Some time we use only Ct value and some time Cq value in Real Time-PCR gene expression studies. I am little bit confused, what is main difference between these?
Add: There is also the name "Cp" for "crossing point" (the point at which the amplification curve crosses the vertical threshold line / noiseband).
It all means the same.
One minor difference in the meaning of such values comes from using a different approach to determin the Cq value: the usualy or conventional method is to use the cycle value at which the (baseline-corrected) amplification curve crosses some arbitrary threshold value. Roch introduced a different method that should remove the need of defining an arbitrary threshold value: the second derivative maximum (SDM) method. Here, the Cq is defined as the cycle at which the curvature of the amplification curve is maximal. So there is a different meaning here (and the names "Ct" or "Cp" are actually not correct in theis case, because there is no threshold and no crossing involved). Due to the fact that the threshold is chosen to cut the amplification curves in thier early exponential phase (where the curvature is neccesarily maximal, too), both methods yield quite similar (bot not identical!) values (and so even here Ct and Cp were sometimes used synonyousely to Cq). However, the SDM method never worked very robustly and Roche itself eventually suggested to use "conventionally" calculated Ct values to crosscheck the Cq values obtained with the SDM.
And Roche also used another term "fit points" to designate the cycle values used for quantification. These are in fact really Ct values, estimated from a linear regression fit through the points of the log-linear phase of the amplification curve. But this is only a technical trifle to average out some measurement noise.
There is no difference at all.. Cq was introduced through the MIQE guidelines. Ct means cycle threshold, Cq quantification cycle. But its all the same.
They are all the same, but I recomend using Cq because it was introduced by MIQE guidelines. These guidelines are very useful. Papers published following them are more complete with very important information.
Add: There is also the name "Cp" for "crossing point" (the point at which the amplification curve crosses the vertical threshold line / noiseband).
It all means the same.
One minor difference in the meaning of such values comes from using a different approach to determin the Cq value: the usualy or conventional method is to use the cycle value at which the (baseline-corrected) amplification curve crosses some arbitrary threshold value. Roch introduced a different method that should remove the need of defining an arbitrary threshold value: the second derivative maximum (SDM) method. Here, the Cq is defined as the cycle at which the curvature of the amplification curve is maximal. So there is a different meaning here (and the names "Ct" or "Cp" are actually not correct in theis case, because there is no threshold and no crossing involved). Due to the fact that the threshold is chosen to cut the amplification curves in thier early exponential phase (where the curvature is neccesarily maximal, too), both methods yield quite similar (bot not identical!) values (and so even here Ct and Cp were sometimes used synonyousely to Cq). However, the SDM method never worked very robustly and Roche itself eventually suggested to use "conventionally" calculated Ct values to crosscheck the Cq values obtained with the SDM.
And Roche also used another term "fit points" to designate the cycle values used for quantification. These are in fact really Ct values, estimated from a linear regression fit through the points of the log-linear phase of the amplification curve. But this is only a technical trifle to average out some measurement noise.
Dear Jochen Wilhelm, I am very much thankful to you, how beautifully you explain it, now I am feeling much more confidence in this section. Thanking you sir again.
Yogendra
Dear Jochen Wilhelm, as you mentioned above that a crosscheck with conventionally calculated Ct values is suggested sometime. So I wonder what will happen if 2 values obtained with conventional and SDM method are different? What could I count on?
Look at the amplification curves. Which result is more resonable for the given curves? I would always be more suspicious about SDM because is uses more assumptions about the shape of the curves.
TOF (Take-off point) is other name refer to the same thing (Ct, Cp, Cq) but now Cq is standardized MIQE guidlines.
Ct becomes Cq nowadays but why not change Delta Ct to Delata Cq too. Formula is still in written Delta Ct or Delta Delta Ct but I haven't seen yet Delta Cq or Delta Delta Cq.
I found one document that is using the term Delta Cq instead of Delta Ct. Here it is
http://dharmacon.gelifesciences.com/uploadedfiles/resources/delta-cq-solaris-technote.pdf
So confusing.
In blog post "Why is the PCR amplification efficiency still ignored?" Jan Ruijter consistently uses delta delta Cq (ddCq), not Ct.
However, according to google, delta delta Ct is still most popular.
http://blog.qbaseplus.com/why-is-the-pcr-amplification-efficiency-still-ignored
There is no difference, Ct means cycle threshold whereas, Cq was introduced through the MIQE guidelines, Cq quantification cycle.
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