Sarcoma Targeted Gene Panel [Test in Focus]

Sarcomas are malignant tumors that arise in the bone and soft tissue. With numerous subtypes of sarcoma that can have overlapping histological, immunophenotypic, and clinical features, diagnosis can be extremely challenging. This challenge increases when rare subtypes are encountered for which most pathologists will have little experience. Using only histological and immunophenotypic features can lead to a high rate of inaccurate diagnoses. Published data indicates a substantial number of patients have discordant diagnoses between referring institutions and specialty centers. Supplementing the histologic diagnosis with genetic testing can improve diagnostic accuracy and overall patient management. 

Andre Oliveira, M.D., Ph.D., gives an overview of this testing available through Mayo Clinic Laboratories. He discusses when this testing should be ordered, how this testing compares to previous testing approaches, and what clinical action can be taken due to the results of this testing.

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Useful for:

  • Diagnosing specific soft tissue and bone tumors (sarcoma) based on the observed gene fusions (e.g., PAX3/FOXO1 gene fusion observed in alveolar rhabdomyosarcoma, EWSR1-FLI1 gene fusion for Ewing’s sarcoma, SS18-SSX1/2 gene fusion for synovial sarcoma)

Specimen Requirements

Specimen Type 


Necessary Information

Pathology report (final or preliminary), at minimum containing the following information, must accompany specimen in order for testing to be performed:

1. Patient name

2. Block number must be on all blocks, slides, and paperwork (can be handwritten on the paperwork)

3. Tissue collection date

4. Source of the tissue

Specimen Required

This assay requires at least 10% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 144 mm(2).

-Minimum amount of tumor area: tissue 36 mm(2).

-These amounts are cumulative up to 10 unstained slides and must have adequate percent tumor nuclei.

-Tissue fixation: 10% neutral buffered formalin, not decalcified.

-For specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing in Special Instructions. In this document, the sizes are given as 4mm x 4mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3mm x 1mm x 10 slides: approximate/equivalent to 36mm(2).


Specimen Type: Formalin-fixed, paraffin-embedded (FFPE) tissue

Container/Tube: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block.


Specimen Type: FFPE Tissue

Slides: 1 stained and 10 unstained

Collection Instructions: Submit 1 slide stained with hematoxylin and eosin and 10 unstained, nonbaked slides with 5-micron thick sections of the tumor tissue.

Specimen Type: Cytology slide (direct smears or ThinPrep)

Slide: 1 to 3 slides

Collection Instructions: Submit 1 to 3 slides stained and coverslipped with a preferred total of 5,000 nucleated cells or a minimum of at least 3,000 nucleated cells.

Note: Glass coverslips are preferred; plastic coverslips are acceptable but will result in longer turnaround times.

Additional Information: Cytology slides will not be returned.

Performance Information

Day(s) and Time(s) Test Performed 

Monday-Friday; Varies

Analytic Time

14 days

Alyssa Frank

Alyssa Frank is a Marketing Segment Manager at Mayo Clinic Laboratories. She leads marketing strategies for product management and specialty testing. Alyssa has worked at Mayo Clinic since 2015.