It is seen that most diagnostics kits are Taqman based, now as PCR is quite sensitive, can we settle ourselves with SYBR based kits in a resource-crunch set up?
The main difference between Taqman and normal qPCR is the Taqman uses probes and others use primers. Probe has its own advantage and disadvantage. Similarly for the normal primer based qPCR.
But, basic principle is the same for both and primer based qPCR is sensitive enough for any diagnostic work. I don't see any problem why not.
In my opinion, when dealing with disease diagnostics it is highly recommended to use probes. In general, results generated with probe-based PCR will be more reliable than SYBR GREEN-based. Of course, it also depends on what experiments exactly are you planning. For some purposes SYBR GREEN may be sufficient, but as Florian C Priller
said, you will need more controls and it's more prone to different kind of errors.
"Should and always" in the above answer poses high doubt in the efficiency and accuracy of the dye based qPCR assays. In the case of off target detection, I would say it is not primarily a method based problem, it is a primer based problem. If you are going for diagnostics, you should be well aware & sure about the primer specificity before you are really using it as diagnostic purpose. I am not opposing probe based assays. By that diagnostics assay can be multiplexed but at a higher initial cost. If people dealing with it are not experienced, it is possibility that they are not taking advantage of the probe based assay.
In my opinion, one should be well aware of the pros and cons, but which is better, probes or primer based assay, this can only be answered after analyzing the nuts and bolts of the project.
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