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Test ID: 83367    
Alveolar Rhabdomyosarcoma (ARMS) by Reverse Transcriptase PCR (RT-PCR), Paraffin

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

Supporting the diagnosis of alveolar rhabdomyosarcoma

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

Alveolar rhabdomyosarcoma (ARMS) is a member of the family of rhabdomyosarcomas (tumors composed of cells showing muscle differentiation) that also includes embryonal, botryoid, spindle cell, and pleomorphic types.(1) Alveolar rhabdomyosarcomas include the classical and solid patterns.(1) ARMS is also a member the small round-cell tumor group that includes synovial sarcoma, lymphoma, Wilms tumor, Ewing sarcoma, and desmoplastic small round-cell tumor.


While treatment and prognosis depend on establishing the correct diagnosis, the diagnosis of sarcomas that form the small-round-cell tumor group can be very difficult by light microscopic examination alone, especially true when only small-needle biopsy specimens are available for examination. The use of immunohistochemical stains (eg, desmin, actin, and the nuclear transcription factor markers MyoD and myogenin) are useful in separating rhabdomyosarcomas from other small-round-cell tumors, but do not always distinguish the various subtypes of rhabdomyosarcomas. Expertise in soft tissue and bone pathology are often needed.


Studies have shown that some sarcomas have specific recurrent chromosomal translocations. These translocations produce highly specific gene fusions that help define and characterize subtypes of sarcomas and are useful in the diagnosis of these lesions.(1-4)


Most cases of ARMS have a t(2;13)(q35;q14) reciprocal translocation. This rearrangement juxtaposes 5' portions of the PAX3 gene on chromosome 2 with 3' portion of the FOXO1 gene on chromosome 13 resulting in a chimeric gene in the designated chromosome 13 that encodes a transcriptional regulatory protein in 75% of cases.(1) Another variant t(1;13)(q36;q14) translocation fuses the 5' portion of the PAX7 gene on chromosome 1 with the FOXO1 gene on chromosome 13 in a smaller number of cases (10%). The PAX3-FOXO1 fusion is associated with a worse prognosis than the PAX7-FOXO1 fusion.

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.


Interpretation Provides information to assist in interpretation of the test results

A positive PAX3-FOXO1 or PAX7-FOXO1 result is consistent with a diagnosis of alveolar rhabdomyosarcoma (ARMS).


Sarcomas other than ARMS, and carcinomas, melanomas, and lymphomas are negative for the fusion products.


A negative result does not rule out a diagnosis of ARMS.

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

No significant cautionary statements

Supportive Data

A total of 35 cases including 3 frozen and 32 paraffin-embedded tissue cases diagnosed as alveolar rhabdomyosarcoma (ARMS) by soft tissue pathology experts and by immunohistochemistry were analyzed. All 3 of the frozen tissue cases were also analyzed as paraffin sections for comparison.


The common transcript, PAX3/PAX7-FOXO1, was 89 bp, while the PAX3-FOXO1 was 145 bp and the PAX7-FOXO1 was 133 bp in size. Analysis of the frozen tissues showed all 3 specimens (100%) had the common transcript and the PAX3-FOXO1 transcript (100%). Four rhabdomyosarcomas of other types (embryonal type) were negative for the translocations. Analysis of 32 paraffin tissues showed 23 (71.9%) of cases with the common transcript, while 11 (34.4%) had the PAX3-FOXO1 transcript and none had the PAX7-FOXO1 transcript. The differences between the PAX3/PAX7-FOXO1 and PAX3-FOXO1 could be explained in part by the differences in sensitivity with paraffin-embedded tissues, since the common primers had a size of 89 bp, which made it much less sensitive test in paraffin section. Southern hybridization and sequencing of the RT-PCR products confirmed the findings.


Analysis of other small-round-cell tumors (synovial sarcoma, Ewing sarcoma, and desmoplastic small-round-cell tumor) (n=12) were all negative for the PAX3/PAX7-FOXO1 fusion transcripts.

Clinical Reference Provides recommendations for further in-depth reading of a clinical nature

1. Edwards RH, Chatten J, Xiong QB, Barr FG: Detection of gene fusions in rhabdomyosarcoma by reverse transcriptase polymerase chain reaction assay of archival samples. Diagn Mol Pathol 1997 Apr;6(2):91-97 

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

3. Galili N, Davis RJ, Fredricks 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 

4. Jin L, Majerus J, Oliveira A, et al: Detection of fusion gene transcripts in fresh-frozen and formalin-fixed paraffin-embedded tissue sections of soft tissue sarcomas after laser capture microdissection and RT-PCR. Diagn Mol Pathol 2003;12(4):224-230

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