Test Catalog

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’s 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 in Special Instructions 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.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Method Name
A short description of the method used to perform the test

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

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Sarcoma Targeted Gene Fusion Panel

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 Oncology Somatic NGS Testing 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 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).

 

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

See Specimen Required

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Other Decalcified specimens; bone marrow in EDTA

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)
Frozen
Refrigerated

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’s 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 in Special Instructions 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 diagnosis, prognosis, and therapeutic management of patients. 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 Sarcoma Targeted Gene Fusion Panel in Special Instructions 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

An interpretive report will be provided.

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, indels, 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 1 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 PCR 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 a number of 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 but there are sometimes 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 (FFPE) and cytology samples (86 fusion positive and 25 fusion negative). The NGS assay results were confirmed by RT-PCR and FISH 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;2:475-482. 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;46:95-104. 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;64:2-11. doi: 10.1111/his.12267

4. Quesada J, Amato R: The Molecular Biology of Soft-Tissue Sarcomas and Current Trends in Therapy. Sarcoma 2012:1-15. 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 106:2014;unit 4.21:1-19

6. Mertens F, Tayebwa J: Evolving techniques for gene fusion detection in soft tissue tumours. Histopathology 2014;64:151-162. 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;471:243-255

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;23:227-238. 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;20:653-663. 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 Nov 17;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 Mar;42(3):335-341. doi: 10.1097/PAS.0000000000000993

Special Instructions
Library of PDFs including pertinent information and forms related to the test

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 in Special Instructions 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

No

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.

Monday through Friday

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.

14 to 21 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

Unused portions of blocks will be returned to client. Unused slides are stored indefinitely.

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

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 Regional Manager. 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. This test 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.

81455

Slide Review

88381-Microdissection, manual

 

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports