The SS18 gene is located on chromosome 18q11.2. The SS18 break apart FISH probe is designed to label both ends of the SS18 gene, respectively. A 370 Kb orange probe is designed at the 3′ end of the SS18 gene, and a 580 Kb green probe is designed at the 5′ end of the SS18 gene.

Ninety percent of Synovial Sarcoma patients exhibit the defining chromosomal translocation t(X;18)(p11.2;q11.2). This chromosomal rearrangement creates a fusion between the SS18 gene on chromosome 18 and either SSX1 or SSX2 genes located on the X chromosome.