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Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a probabilistic model (a distribution) parameters (shape) of which will strongly depend on the details of the PCR protocol and the characteristics of the amplicon...

If not, then may be there are forward models that predict the amount of the amplified result from the initial content?

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  • $\begingroup$ You need to know the primer efficiency for this to work, do you know that? $\endgroup$
    – Devon Ryan
    Commented Nov 12, 2019 at 14:39
  • $\begingroup$ @DevonRyan Assume, yes. You can assume I know everything. At this point I want to simply familiarize myself with any such model if there are any. $\endgroup$
    – user75619
    Commented Nov 12, 2019 at 14:46
  • $\begingroup$ Have you considered just using a qPCR calculator such as this nebiocalculator.neb.com./#!/qPCRGen ? The model of qPCR is pretty simple really, so there are a few of these premade. $\endgroup$
    – Devon Ryan
    Commented Nov 12, 2019 at 14:53
  • $\begingroup$ This is qPCR based on CT number, it is common place to identify patient viraemia for example $\endgroup$
    – M__ ♦
    Commented Nov 12, 2019 at 16:18

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The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency). NCBI

In this article on research gate they said amplifx was the software you were looking for to, calculate "(i.e. expected efficiency in PCR reaction)". The amplifx even mentions "Testing primers in in silico PCR".

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