EWSR1 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:

EWSR1 rearrangement is found in Ewing and Ewing-like small round cell sarcomas, as well as several other types of sarcoma. EWSR1 rearrangements have also been found in other tumors, including angiomatoid fibrous histiocytoma and hyalinizing clear cell carcinoma of salivary gland.

HOW THE TEST WORKS:

The EWSR1 gene rearrangement by FISH assay is designed to identify EWSR1 gene rearrangement on chromosome 22q12. It utilizes a Vysis LSI EWSR1 (22q12) Dual Color Break Apart Rearrangement Probe set. The probe set includes two FISH probes. The first probe flanks the 5' (centromeric) side of the EWSR1 gene, producing an orange signal while the second probe flanks the 3' (telomeric) side of the EWSR1 gene, producing a green 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.

The test was validated by the UCSF Clinical Cancer Genomics Laboratory (CCGL) to confirm performance characteristics, in compliance with current guidelines for clinical implementation

SPECIMEN REQUIREMENTS FOR A SUCCESSFUL TEST:

Blocks selected for EWSR1 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.

HOW TO ORDER THE TEST:

UCSF Clinicians — this test can be ordered through Pathology
Outside Physicians — this test can be ordered with the CCGL Requisition Form

For all specimens, an interpretation of this test by a laboratory physician will automatically be performed and billed for separately.