Characterization of a variant SYT-SSX1 synovial sarcoma fusion transcript

Synovial sarcoma is characterized cytogenetically by an X;18 translocation [t (X;18) (p11;q11)] that results in the fusion of the SYT gene from chromosome 18 to either of two highly homologous genes at Xp11, SSX1 or SSX2. Heterogeneity within the synovial sarcoma fusion junctions is rare. Examination of a primary monophasic synovial sarcoma for an SYT-SSX fusion transcript by reverse-transcription polymerase chain reaction revealed a smaller-than-expected product. Direct sequencing of the product disclosed a novel SYT-SSX1 fusion transcript that contained an additional 51 bp of normal SSX1 sequence but lost 135 bp of the SYT sequence. Detection of synovial sarcoma hybrid transcripts is useful for diagnosis and should include the recognition of distinct variants.