I used to work on copy number test using Taqman real time PCR and now transfer to digital PCR. I am wondering if anyone had experiences in comparison on same cohort between real-time and digital PCR copy numbers?
Caroline Weydert
This will depend on how good your qPCR standard and assay was.
Some assays translate almost 1:1, others are very surprising .... (I have seen CN of 8 instead of 4; 125 instead of 25; ddPCR results were confirmed with NGS afterwards ....)
Another point to consider is the ploidy of your reference gene. For a new cell type or animal model, .... I would advice to take 3 reference genes the first run and check that the ratio is 1:1:1 and that those genes are actually stable.
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