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HelpTest Code FOXOF Alveolar Rhabdomyosarcoma (ARMS), 13q14 (FOXO1 or FKHR) Rearrangement, FISH, Tissue
Reporting Name
FOXO1 (13q14), ARMS, FISH, TsUseful For
Supporting the diagnosis of alveolar rhabdomyosarcomas when used in conjunction with an anatomic pathology consultation
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| _PBCT | Probe, +2 | No, (Bill Only) | No |
| _PADD | Probe, +1 | No, (Bill Only) | No |
| _PB02 | Probe, +2 | No, (Bill Only) | No |
| _PB03 | Probe, +3 | No, (Bill Only) | No |
| _IL25 | Interphases, <25 | No, (Bill Only) | No |
| _I099 | Interphases, 25-99 | No, (Bill Only) | No |
| _I300 | Interphases, >=100 | No, (Bill Only) | No |
Testing Algorithm
This test includes a charge for the probe application, analysis, and professional interpretation of results for one probe set (2 individual fluorescence in situ hybridization probes). No analysis charges will be incurred if an insufficient number of representative cells are available for analysis.
Appropriate ancillary probes may be performed at consultant discretion to render comprehensive assessment. Any additional probes will have the results included within the final report and will be performed at an additional charge.
Method Name
Fluorescence In Situ Hybridization (FISH)
Performing Laboratory
Mayo Clinic Laboratories in Rochester
Specimen Type
TissueOrdering Guidance
This test does not include a pathology consultation. If a pathology consultation is requested, order PATHC / Pathology Consultation, and appropriate testing will be added at the discretion of the pathologist and performed at an additional charge.
Multiple oncology (cancer) gene panels are also available. For more information see Hematology, Oncology, and Hereditary Test Selection Guide.
Additional Testing Requirements
Confirmation testing by next-generation sequencing to resolve atypical or unbalanced fluorescence in situ hybridization results of this gene region is available, order SARCP / Sarcoma Targeted Gene Fusion/Rearrangement Panel, Next-Generation Sequencing, Tumor.
Shipping Instructions
Advise Express Mail or equivalent if not on courier service.
Necessary Information
1. A pathology report is required for testing to be performed. If not provided, appropriate testing and/or interpretation may be compromised or delayed. Acceptable pathology reports include working drafts, preliminary pathology, or surgical pathology reports.
2. The following information must be included in the report provided.
1. Patient name
2. Block number - must be on all blocks, slides, and paperwork
3. Date of collection
4. Tissue Source
3. A reason for testing must be provided. If this information is not provided, an appropriate indication for testing may be entered by Mayo Clinic Laboratories.
Specimen Required
Submit only 1 of the following specimens:
Preferred
Specimen Type: Tissue block
Collection Instructions: Submit a formalin-fixed, paraffin-embedded (FFPE) tumor tissue block. Blocks prepared with alternative fixation methods will be attempted but are less favorable for successful results by FISH testing; provide fixation method used.
Additional Information:
1. Paraffin-embedded specimens can be from any anatomic location (skin, soft tissue, lymph node, etc).
2. Bone specimens that have been decalcified will be attempted for testing, but the success rate is approximately 50%.
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Acceptable
Specimen Type: Tissue slides
Slides: 1 Hematoxylin and eosin stained and 4 unstained?
Collection Instructions: Submit 4 consecutive unstained, positively charged, unbaked slides with 5 micron-thick sections of the tumor tissue and 1 slide stained with hematoxylin and eosin.
Specimen Minimum Volume
Slides: 1 Hematoxylin and eosin stained and 2 unstained
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Tissue | Ambient (preferred) | ||
| Refrigerated | |||
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Reference Values
An interpretive report will be provided.
Day(s) Performed
Monday through Friday
CPT Code Information
88271 x 2, 88291-DNA probe, each (first probe set), Interpretation and report
88271 x 2-DNA probe, each; each additional probe set (if appropriate)
88271-DNA probe, each; coverage for sets containing 3 probes (if appropriate)
88271 x 2-DNA probe, each; coverage for sets containing 4 probes (if appropriate)
88271 x 3-DNA probe, each; coverage for sets containing 5 probes (if appropriate)
88274 w/modifier 52-Interphase in situ hybridization, <25 cells, each probe set (if appropriate)
88274-Interphase in situ hybridization, 25 to 99 cells, each probe set (if appropriate)
88275-Interphase in situ hybridization, 100 to 300 cells, each probe set (if appropriate)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| FOXOF | FOXO1 (13q14), ARMS, FISH, Ts | 93807-6 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 52211 | Result Summary | 50397-9 |
| 52213 | Interpretation | 69965-2 |
| 52389 | Result | 62356-1 |
| CG752 | Reason for Referral | 42349-1 |
| 52214 | Specimen | 31208-2 |
| 52215 | Source | 31208-2 |
| 52216 | Tissue ID | 80398-1 |
| 52217 | Method | 85069-3 |
| 54592 | Additional Information | 48767-8 |
| 52824 | Disclaimer | 62364-5 |
| 52218 | Released By | 18771-6 |
Clinical Information
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.
Most cases of ARMS are associated with the rearrangement of the FOXO1 gene on chromosome 13. Detection of a FOX01 rearrangement by FISH may help to support a histologic diagnosis of ARMS.
Interpretation
FOXO1 will be clinically interpreted as positive or negative.
A neoplastic clone is detected when the percent of cells with an abnormality exceeds the normal cutoff for the FOXO1 probe set.
A positive result is consistent with rearrangement of the FOXO1 gene and likely reflects FOXO1 fusion with a partner gene. The significance of this finding is dependent on the clinical and pathologic features.
A positive result is consistent with rearrangement of the FOXO1 gene, likely reflects FOXO1 fusion with a partner gene, and is consistent with a subset of alveolar rhabdomyosarcomas (ARMS). The significance of this finding is dependent on the clinical and pathologic features.
A negative result suggests a FOXO1 gene rearrangement is not present but does not exclude the diagnosis of ARMS.
Cautions
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.
This fluorescence in situ hybridization (FISH) assay does not rule out other chromosome abnormalities.
Fixatives other than formalin (eg, Prefer, Bouin's) may not be successful for FISH assays. Non-formalin fixed specimens will not be rejected.
Paraffin-embedded tissues that have been decalcified may not be successful for FISH analysis. The success rate of FISH studies on decalcified tissue is approximately 50%, but FISH will be attempted if sufficient tumor is present for analysis.
FISH studies will be attempted if sufficient tumor is present for analysis. The pathologist reviewing the hematoxylin and eosin-stained slide may find it necessary to cancel testing if insufficient tissue/tumor is available for testing.
If no FISH signals are observed post-hybridization, the case will be released indicating a lack of FISH results.
Clinical Reference
1. 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;5(3):230-235
2. 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;86(6):547-556
3. Barr FG. Gene fusions involving PAX and FOX family members in alveolar rhabdomyosarcoma. Oncogene. 2001;20(40):5736-5746
4. WHO Classification of Tumours Editorial Board. Soft tissue and bone tumours. 5th ed. IARC; 2020. WHO Classification of Tumours Series. Vol. 3, 203-208
Method Description
The test is performed using a commercially available FOXO1 dual-color, break-apart strategy probe (BAP). Formalin-fixed, paraffin-embedded tissues are cut at 5 microns and mounted on positively charged glass slides. The selection of tissue and the identification of target areas on the hematoxylin and eosin (H and E)-stained slide are performed by a pathologist. Using the H and E-stained slide as a reference, target areas are etched with a diamond-tipped engraving tool on the back of the unstained slide to be assayed. The probe set is hybridized to the appropriate target areas, and 2 technologists independently analyze 50 interphase nuclei (100 total) with the results expressed as the percent of abnormal nuclei.(Unpublished Mayo method)
Report Available
7 to 10 daysSpecimen Retention Time
Slides and H&E used for analysis are retained by the laboratory in accordance with regulatory requirements. Client provided paraffin blocks and extra unstained slides (if provided) will be returned after testing is complete.Test Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.Forms
If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.