Sequence analysis of translocation t (X; 18) genomic breakpoints characterized in synovial sarcoma

OBJECTIVE: To analyze the DNA sequence characteristics of translocation t (X; 18) genomic breakpoints and to study the mechanism underlying chromosomal translocation t (X; 18) in synovial sarcoma. METHODS: Two cases of synovial sarcoma were studied utilizing long-distance polymerase chain reaction (PCR) and sequence analysis to amplify the genomic DNA of translocation t (X; 18) breakpoints. RESULTS: Translocation t (X; 18) was detected in both cases, which generated SYT-SSX1 and SYT-SSX2 fusion gene respectively. Sequence analysis revealed that intron 10 of SYT was fused to the intron 4 of SSX1 or SSX2. Sequences highly homologous to consensus recognition motifs of translin were found adjacent to breakpoints in all three genes. Breakpoints in the three genes were close to or even at several palindromic oligomer sequences. The breaks in intron 4 of SSX1 and SSX2 were near an Alu sequence. No Alu or other repetitive sequences were found 500 bp upstream or downstream from the break in intron 10 of SYT. One topoisomerase II consensus site was found between the two breakpoints but with considerable distance from intron 10 of SYT. CONCLUSIONS: All three genes involved in synovial sarcomas contain characteristic sequence motifs in the breakpoint regions which may play an important role in the genesis of chromosomal translocation in synovial sarcoma.