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What are exogeneous and endogeneous controls? - (Apr/19/2011 )


Can anyone tell me what are exogeneous and endogeneous controls? when do we use? which one is reliable?



Exogenous control - A control that is spiked in the sample. For example, DNAs with known concentrated and sequences added to samples as controls.

Endogenous control - A control that is present in the sample. For example Actin RNA in a RNA sample.



exogenous controls are DNAs that are spiked from outside into your sample, there are 2 types of exogenous controls:

1) heterologous controls where you end up with two primer pairs in the tube + a spiked DNA from outside (can also be in a defined number of copies), e.g. you want to control if a PCR reaction happened in your tube to exclude false negatives.

2) competitive exogenous control: one primer pair but probes labeled with different fluorescent dyes, again + spiked DNA from outside (in defined copy number). So, the two target DNAs (your target + control sequence) compete for the primers.

Endogenous control: as the name implies, this control uses a DNA which is component of your sample cDNA. this is commonly termed as a "housekeeping gene". This sort of control is mostly used in real-time PCR to normalize for different cDNA loading amounts. Here, for instance, you can also control for different efficiencies of the RT enzyme during the cDNA reaction.


An exogenous control is a control DNA spiked into your DNA samples. For example adding 100 ng of a 200 bp template to your cDNA sample of unknown concentration. This is typically used when you need to quantify a given amount of template; for example to quantify the amount of viral DNA in a blood sample based on known quantities of control/exogenous virus.

An endogenous control is basically a control that is already present in your DNA sample. For example the typical GAPD gene used for Northern blots and PCR. You typically use this when you are comparing the expression of a gene of interest across multiple samples. You basically use the endogenous control to normalize the amount of DNA template in all your samples.

Either one can be very reliable if used appropriately.


Hi Ivan,

Thank you for your explanation. It was really helpful.

Kartheek :)