What are the limitations of Fluorescence in situ hybridization (FISH)?

One drawback of FISH is it has a restriction on the number of probes that can be utilized simultaneously, typically involving only two or three colors. It also requires expertise and is not able  to detect uniparental disomy. One drawback of interphase FISH is its tendency to produce a relatively high rate of false positives. This occurs because when observing the three-dimensional structure of a nucleus in a two-dimensional view, two signals may appear to overlap even if they are not colocalized. Interphase FISH also doesn't offer positional information and metaphase FISh requires cell culturing. Cross-hybridization may also occur, where the probe attaches to regions containing repetitive sequences.