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Comparision of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

Whale, A.S., Huggett, J.F., Cowen, S., Speirs, V., Shaw, J., Ellison, S., Foy, C.A., Scott, D.J.

One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.

Citation

Whale, A.S., Huggett, J.F., Cowen, S., Speirs, V., Shaw, J., Ellison, S., Foy, C.A., Scott, D.J. "Comparision of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation" Nucleic Acids Research (2012): e82