Use Of Digital PCR For Improved Copy Number Quantification

Ariane De Ganck1, Annelies Dheedene2, Björn Menten2, Jan Hellemans1, Jo Vandesompele1
1Biogazelle, Zwijnaarde, Belgium; 2center for medical genetics, Ghent University, Ghent, Belgium


Although the expertise of Biogazelle is historically based on quantitative PCR, we welcome the opportunity to be able to offer digital droplet PCR to our customers for a number of cases were qPCR could not fulfill their needs.
Here we present a pilot study for the genetic characterization of cell banks used for the production of recombinant therapeutic proteins. Determination of transgene copy number and genetic stability are important parameters for recombinant protein production. Using ddPCR, a markedly higher accuracy and precision in terms of copy number determination was obtained. Moreover fewer replicate reactions are necessary compared to qPCR. This study paves the way for ddPCR to become the gold standard for transgene copy number determination.
A second case study we will present is part of an internal R&D project in collaboration with Ghent University set up to discover the ddPCR boundaries for noninvasive prenatal diagnosis (NIPD) of chromosomal aneuploidies. The discovery of cell-free fetal nucleic acids in maternal plasma has opened up new possibilities in this context. Our current results support the use of ddPCR to determine chromosomal aneuploidy in post-natal samples. More efforts in terms of assay design, multiplexing strategy and data normalization are ongoing to improve accuracy and precision to enable the use of ddPCR for NIPD.
The results obtained in these two case studies confirm the unique potential of ddPCR for copy number analysis in both clinical and research settings.

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