Fluorescent in situ Hybridization (FISH) is a method for roughly mapping DNA. It is useful in helping order the fragments of DNA, or contigs. Properly ordering the fragments helps eliminate potential discontinuities.
To cause the hybridization of the genetic material with the fluorescent marker, the marker is added in solution to the sample DNA (Fig. 1). The total solution is then incubated. Once the incubation time (2 hours at 46 degrees C) is complete, cold (0 degree C) PBS solution is added. This decrease in temperature helps slow the loss of fluorescent intensity.
Once the sample is prepared, it can be analyzed using a flow cytometer. A flow cytometer measures the light scatter and fluorescence of the sample. These measurements can then be analyzed using data analysis software.
Figure 1: Fluorescent in situ hybridization depiction. (Image from: http://www.biovisible.com/FISHex.jpg)
Besides helping orient the contig, FISH is a useful method because the cells do not need to be actively dividing for the method to work. Previous methods needed the cells to be currently dividing to yield results, so this method was highly beneficial with that flexibility.
Another benefit of FISH is that you can probe for a desired gene. If you know what you are looking for, it makes it simpler to do so. A single strand of the DNA is taken and fluorescent tags are added. They bind to specific bases in the DNA, causing them to fluoresce.
The signal to noise ratio of this procedure can be increased by: intermediate probe concentrations, adding detergent to the buffer solution, or washing after hybridization. To analyze two segment types at once, probes that target different regions can be implemented – one with fluorescein and one with tetramethylrhodamine, for example.
To get good readings, a proper amount of probes must be used. Too many probes leads to non-specific binds and false readings. Too few probes results in insufficient binding and low fluorescence.
The Human Genome Project and Cancer 
