinese hamster ovary (CHO) cells are the host cell of choice for manufacturing of monoclonal antibody (mAb) drugs in the biopharmaceutical industry. Host cell DNA is an impurity of such manufacturing process and must be controlled and monitored in order to ensure drug purity and safety. A conventional method for quantification of host residual DNA in drug requires extraction of DNA from the mAb drug substance with subsequent quantification of the extracted DNA using real-time PCR (qPCR). Here we report a method where the DNA extraction step is eliminated prior to qPCR. In this method, which we have named ‘direct resDNA qPCR’, the mAb drug substance is digested with a protease called KAPA in a 96-well PCR plate, the protease in the digest is then denatured at high temperature, qPCR reagents are added to the resultant reaction wells in the plate along with standards and controls in other wells of the same plate, and the plate subjected to qPCR for analysis of residual host DNA in the samples. This direct resDNA qPCR method for CHO is sensitive to 5.0fg of DNA with high precision and accuracy and has a wide linear range of determination. The method has been successfully tested with four mAbs drug, two IgG1 and two IgG4. Both the purified drug substance as well as a number of process intermediate samples, e.g., bioreactor harvest, Protein A column eluate and ion-exchange column eluates were tested. This method simplifies the residual DNA quantification protocol, reduces time of analysis and leads to increased assay sensitivity and development of automated high-throughput methods.