SS18 (SYT) Rearrangement by FISH

Performing Lab:

UCSF Clinical Cancer Genomics Lab

CPT Code:

88377

Specimen Type
Formalin-fixed, paraffin-embedded tissue on six (6) unstained slides (5 microns thick) on charged glass. One adjacent hematoxylin and eosin stained (H&E) slide should also be included. Slides should be labeled with pathology case number and block identification. Cytology smears may also be used for testing if there is sufficient tumor present. Contact the laboratory at 415.502.3252 or [email protected] if testing on a cytology smear is desired.
Methodology: Fluorescence in-situ hybridization (FISH)
Turnaround Time: 7-14 days

TEST INDICATIONS:

SS18 (SYT) rearrangement is the pathognomonic genomic change in synovial sarcoma, and the presence of SS18 rearrangement therefore helps to confirm that diagnosis.

HOW THE TEST WORKS:

The SS18 (SYT) gene rearrangement by FISH assay is designed to identify SS18 gene rearrangement on chromosome 18q11.2. It utilizes a Vysis LSI SS18 (18q11.2) Dual Color Break Apart Rearrangement Probe set. The probe set includes two FISH probes. The first probe flanks the 3' (centromeric) side of the SS18 gene, producing a green signal while the second probe flanks the 5' (telomeric) side of the SS18 gene, producing an orange signal. Formalin-fixed, paraffin-embedded tissue on one glass slide is de-paraffinized and then treated with pepsin to digest tissue proteins and allow for probes to reach target DNA. The DNA is then heat denatured and subsequently allowed to hybridize with the probe set. After hybridization, the slides are washed to remove any of the excess unbound probes and the nuclei are counterstained with DAPI (4,6 diamidino-2-phenylidole). Enumeration of the fusion and break-apart signals is conducted by microscopic examination of cell nuclei using a fluorescence microscope equipped with appropriate excitation and emission filters.

LIMITATIONS OF THE TEST:

The clinical interpretation of this test should be evaluated within the context of the patient's medical history, other diagnostic tests, and the histologic and immunohistochemical features of the tumor.

SS18 (SYT) gene rearrangement by FISH was validated by the UCSF Clinical Cancer Genomics Laboratory (CCGL) to confirm performance characteristics, in compliance with current guidelines for clinical implementation

HOW TO ORDER THE TEST:

Blocks selected for SS18 (SYT) gene rearrangement testing must contain tumor tissue. The assay is optimized for formalin-fixed tissue; tissue processed with other fixatives will not be rejected, but may not provide interpretable results. Decalcified specimens are usually unsuitable for FISH testing but an attempt at hybridization will be performed. An adjacent H&E-stained slide must be included. Contact the laboratory at 415.502.3252 or [email protected] if the specimen suitability is uncertain. Label slides with pathology case number and block identification.

Specimen rejection criteria include: All required slides not included. Insufficient tumor tissue present on slide as determined by pathologist. Outside slides not labeled or not accompanied by printed copy of test order.