A standard curve can be generated using a 10-fold dilution of a template amplified on a real-time system (Example: ABI 7500). Each dilution can assayed in triplicate(its always better to do in duplicates or in triplicates).
Below are the data generated after a Real time PCR run.
Ct
|
Log
DNA dilution |
36.47
|
10^-6
|
33.83
|
10^-5
|
29.49
|
10^-4
|
26.85
|
10^-3
|
23.11
|
10^-2
|
20.14
|
10^-1
|
17.16
|
10^0
|
The template used for this purpose can be a target with known concentration (e.g., nanograms of genomic DNA or copies of plasmid DNA) or a sample of unknown quantity (e.g., cDNA). Here plasmid is used as the template for the reaction.
Below is the standard curve graph generated using the data obtained after the PCR run, here Ct value is plotted against log DNA dilution.
Standard Curve qPCR |
If perfect doubling occurs with each amplification cycle, the spacing of the fluorescence curves will be determined by the equation 2^n =dilution factor, where n is the number of cycles between curves at the fluorescence threshold (in other words, the difference between the Ct values of the curves).
for example, with a 10-fold serial dilution of DNA, 2^n = 10. Therefore, n = 3.32, and the Ct values should be separated by 3.32 cycles.
Amplification efficiency denoted by E can be calculated from the below equation:
E = 10^(-1/slope);
From the standard Curve chart (y = mx + b)
where m is the slope;
b is the intercept;
slope (m) = – 3.2746
Amplification efficiency E = 10^(-1/-3.2746) = 2.02
Amplification efficiency is also frequently presented as a percentage, that is, the percent of template that was amplified in each cycle.
To convert E into a percentage:
% Efficiency = (E – 1) x 100%
% Efficiency = (2.0 – 1) x 100% = 100%.
An efficiency close to 100% is the best indicator of a robust, reproducible assay. Low reaction efficiencies < 90% may be caused by poor primer design or by suboptimal reaction conditions. Reaction efficiencies >100% may indicate pipetting error in your serial dilutions or co-amplification of nonspecific products, such as primer-dimers.
When using the method described above to determine amplification efficiency, the presence of inhibitor can also result in an apparent increase in efficiency. This is because samples with the highest concentration of template also have the highest level of inhibitors, which cause a delayed Ct, whereas samples with lower template concentrations have lower levels of inhibitors, so the Ct is minimally delayed. As a result, the absolute value of the slope decreases and the calculated efficiency appears to increase. If the reaction efficiency is <90 nbsp="" or="">105%, one should modify the assay by redesigning your primers and probes. 90>
Reference
PCR Application guide Bio-Rad
Mathematics in molecular biology and Biotechnology
Internet Sources
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