Test ID: 83367
Alveolar Rhabdomyosarcomas (ARMS) by Reverse Transcriptase PCR (RT-PCR), Paraffin
Secondary ID 
A test code used for billing and in test definitions created prior to November 2011
NY State Approved Indicates the status of NY State approval and if the test is orderable for NY State clients.
Useful For Suggests clinical disorders or settings where the test may be helpful
Supporting the diagnosis of alveolar rhabdomyosarcoma
Additional Tests Lists test(s) that are always performed, at an additional charge, with the initial test(s)
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| 60254 | AP Special Studies Review | No | Yes |
Testing Algorithm Delineates situation(s) when tests are added to the initial order. This includes reflex and additional tests.
This test is performed in conjunction with 60254 AP Special Studies Review. Additional testing may be performed after review by pathologist. Upon approval from the requesting clinician, 60254 AP Special Studies Review could be changed to 5439 Surgical Pathology Consultation, if determined to be more appropriate.
Special Instructions and Forms Describes specimen collection and preparation information, test algorithms, and other information pertinent to test. Also includes pertinent information and consent forms to be used when requesting a particular test
Method Name A short description of the method used to perform the test
Reverse Transcriptase Polymerase Chain Reaction (RT-PCR)/Gel Electrophoresis
(PCR is utilized pursuant to a license agreement with Roche Molecular Systems, Inc.)
Reporting Name A shorter/abbreviated version of the Published Name for a test; an abbreviated test name
Aliases Lists additional common names for a test, as an aid in searching
FOXO1A
PAX
Rhabdomyosarcoma
ALRSH
Specimen Type Describes the specimen type needed for testing
Specimen Required Defines the optimal specimen. This field describes the type of specimen required to perform the test and the preferred volume to complete testing. The volume allows automated processing, fastest throughput and, when indicated, repeat or reflex testing.
A pathology/diagnostic report and a brief history are required.
Specimen Type:
Preferred: Formalin-fixed, paraffin-embedded (FFPE) tissue
Acceptable: Unstained slides; slides may be stained and/or scraped
Collection Instructions:
1. Process all specimens into FFPE blocks prior to submission.
2. If submitting slides, a minimum of ten, 4- to 5-micron thick, unstained slides are required.
Additional Information:
1. A quality specimen is essential for evaluation. Submit only tissue containing tumor cells; minimal tissue is required for evaluation.
2. Special stains performed outside Mayo Medical Laboratories and included with the case may be repeated and charged at the reviewing pathologist's discretion. Testing requested by the referring physician may not be performed if deemed unnecessary by Mayo Clinic pathologist.
Forms: If not ordering electronically, submit a Pathology/Cytology Request Form (Supply T246) with the specimen.
Reject Due To Identifies specimen types and conditions that may cause the specimen to be rejected
| Hemolysis | NA |
| Lipemia | NA |
| Icterus | NA |
| Other | Decalcified specimens |
Specimen Stability Information Provides a description of the temperatures required to transport a specimen to the laboratory. Alternate acceptable temperature(s) are also included.
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Ambient (preferred) | |
| Refrigerated | ||
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 FOXO1A 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 FOXO1A gene on chromosome 13 in a smaller number of cases (10%). The PAX3-FOXO1A fusion is associated with a worse prognosis than the PAX7-FOXO1A 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.
Negative
Interpretation Provides information to assist in interpretation of the test results
A positive 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
Reliable results are dependent on adequate specimen collection and processing. This test has been validated on formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause PCR failure.
Clinical diagnosis and therapy should not be based solely on this assay. The results should be considered in conjunction with clinical information, histologic evaluation, and additional diagnostic tests.
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+7/FOXO1A, was 89 bp, while the PAX3/FOXO1A was 145 bp and the PAX7/FOXO1A was 133 bp in size. Analysis of the frozen tissues showed all 3 specimens (100%) had the common transcript and the PAX3/FOXO1A 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/FOXO1A transcript and none had the PAX7/FOXO1A transcript. The differences between the PAX 3+7/FOXO1A and PAX3/FOXO1A 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 sarcomas, Ewing sarcoma, and desmoplastic small-round-cell tumors) (n=12) were all negative for the PAX 3+7/FOXO1A 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;6:91-97
2. Ladanyi M, Bridge JA: Contribution of molecular genetic data to the classification of sarcomas. Hum Pathol 2000;31:532-538
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;5:230-235
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;12:224-230
Method Description Describes how the test is performed and provides a method-specific reference
The paraffin-embedded tissue is deparaffinized, lysed, and digested. RNA is extracted using either the TRIzol kit (Invitrogen) or High Pure FFPE RNA Micro kit (Roche). DNase digestion is performed. RNA is converted to cDNA via reverse transcription; the cDNA is amplified via PCR. Primers specific for the alveolar rhabdomyosarcoma PAX3-FOXO1A and PAX7-FOXO1A transcripts are used. Controls are run with each specimen to assess possible contamination issues and overall test performance. The PCR products are separated by gel electrophoresis and stained with ethidium bromide. The agarose gel is viewed under ultraviolet light and photographed to document the results. The results are interpreted and reported by a working group pathologist. In some cases, the specimen is further analyzed by FISH and/or sequencing.(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;6:91-97)
Day(s) and Time(s) Test Performed Outlines the days and times the test is performed. This field reflects the day and time the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time required before the test is performed. Some tests are listed as continuously performed, which means assays are performed several times during the day.
Monday through Friday; 8 a.m.–4:30 p.m.
Analytic Time Defines the amount of time it takes the laboratory to setup and perform the test. This is defined in number of days. The shortest interval of time expressed is "same day/1 day," which means the results may be available the same day that the sample is received in the testing laboratory. One day means results are available 1 day after the sample is received in the laboratory.
Maximum Laboratory Time Defines the maximum time from specimen receipt at Mayo Medical Laboratories until the release of the test result
Specimen Retention Time Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location The location of the laboratory that performs the test
Test Classification Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer's instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR), Investigation Use Only (IUO) product, or a Research Use Only (RUO) product.
CPT Code Information Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Medical Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
81401x2
LOINC® Code Information Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the result codes returned for this test or profile.
| Result ID | Reporting Name | LOINC Code |
|---|---|---|
| 83367 | Alveolar Rhabdomyosarcoma,RT-PCR,PF | In Process |
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