Despite its advantages, CISH does have some limitations. The resolution of CISH may be lower than that of fluorescent-based techniques like FISH, which can limit its ability to detect very small or closely spaced targets. Additionally, the enzymatic amplification steps in CISH can sometimes lead to background staining, which may complicate the interpretation of results. Another limitation is that the sensitivity of CISH may be lower than other nucleic acid detection methods, such as PCR. Therefore, CISH may not be suitable for detecting very low abundance targets. The technique also requires careful optimization and control experiments to ensure specificity and sensitivity.
