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Test Code SARCP Sarcoma Targeted Gene Fusion/Rearrangement Panel, Next-Generation Sequencing, Tumor


Ordering Guidance


Multiple oncology (cancer) gene panels are available. For more information see Hematology, Oncology, and Hereditary Test Selection Guide.



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 over 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 this document, the sizes are given as 4 mm x 4 mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3 mm x 1 mm x 10 slides: approximate/equivalent to 36 mm(2).

 

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 to 3 slides

Collection Instructions: Submit 1 to 3 slides stained and coverslipped with a preferred total of 5000 nucleated cells or a minimum of at least 3000 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.


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 sarcoma, SS18-SSX1/2 gene fusion for synovial sarcoma)

Genetics Test Information

This test evaluates 138 gene targets for the presence of somatic gene fusions and also assesses for common BCOR internal tandem duplications. See Sarcoma Targeted Gene Fusion Panel and Common BCOR Tandem Duplications for details regarding the targeted gene regions identified by this test.

 

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.

Testing Algorithm

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

Reporting Name

Sarcoma Targeted Gene Fusion Panel

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

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

Reject Due To

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded
Bone marrow in EDTA
Reject

Reference Values

An interpretive report will be provided.

Supportive Data

In a verification study, this next-generation sequencing (NGS) assay was performed in 111 sarcoma formalin-fixed, paraffin-embedded and cytology samples (86 fusion positive and 25 fusion negative). The NGS assay results were confirmed by reverse transcription-polymerase chain reaction and fluorescence in situ hybridization tests. The overall accuracy of the NGS assay was 95.5% (106/111). No targeted gene fusions were detected in 20 negative control samples (100% specificity).

Day(s) Performed

Varies

Report Available

10 to 14 days

Specimen Retention Time

FFPE tissue block: Unused portions of FPPE blocks will be returned; Unused, unstained slides: 5 years; Stained slides: Indefinitely

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

81456

88381

LOINC Code Information

Test ID Test Order Name Order LOINC Value
SARCP Sarcoma Targeted Gene Fusion Panel 95124-4

 

Result ID Test Result Name Result LOINC Value
606430 Result Summary 50397-9
606431 Result 95123-6
606432 Interpretation 69047-9
606433 Additional Information 48767-8
606434 Method 85069-3
606435 Disclaimer 62364-5
606436 Specimen 31208-2
606437 Source 39111-0
606452 Tissue ID 80398-1
606438 Released By 18771-6

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Forms

If not ordering electronically, complete, print, and send a Oncology Test Request (T729) with the specimen.