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Test ID SARCP Sarcoma Targeted Gene Fusion/Rearrangement Panels, Next-Generation Sequencing, Tumor


Advisory Information


For formalin-fixed, paraffin-embedded (FFPE), at least 10% tumor content (% of tumor cell nuclei relative to the total number of cell nuclei in the specimen) with at least 15,000 cells is required for this assay. The amount of tumor tissue needed is dependent on a variety of pre-analytical factors (eg, cellularity, ischemic time, fixation). In general, the specimen adequacy for this test is approximately 4 squares (approximately 144 mm[2]) of tumor tissue (can be over multiple slides) or 15,000 total cells. For cytology smears, at least 5000 tumor cells are required.



Necessary Information


Either Sarcoma Targeted Gene Fusion Panel or Custom Gene Fusion Panel must be selected. If Custom Gene Fusion Panel is selected, a Gene List ID must accompany the order (generated through the Custom Gene Ordering Tool: https://orders.mayocliniclabs.com/en/tools/gene_panels/).

 

Pathology report must accompany specimen in order for testing to be performed.



Specimen Required


Preferred:

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

Container/Tube: Tissue block

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

 

Acceptable:

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: 1-2 slides

Collection Instructions: Submit 1-2 slides stained and coverslipped with at least 5,000 total nucleated cells

Additional Information: Cytology slides will not be returned.


Useful For

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

Genetics Test Information

There are 2 ordering options associated with this test. One of the 2 options below must be selected when this test is ordered.

 

Comprehensive Sarcoma Targeted Gene Fusion Panel

This ordering option evaluates 138 gene targets for the presence of somatic gene fusions. See Sarcoma Targeted Gene Fusion Panel in Special Instructions for details regarding the targeted gene regions identified by this test.

 

Custom Sarcoma Targeted Gene Fusion Panel

This ordering option provides a customizable panel in which a subset of the 138 gene targets can be selected to aid in the diagnosis and evaluation of sarcomas. This would allow for selection of a single gene or gene fusion.

 

If the custom panel option is selected, a unique Gene List ID must be created using the Gene Selection Application. The Gene List ID must be included with the test order. The Gene List ID can be created here: https://orders.mayocliniclabs.com/en/tools/gene_panels/.

 

For a demonstration of this application, Custom Gene Ordering tutorial, click here: https://vimeo.com/299737728/23d56922f1

 

See Frequently Asked Questions: Custom Gene Ordering Tool in Special Instructions.

 

Targeted genes: ACTB, AHRR, ALK, ASPSCR1, ATF1, ATIC, BCOR, BRD3, BRD4, CAMTA1, CARS, CCNB3, CDH11, CDX1, CD63, CEP128, CIC, CITED2, CLTC, CNBP, COL1A1, COL1A2, COL3A1, COL6A3, CREB1, CREB3L1, CREB3L2, CSF1, CXorf67, C11orf95, DDIT3, DUX4, DVL2, EML4, EPC1, EP400, ERG, ETV1, ETV4, ETV6, EWSR1, FEV, FGFR1, FLI1, FN1, FOSB, FOXO1, FOXO4, FUS, GLI1, HAS2, HEY1, HMGA2, IRF2BP2, JAZF1, KIRREL, KLF17, LAMTOR1, LPP, MAML3, MBTD, MEAF6, MED12, MIR143HG, MKL2, MYH9, NAB2, NCOA1, NCOA2, NFATC2, NFIB, NOTCH1, NOTCH2, NR4A3, NTRK1, NTRK3, NUMA1, NUTM1, NUTM2B, OMD, OPHN1, PATZ1, PAX3, PAX7, PBX1, PBX3, PDGFB, PDPN, PHF1, PLAG1, PLPP3, POU5F1, PPFIBP1, PRDM10, PRKCA, PRKCB, PRKCD, RAB2A,RAD51B, RANBP2, RNF213, RRAGB, SEC31A, SERPINE1, SETBP1, SFMBT1, SMARCA5, SP3, SQSTM1, SRF, SRSF3, SSX1, SSX2, SSX4, SS18, SS18L1, STAT6, SUZ12, S100A10, TAF15, TCF12, TEAD1, TFE3, TFG, THRAP3, TPM3, TPM4, TPR, USP6, VCL, VGLL2, WT1, WWTR1, YAP1, YWHAE, ZC3H7B, ZFP36, and ZNF444.

Highlights

This test uses RNA-based next-generation sequencing to evaluate sarcomas for gene fusions that involve at least 1 of 138 genes.

 

This panel can be modified to interrogate a customized list of gene fusion targets associated with sarcoma. Single gene fusions or single gene targets can be ordered using the Custom Sarcoma Targeted Gene Fusion Panel.

Testing Algorithm

When this test is ordered, slide review will always be performed at an additional charge.

 

This test includes the option of ordering a predefined comprehensive gene fusion panel or the option to create a custom gene fusion panel. Pricing for the Custom Gene Fusion Panel will be based on the number of genes selected (1-4, 5-50, and 50+).

Method Name

Polymerase Chain Reaction (PCR)-Based Next-Generation Sequencing

Reporting Name

Sarcoma Targeted Gene Fusion Panels

Specimen Type

Varies

Specimen Minimum Volume

Tissue: Entire block.
Slides: 1 stained with hematoxylin and eosin (H and E) and 2 or more unstained nonbaked slides

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Frozen 
  Refrigerated 

Reference Values

An interpretive report will be provided.

Day(s) and Time(s) Performed

Monday through Friday; Varies

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

81455 (If Applicable)

81445 (If Applicable)

81405 (If Applicable)

81406 (If Applicable)

81407 (If Applicable)

81408 (If Applicable)

81479 (If Applicable)

88381

LOINC Code Information

Test ID Test Order Name Order LOINC Value
SARCP Sarcoma Targeted Gene Fusion Panels In Process

 

Result ID Test Result Name Result LOINC Value
MG132 Client Provided Sub-Panel 19145-2
MG133 Gene List ID or NA 48018-6
606430 Result Summary 50397-9
606431 Result In Process
606432 Interpretation 69047-9
606433 Additional Information 48767-8
606434 Method 49549-9
606435 Disclaimer 62364-5
606436 Specimen 31208-2
606437 Source 39111-0
606452 Tissue ID 80398-1
606438 Released By 18771-6

NY State Approved

Yes

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
G176 Sarcoma Targeted Gene Fusion Panel No, (Bill Only) No
G178 Oncology Custom Gene Panel Tier 1 No, (Bill Only) No
G179 Oncology Custom Gene Panel Tier 2 No, (Bill Only) No
G181 Oncology Custom Gene Panel Tier 3 No, (Bill Only) No