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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.


Secondary ID

606427

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.

Method Name

Polymerase Chain Reaction (PCR)-based Next-Generation Sequencing (NGS)

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

Clinical Information

Molecular analysis of biomarkers is increasingly being utilized in oncology practices to support and guide patient diagnosis, prognosis, and therapeutic management. Chromosomal translocations, interstitial deletions, and inversions that lead to gene fusions are common in various sarcomas, such as Ewing sarcoma and rhabdomyosarcoma. This next-generation sequencing assay is used to detect specific gene fusions to assist in the diagnosis of sarcomas. See Method Description for details regarding the targeted gene regions identified by this test.

Reference Values

An interpretive report will be provided.

Interpretation

The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.

Cautions

This assay is not validated for the detection of point variations, deletions-insertions, copy number alterations, or gene expression.

 

This assay may detect gene fusions that are present at the RNA level, but not the DNA level, that result from cis splicing of adjacent genes or trans-splicing.(1)

 

This panel can detect in-frame and out-of-frame fusions. There may be lower sensitivity in detecting out-of-frame fusions such as exon-intron, intron-intron, or big insertions. This assay will only detect fusions involving at least one gene in the defined genes of interest list.

 

This assay will only detect fusions involving gene transcripts that have been defined in UCSC Genome Browser (March 2012 version) available from Illumina's iGenomes Project.(2)

 

Reliable results are dependent on adequate specimen collection and processing. This test has been validated on cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure.

 

A negative result does not rule out the presence of a gene fusion that may be present but below the limits of detection of this assay (tumor cells comprise <10% of the cell population; targeted fusion read coverage with <10 unique fusion molecules in a sample).

 

The limit of detection of this assay for specific gene fusions is dependent on several variables, including decreased sensitivity with decreased tumor percentage and decreased sensitivity with decreased level of expression of the gene fusion.

 

RNA is particularly labile and degrades quickly. Rapid preservation of the tumor sample after collection reduces the likelihood of degradation. Still, there can be biological factors, such as tumor necrosis, which interfere with obtaining a high-quality RNA specimen despite rapid preservation.

 

The presence or absence of a fusion may not be predictive of response to therapy or prognosis in all patients.

 

Fusions of uncertain significance may be identified.

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).

Clinical Reference

1. Jia Y, Xie Z, Li H. Intergenically spliced chimeric RNAs in cancer. Trends Cancer. 2016;2(9):475-484. doi:10.1016/j.trecan.2016.07.006

2. Jo VY, Fletcher CD. WHO classification of soft tissue tumours: an update based on the 2013 (fourth) edition. Pathology. 2014;46(2):95-104. doi:10.1097/PAT.0000000000000050

3. Fletcher CD. The evolving classification of soft tissue tumours - an update based on the new 2013 WHO classification. Histopathology. 2014;64(1):2-11. doi:10.1111/his.12267

4. Quesada J, Amato R. The molecular biology of soft-tissue sarcomas and current trends in therapy. Sarcoma. 2012;2012(3):849456. doi:10.1155/2012/849456

5. Podnar J, Deiderick H, Huerta G, Hunicke-Smith S. Next-generation sequencing RNA-seq library construction. Curr Protoc Mol Biol. 2014;106:4.21.1-4.21.19

6. Mertens F, Tayebwa J. Evolving techniques for gene fusion detection in soft tissue tumours. Histopathology. 2014;64(1):151-162. doi:10.1111/his.12272

7. AI-Zaid T, Wang WL, Somaiah N, Lazar AJ. Molecular profiling of sarcomas: new vistas for precision medicine. Virchows Arch. 2017;471(2):243-255

8. Gao Q, Liang WW, Foltz SM, et al. Driver fusions and their implications in the development and treatment of human cancers. Cell Rep. 2018;23(1):227-238. doi:10.1016/j.celrep.2018.03.050

9. Lam SW, Cleton-Jansen AM, Cleven AHG, et al. Molecular analysis of gene fusions in bone and soft tissue tumors by anchored multiplex PCR-based targeted next-generation sequencing. J Mol Diagn. 2018 Sep;20(5):653-663. doi:10.1016/j.jmoldx.2018.05.007

10. Roy A, Kumar V, Zorman B, et al. Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. Nat Commun. 2015;6:8891. doi:10.1038/ncomms9891

11. Marino-Enriquez A, Lauria A, Przybyl J, et al. BCOR Internal tandem duplication in high-grade uterine sarcomas. Am J Surg Pathol. 2018;42(3):335-341. doi:10.1097/PAS.0000000000000993

Method Description

RNA-based next-generation sequencing is performed to test for the presence of rearrangements involving targeted regions of 138 fusion genes. See Sarcoma Targeted Gene Fusion Panel and Common BCOR Tandem Duplications for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)

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

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.

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.