Break-apart probes target two areas of a specific gene sequence. Usually, a green fluorescent label is used on one end of a gene sequence and a red fluorescent label is used on the other end of the gene sequence. When the gene sequences are intact (still close together), the green and red signals will usually fluoresce as a yellow signal, known as a fusion signal. This is illustrated in the top diagram.
The analyst reading the case must be highly experienced to determine the width of the green and red signals. If the green and red signals are closer than the width of ONE signal, they are said to be INTACT.
When a break in the gene sequence occurs, the green and red signal will NOT be close together anymore and will thus appear as separate green and red signals.
The lower image is an example of the clinical use of a break-apart probe. In this synovial sarcoma probe SS18 image, we see a chromosomal translocation t(X;18, which) is seen in greater than 90% of all synovial sarcomas. There have been synovial cases without t(X;18), but this is rare. This translocation has not been reported in any other soft-tissue sarcomas.