Test Catalog

Test ID: FOXOF    
Alveolar Rhabdomyosarcoma (ARMS), 13q14 (FOXO1 or FKHR) Rearrangement, FISH, Tissue

Useful For Suggests clinical disorders or settings where the test may be helpful

Supporting the diagnosis of alveolar rhabdomyosarcomas (ARMS) when used in conjunction with an anatomic pathology consultation


Aiding in the diagnosis of ARMS when reverse transcriptase-PCR results are equivocal or do not support the clinical picture

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

This test does not include a pathology consult. If a pathology consultation is requested, PATHC / Pathology Consultation should be ordered and the appropriate FISH test will be ordered and performed at an additional charge.


This test includes a charge for application of the first probe set (2 FISH probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Rhabdomyosarcomas are a heterogeneous group of malignant tumors showing skeletal muscle differentiation. They can be divided into 3 subtypes: alveolar, embryonal, and pleomorphic. The rarer alveolar rhabdomyosarcomas (ARMS) are seen in older children, are more likely to occur in limbs, and are associated with higher stage disease and an unfavorable prognosis.


The alveolar form consists of 2 variants; classic and solid. The classic form is characterized by small round cells with dark hyperchromatic nuclei containing distinct nucleoli, held together by strands of intercellular collagen, thereby creating a cellular architecture resembling the alveolar spaces of the lungs. The solid form is characterized by a similar cellular morphology but without the formation of alveolar spaces. ARMS are also members of the small round cell tumor group that includes synovial sarcoma, lymphoma, Wilms tumor, Ewing sarcoma, and desmoplastic small round cell tumor.


Most cases of ARMS (75%) are associated with a t(2;13)(q35;q14), where a chimeric gene is formed from the rearrangement of the PAX3 gene on chromosome 2 and the FOXO1(FKHR) gene on chromosome 13. A small subset of ARMS patients (10%) are associated with a variant translocation, t(1;13)(q36;q14), involving the PAX7 gene of chromosome 1 and the FOXO1 gene. Detection of these transcripts by RT-PCR (ARMS / Alveolar Rhabdomyosarcoma by Reverse Transcriptase PCR [RT-PCR]), which allows specific identification of the t(2;13) and t(1;13), has greatly facilitated the diagnosis of ARMS tumors. FISH analysis (using the FOXO1 probe) adds the ability to detect variant FOXO1 rearrangements not detectible by PCR, and will often yield results when the quality of the available RNA is poor or the PCR results are equivocal.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation Provides information to assist in interpretation of the test results

A neoplastic clone is detected when the percent of cells with an abnormality exceeds the normal cutoff for the FOXO1 FISH probe.


A positive result suggests rearrangement of the FOXO1 gene region at 13q14 and is consistent with a subset of alveolar rhabdomyosarcomas (ARMS).


A negative result suggests FOXO1 gene rearrangement is not present, but does not exclude the diagnosis of alveolar rhabdomyosarcomas (ARMS).

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This test is not approved by the US Food and Drug Administration and it is best used as an adjunct to existing clinical and pathologic information.


Fixatives other than formalin (eg, Prefer, Bouin) may not be successful for FISH assays, however, nonformalin-fixed samples will not be rejected.


Paraffin-embedded tissues that have been decalcified are generally unsuccessful for FISH analysis. The pathologist reviewing the hematoxylin and eosin-stained slide may find it necessary to cancel testing.

Supportive Data

FISH analysis was performed on 42 formalin-fixed paraffin-embedded tissue samples, including 17 rhabdomyosarcomas and 25 noncancerous soft tissue control specimens (from various anatomic locations). The normal controls were used to generate a normal cutoff for this assay. Rearrangement of FOXO1 was identified in 10 of 17 (59%) of alveolar rhabdomyosarcoma specimens.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Fletcher CDM, Unni K, Mertens F: World Health Organization Classification of Tumours. Pathology and Genetics of Tumours of Soft Tissue and Bone. IARC: Lyon 2002, pp 150-152

2. Galili N, Davis RJ, Fredericks WJ, et al: Fusion of a fork head domain gene to PAX3 in the solid tumor alveolar rhabdomyosarcoma. Nat Genet 1993 Nov;5(3):230-235

3. Nishio J, Althof PA, Bailey JM, et al: Use of a novel FISH assay on paraffin-embedded tissues as an adjunct to diagnosis of alveolar rhabdomyosarcoma. Lab Invest 2006 Jun;86(6):547-556

4. Ladanyi M. Bridge JA: Contribution of molecular genetic data to the classification of sarcomas. Hum Pathol 2000 May;31(5):532-538

5. Lae ME, Roche PC, Jin L, et al: Desmoplastic small round cell tumor: a clinicopathologic, immunohistochemical, and molecular study of 32 tumors. Am J Surg Pathol 2002 Jul;26(7):823-835

6. Barr FG: Gene fusions involving PAX and FOX family members in alveolar rhabdomyosarcoma. Oncogene 2001 Sep 10;20(40):5736-5746