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Accuracy and sensitivity of residual DNA detection by QPCR is not predicted by target copy number
Author(s) -
Verardo Megan L.,
Carvalho Juliane G.,
Delgado Dora N.,
Kuhns Scott T.
Publication year - 2011
Publication title -
biotechnology progress
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 129
eISSN - 1520-6033
pISSN - 8756-7938
DOI - 10.1002/btpr.731
Subject(s) - chinese hamster ovary cell , gene , biology , dna , genomic dna , polymerase chain reaction , biopharmaceutical , real time polymerase chain reaction , dna extraction , reference genes , microbiology and biotechnology , computational biology , cell culture , genetics
A major issue in the use of mammalian cell culture in biopharmaceutical manufacturing is the removal of process related impurities, such as residual host cell DNA, during the product purification process. To ensure that sufficient DNA removal is achieved during purification, it is essential to have an accurate and sensitive assay for host cell DNA. The quantitative polymerase chain reaction (QPCR) is widely used for this purpose; however, the extent to which the choice of QPCR gene target can have an impact on final results requires further understanding. In the present study, we examined the relationship between the genomic copy number of eight different Chinese Hamster ovary (CHO) gene targets and the sensitivity and accuracy afforded by those targets in a residual host cell DNA QPCR assay. We also evaluated the use of each gene target for accurate measurement of residual DNA clearance using in‐process purification samples from two CHO production cell lines. Our results revealed a correlation between gene target abundance and the potential sensitivity for use in a QPCR assay. However, we found that higher copy number gene targets do not provide the highest measurement or reveal the largest clearance of residual host cell DNA from purification samples. These findings suggest that different DNA sequences may clear or degrade at differential rates and highlight unexpected considerations that must be made in the choice of QPCR gene target when designing QPCR assays. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2012