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Myxoid Liposarcoma, Synovial Sarcoma, Ewing Sarcoma, Alveolar Rhabdomyosarcoma by FISH Analysis

FISH, paraffin FISH, genetic, CHOP (DDIT3) gene rearrangement associated with t(12;16) in myxoid liposarcoma, SYT (SS18) gene rearrangement (18q11.2) in synovial sarcoma, EWSR1 gene rearrangement for t(v;22q) in Ewing's sarcoma, FOX01 gene rearrangement (13q14) in alveolar rhabdomyosarcoma, MDM2 gene amplification to differentiate between well-differentiated liposarcoma and benign lipoma.

Test Codes

Please contact the Cytogenetics Laboratory if assistance with ordering in EPIC or SOFT is needed. Paraffin, EPIC: LAB1231025; Solid Tumor, CHOP Break Apart by FISH, EPIC: LAB2111363; EWSR1 Rearrangement (22Q12) by FISH, EPIC: LAB2111387

Department

Cytogenetics

Specimen Collection Criteria

Collect: Tumor biopsy for culture or paraffin tissue section with concurrent H/E slide with the region of interest designated on the slide. A copy of the requisition must be sent with the specimen. 

Physician Office/Draw Specimen Preparation

Do not freeze specimen. Maintain specimens at room temperature (20-25°C or 68-77°F) prior to courier pickup. For delays in transport (greater than 48 from the time of collection), refrigerate (2-8°C or 36-46°F) the specimen.

Preparation for Courier Transport

Transport: Tumor biopsy or paraffin tissue section with concurrent H/E slide, at room temperature (20-26°C or 68-78.8°F) or refrigerated (2-8°C or 36-46°F).

Rejection Criteria

Specimens arriving in the Laboratory 4 days or more following the original collection date.

Fixed or frozen specimens. 

In-Lab Processing

Specimens are processed immediately upon receipt in the Laboratory.

Storage

Specimen Stability for Testing:

Room Temperature (20-26°C or 68-78.8°F): 48 hours
Refrigerated (2-8°C or 36-46°F): 96 hours
Frozen (-20°C/-4°F or below): Unacceptable

Specimen Storage in Department Prior to Disposal:

Refrigerated (2-8°C or 36-46°F): 7 days. A backup in situ culture is maintained for two weeks after the case has been signed out.

Laboratory

Royal Oak Cytogenetics Laboratory

Performed

Monday – Friday, 8:00 am – 5:00 pm.
Results available within 7 days of receipt in the Laboratory.

Reference Range

Positive or negative for a neoplastic clone. An interpretative report will be provided.

Test Methodology

Fluorescence In Situ Hybridization (FISH) Analysis.

Interpretation

A neoplastic clone is detected when the percent of cells with an abnormal probe hybridization pattern indicative of gene rearrangement exceeds the threshold (normal reference range) established for each probe.

Clinical Utility

Solid tumor cytogenetics can be an invaluable tool for diagnosing tumors of equivocal morphology. Unfortunately, as compared with hematological malignancies that are readily amenable to chromosome analysis, solid tumors present unique challenges, which can preclude an accurate cytogenetic diagnosis using conventional techniques. These include: 1) unpredictable growth of neoplastic cells in tissue culture, 2) overgrowth of neoplastic cells by "reactive" non-neoplastic cells, 3) destruction of tumor cultures by bacterial or fungal infection, and 4) failure of cells to grow in culture due to tissue non-viability. Fluorescence in situ hybridization (FISH) can overcome these problems as the assay can be performed on paraffin embedded tissue sections, which provides an opportunity to correlate cytogenetic events with morphology. Of course, these assays can also be performed on cultured cell preparations and can provide a definitive answer provided that the cells growing in culture are neoplastic. 

The diagnosis of four solid tumors, in particular, can be aided by FISH analysis. These include myxoid liposarcoma, synovial sarcoma, Ewing sarcoma, and alveolar rhabdomyosarcoma. Myxoid liposarcoma (as well as round cell liposarcoma) is associated with the t(12;16)(q13;p11) which leads to fusion of the CHOP gene at 12p13 and the FUS gene at 16p11. Synovial sarcoma is associated in more than 90% of cases with the t(X;18)(p11.2;q11.2) that results in fusion of the SYT gene on chromosome 18 with one of two genes on the X chromosome (SSX1 or SSX2). Ewing sarcoma is associated with rearrangement of the EWSR1 gene on chromosome 22q with one of several partner genes, the most common being the FLI1 gene on chromosome 11 as a result of the t(11;22)(q24;q12). Alveolar rhabdomyosarcoma is associated with rearrangement of the FOX01 gene that occurs as a result of the fusion of PAX3-FOX01 or PAX7-FOX01 genes. MDM2 gene amplification is often observed in liposarcomas including atypical lipomatous tumor/well-differentiated liposarcoma and dedifferentiated liposarcoma but is absent in benign lipomatous tumors.

Five solid tumor FISH assays are offered:

• CHOP gene rearrangement associated with t(12;16) in myxoid liposarcoma
• SYT gene rearrangement (18q11.2) in synovial sarcoma
• EWSR1 gene rearrangement for t(v;22q) in Ewing's sarcoma
• FOX01 gene rearrangement (13q14) in alveolar rhabdomyosarcoma
• MDM2 gene amplification to differentiate between well-differentiated liposarcoma and benign lipoma

CPT Codes

88271x1 (DNA probe, each), 88275x1 (Interphase analysis, 100-300 cells).

Contacts

Last Updated

3/7/2025