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Also known as: FKHR FISH, alveolar rhabdomyosarcoma FISH, FOXO1/PAX3, FOXO1/PAX7

Test category:

Oncology - Sarcoma

Use of Test


The FOXO1 (also known as FKHR) locus is rearranged in around 80% of cases of Alveolar Rhabdomyosarcoma (RMS). 60% have a PAX3-FOXO1 fusion, and 20% a PAX7-FOXO1 fusion.


Diagnosis of RMS is often problematic histologically, and positivity for a FOXO1 gene fusion is a useful diagnostic aid. The presence of a FOXO1 gene fusion also has prognostic implications.

Ethical Considerations:

This is an assay for non-heritable mutations. It does not raise issues of ethics or consent that are different from most other investigations ordered in the routine care of a patient.


Fluorescent in situ hybridisation (FISH) analysis using probes to detect gene fusions involving the FOXO1 gene, including fusions with the PAX3 and PAX7 genes. This test is performed on thin sections of tissue, so some cells in the section may be sliced by the process, and only contain some of the regions of interest. Sections may contain bony, fatty or necrotic material, which may interfere with processing and/or analysis. Dense tissue also makes identification of individual cells difficult. The accuracy of the results is dependent on the correct identification of tumour on the sections provided, and the assumption that positive results will be identified by a large proportion of cells within the tumour having a rearrangement.

Requesting the Test


This test is usually requested by an oncologist.

Request form:

Download the solid tumour somatic mutation request form.

Sample required:

Formalin-fixed, paraffin embedded tissue (FFPE) - 15 sections of 4 uM thickness, dried overnight at 37°C onto charged/coated slides.

Special instructions:

Please stain the first section with H&E, and label each slide with patient and block identifiers. Label the unstained sections sequentially (slides 2-15). The request should be accompanied by the somatic mutation request form (above) and a copy of the original histopathology report.

Turnaround time:

5 business days.


Up to $410.

If more information is required, the requesting clinician can call our laboratory on (07) 3377 8573.


This test is not rebated by Medicare. The laboratory assumes that the patient or client has provided informed financial consent for the test.

Click here for our billing policy.