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Incorporate New Technology to Streamline Cell Line Characterization and Deliver Better Data
Rethink your therapeutic antibody cell line development process with copy number measurement and genome edit detection that’s accurate, precise, and requires fewer cells than qPCR.
Start a Conversation with a SpecialistOne of the bottlenecks in bringing a therapeutic antibody to IND,1 is that stable cell line development can take anywhere from several months to an entire year.1 Thus, any efficiencies that can speed up the cell line development process can have a big impact on the speed of your entire development program.
However, changing well-established workflows can feel daunting. You need to achieve significant benefits to feel like the change is worthwhile.
Making the switch from qPCR to Droplet Digital™ PCR (ddPCR™) for measuring the copy number of your antibody expressing gene and detecting genome edits is one process change that is definitely worth considering.
The switch to ddPCR does more than deliver accurate and reliable data. With the ability to provide absolute quantification using much less sample and accuracy over a wide range of copy numbers, ddPCR can streamline your cell line development workflows and help you choose the best clones earlier to accelerate development.
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Did you know?
A sample of the first monoclonal antibody approved for therapeutic use in humans, Orthoclone OKT3 Muromonab-CD3, is stored in the National Museum of American History. The sample was donated by the company that discovered and developed the mAb, Ortho Pharmaceuticals.2
How ddPCR Technology Delivers Better Data
Compared to qPCR, ddPCR offers a number of technical advantages that can provide more accurate and reliable data for making critical decisions in cell line development:
Higher sensitivity
With higher sensitivity and absolute quantitation, you can find the best clones earlier in the process, speeding development
Increased signal-to-noise
Enrich for rare targets by reducing competition that comes from high-copy templates
Measurement accuracy regardless of copy number
Reducing competition from high-copy templates also ensures accurate quantification regardless of target copy number
Removal of PCR efficiency bias
Error rates are reduced by removing the amplification efficiency reliance of qPCR, enabling accurate quantification of targets
Simplified quantification
A standard curve is not required for absolute quantification
Less sample required
Because a standard curve is not needed for absolute quantification, you can obtain reliable copy number measurement with fewer reactions and, thus, fewer cells
How ddPCR Technology Simplifies Cell Line Development
Compared to qPCR, ddPCR can streamline stable cell line characterization, improving efficiency and accelerating development:
Make decisions earlier
With higher sensitivity and the ability to obtain accurate quantification without the need for a standard curve, quantification with ddPCR requires less input sample than qPCR. As a result, you require much fewer cells — ddPCR can detect events at frequencies as low as 0.05% with a minimum input of 6000 cells — and can analyze your sample at an earlier stage than with qPCR.
Another advantage of not needing to set up a standard curve is that you need fewer reactions to measure the copy number of your target gene. While ddPCR does include an additional droplet generation step and read-out step, these steps are highly automated and are compatible with 96-well plate formats.
Spend less on growth media and reagents
Along with the time savings you achieve with the need for fewer cells, you also save on the costs for culture media and related reagents and consumables.
Using ddPCR in Cell Line Development
Copy Number Variation (CNV)
Accurate CNV quantification in single wells.
Genome Edit Detection Assays
Detection of HDR (Homology Directed Repair) and NHEJ events (Non-homologous end joining events) by CRISPR-Cas9 or other genome editing tools.
Resources
Publications
Droplet digital PCR: A comprehensive tool for genetic analysis and prediction of bispecific antibody assembly during cell line development. Heinzelmann D. et al. N Biotechnol. 2023 Dec 25:78:42-51. DOI: 10.1016/j.nbt.2023.10.001. Epub 2023 Oct 3. PMID: 37797917.
Systematic Quantification of HDR and NHEJ Reveals Effects of Locus, Nuclease, and Cell Type on Genome-Editing. Miyaoka Y. et al. Sci Rep. 2016 Mar 31;6:23549. DOI: 10.1038/srep23549. PMID: 27030102; PMCID: PMC4814844.
Transcriptome and Proteome Analysis of Steady-State in a Perfusion CHO Cell Culture Process. Bertrand V. et al. Biotechnol Bioeng. 2019 Aug;116(8):1959-1972. DOI: 10.1002/bit.26996. Epub 2019 May 7. PMID: 30997936.
Documents
Advancing Cell Line Development to Streamline Biopharmaceutical Production
Explore four areas that advance cell line development for biologics including cell line selection, genetic clonality and stability, and host cell engineering.
Copy Number Determination: The Pursuit of Accuracy
Learn how ddPCR™ technology can accurately and absolutely identify copy number differences for measuring CNV for cell lines producing therapeutic antibodies.
Streamlining Genetic Engineering in Antibody Discovery with Droplet Digital™ PCR
Discover out how ddPCR™ technology is a rapid and sensitive technique that can enable faster, more accurate confirmation of cell line edits.
Mycoplasma Detection during Biotherapeutic Development
Learn how ddPCR™ technology is a reliable, sensitive, and rapid approach for detecting Mycoplasma contamination and ensuring the safety of biotherapeutics.
Using Droplet Digital™ PCR to Detect Mycoplasma Contamination
Learn how traditional methods for detecting Mycoplasma fall short, the challenges associated, and how ddPCR™ technology can improve contamination detection.
Switching from qPCR to ddPCR™ Technology for Impurities Testing
Find out how switching from qPCR to ddPCR™ technology for contamination detection can ensure antibody therapeutic safety, potency, and consistency.
References
- Vuksanaj K. Mapping the Future of Cell Culture and Cell Line Development. GEN - Genetic Engineering and Biotechnology News. Published August 2, 2021. Accessed December 8, 2021. https://www.genengnews.com/insights/mapping-the-future-of-cell-culture-and-cell-line-development/
- Orthoclone OKT3 Muromonab-CD3. National Museum of American History. Accessed December 7, 2021. https://americanhistory.si.edu/collections/search/object/nmah_1000965
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