Real Time PCR

Real Time PCR
A useful new approach?

Statistical Problems?
Reverse transcription followed by Polymerase Chain Reaction
Considered to be the most sensitive method for the detection and quantification of gene expression levels.
Used as a follow-up when a particular gene is suggested in micro-array studies.
Potential problems with sensitivity, specificity and reproducibility.
Fluorescence trajectory
Plot of sigmoid fluorescence trajectory
Accumulation of fluorescence is proportional to the accumulation of amplification products.
Cn = C0 (E)n = k Rn =k R0(E)n
where C0 is the initial concentration
Cn is the concentration at cycle n,
E is the amplification efficiency,
and R0 and Rn are equivalent
measures of fluorescence.

The normal practice is to record the cycle number where the fluorescence rises appreciably above the background fluorescence.
The commonly used value (CP) is the second derivative maximum value (SDM). This is measured in triplicate for each sample.
Absolute versus Relative Measurement

In principle we can produce an absolute measurement by use of an external standard.
However there are various practical difficulties with this and it is much easier to compare the concentration in a test sample against a control. Then the proportionality constant cancels out .
Expression ratio
Expression ratio = C0test / C0cont
= E (CPcont - CPtest)
The CP values are averages of the triplicate readings.
As all genes might change expression in the test sample, the expression ratio is usually calculated for the target gene relative to a reference gene.
i.e. Relative Exp. Ratio = Φ
= Target Exp. Ratio/ Ref. Exp. Ratio.
(Pfaffl et al, 2002)
Reference Genes
Initially housekeeping genes were recommended, e.g. GAPDH, albumin, actin, etc.
However a recent study (Radonic et al, 2003) has suggested that a transcription-related gene RPII is a useful general reference gene but that using several reference genes is desirable.
Amplification Efficiency
E is a value between 1 (no amplification) and 2 (complete amplification). There is evidence that E varies between genes, experimental conditions, etc, necessitating constant estimation in each situation.
Initially E was estimated by assaying serial dilutions of a gene sample and regressing mean CP against log10Conc.
Accuracy of estimated E
Even when the correlation is close to -1 and the R2 value close to 100%, it is important to calculate a standard error for the estimated amplification efficiency, E.
This can easily be done using a Taylor’s series approximation.
Given that Beta hat is the estimated slope
Standard error of estimated slope = 0.3110
Estimated E = 1.8848
Standard error of estimated E = 0.1023
Alternative Method
E can also be estimated by regressing
log10(fluorescence – background)
against cycle number for the data in the exponential phase.
There are methods for choosing which points are in the exponential phase (Tichopad et al, 2003)
The estimated slope is minus the estimated slope from the previous method and the formula for the standard error is unchanged.
The two methods seem to give very similar estimates for E.
Sources of Error
In order to calculate the standard error of the relative expression ratio, Φ,
we must allow for variability in the four CP values and two E values.
Any between run variability can be ignored because we are looking at differences between test and control.
Again using Taylor’s Series
Illustrative Example
Let us take a case of down-regulation where we look at 1/Φ. The formula for the standard error is as above but with Φ replaced by 1/Φ.
CPtarget,test = 32.61; CPtarget,control = 25.88;
CPref,test = 22.35; CPref,control = 22.53;
Etarget =1.670 and Eref = 1.885.
This gives 1/Φ = 1.12/0.032 = 35.35.
SE(Etarget) = 0.036 and SE(Eref) = 0.102
If we take the standard errors of the CP means to be 0.2 which given the literature seems to be a fair estimate,
then we find that the standard error of the estimate of 1/Φ is 9.64. Thus the sampling error on our estimate of 35.35 is large;
Two standard errors being 19.28.
Potential ways to reduce variability
If E only varies between genes and can be accurately determined as a reference this could reduce S.E. (E). Acceptable assumption?
Taking more than three CP readings would reduce the S.E. (CP).
Do we need to look relative to a reference gene?
Conclusion
This seems potentially a very useful technique but it is important that a standard error is put on the expression ratio obtained and that efforts are made to reduce sampling error.