Test Id : SARCP
Sarcoma Targeted Gene Fusion/Rearrangement Panel, Next-Generation Sequencing, Tumor
Useful For
Suggests clinical disorders or settings where the test may be helpful
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
Provides information that may help with selection of the correct genetic test or proper submission of the test request
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.
Additional Tests
Lists tests that are always performed, at an additional charge, with the initial tests.
Test Id | Reporting Name | Available Separately | Always Performed |
---|---|---|---|
SLIRV | Slide Review in MG | No, (Bill Only) | Yes |
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
When this test is ordered, slide review will always be performed at an additional charge.
Method Name
A short description of the method used to perform the test
Polymerase Chain Reaction (PCR)-based Next-Generation Sequencing (NGS)
NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.
Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test
Aliases
Lists additional common names for a test, as an aid in searching
Fusion
Fusion panel
Gene fusion
Gene fusion targets
Gene rearrangement
Next Gen Sequencing Test
Oncology panel
Rearrangement
Rearrangement panel
Sarcoma
Sarcoma fusion
Sarcoma panel
SARCP
Transcript variant
NAB2
STAT6
USP6
BCOR
EWSR1
FLI1
SS18
SSX1
SSX2
PAX3
PAX7
FOXO1
YWHAE
NUTM1
HEY1
NCOA2
ALK
JAZF1
SUZ12
DDIT3
FUS
CREB3L1
PDGFB
TFE3
ATF1
ERG
FEV
WT1
Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
When this test is ordered, slide review will always be performed at an additional charge.
Specimen Type
Describes the specimen type validated for testing
Varies
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
Defines the optimal specimen required to perform the test and the preferred volume to complete testing
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.
Special Instructions
Library of PDFs including pertinent information and forms related to the test
Forms
If not ordering electronically, complete, print, and send a Oncology Test Request (T729) with the specimen.
Specimen Minimum Volume
Defines the amount of sample necessary to provide a clinically relevant result as determined by the testing laboratory. The minimum volume is sufficient for one attempt at testing.
See Specimen Required
Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected
Specimens that have been decalcified (all methods) Specimens that have not been formalin-fixed, paraffin-embedded Bone marrow in EDTA | Reject |
Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included
Specimen Type | Temperature | Time | Special Container |
---|---|---|---|
Varies | Ambient (preferred) | ||
Refrigerated | |||
Frozen |
Useful For
Suggests clinical disorders or settings where the test may be helpful
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
Provides information that may help with selection of the correct genetic test or proper submission of the test request
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
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.
When this test is ordered, slide review will always be performed at an additional charge.
Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test
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
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.
An interpretive report will be provided.
Interpretation
Provides information to assist in interpretation of the test results
The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.
Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances
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
Recommendations for in-depth reading of a clinical nature
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
Describes how the test is performed and provides a method-specific reference
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)
PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information
Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.
Varies
Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.
Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded
Performing Laboratory Location
Indicates the location of the laboratory that performs the test
Fees :
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.
- Authorized users can sign in to Test Prices for detailed fee information.
- Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
- Prospective clients should contact their account representative. For assistance, contact Customer Service.
Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.
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
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.
CPT codes are provided by the performing laboratory.
CPT codes are provided by the performing laboratory.
81456
88381
LOINC® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.
Test Id | Test Order Name | Order LOINC Value |
---|---|---|
SARCP | Sarcoma Targeted Gene Fusion Panel | 95124-4 |
Result Id | Test Result Name |
Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
|
---|---|---|
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 |