Test Catalog

Test Id : MCSRC

MayoComplete Comprehensive Sarcoma Panel, Next-Generation Sequencing, Tumor

Useful For
Suggests clinical disorders or settings where the test may be helpful

Primarily for identifying mutations that help in the diagnosis of specific soft tissue and bone tumors (sarcoma)

 

Secondarily for identifying mutations that have therapeutic or prognostic significance

 

Assessment of microsatellite instability for immunotherapy decisions

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the ALK, APC, BAP1, BCOR (exon 15), BRAF, CDKN2A, CTNNB1, DICER1, EED, EGFR, FGFR4, GNA11, GNA14, GNAQ, GNAS, H3-3A, H3-3B, KIT, MDM2, MED12, MYOD1, NF1, PDGFRA, PDGFRB, PTPRD, ROS1, SMARCB1, SUZ12, TERT-promoter, TP53, and TSC2 genes. In addition, this test evaluates 138 gene targets for the presence of somatic gene fusions. It also assesses for microsatellite instability status and BCOR internal tandem duplications. See Targeted Genes and Methodology Details for MayoComplete Sarcoma Panels and Targeted Genes Fusions and Methodology Details for MayoComplete Sarcoma Panel for details regarding the targeted gene regions evaluated by this test.

 

This test is performed to evaluate for somatic mutations within solid tumor samples. It does not assess for germline alterations within the genes listed.

Highlights

This test evaluates formalin-fixed, paraffin-embedded tumor or cytology slides to assist in the diagnosis and management of patients with sarcoma.

Microsatellite instability (MSI) status is determined (microsatellite stable, MSI-High) as part of this test and is often clinically actionable for determining the efficacy of immunotherapy in solid tumors.

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

Sequence Capture and Targeted Next-Generation Sequencing (NGS) and Polymerase Chain Reaction (PCR)-based NGS

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

MayoComplete Sarcoma Panel

Aliases
Lists additional common names for a test, as an aid in searching

ATF1

BCOR

BCOR duplication

BRAF

CREB3L1

DDIT3

ERG

EWSR1

FEV

FLI1

FOXO1

FUS

Fusion

Fusion panel

Gene fusion

Gene fusion targets

Gene rearrangement

HEY1

Internal Tandem Duplication

JAZF1

Microsatellite Instability

MSI

NAB2

NCOA2

Next Gen Sequencing Test

NGS

NUTM1

Oncology panel

PAX3

PAX7

PDGFB

Rearrangement

Rearrangement panel

Sarcoma

Sarcoma fusion

Sarcoma panel

SARCP

SS18

SSX1

SSX2

STAT6

SUZ1

TERT

TERT Promoter

TP53

TFE3

Transcript variant

Tumor Panel

USP6

WT1

YWHAE

Mayo Complete

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

A pathology report (final or preliminary), at minimum containing the following information, must accompany specimen 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 20% tumor nuclei.

-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 360mm(2)

-Minimum amount of tumor area: tissue 72mm(2)

-These amounts are cumulative over up to 15 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 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: Tissue block

Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block with acceptable amount of tumor tissue.

 

Acceptable:

Specimen Type: Tissue slides

Slides: 1 Stained and 15 unstained

Collection Instructions: Submit 1 slide stained with hematoxylin and eosin and 15 unstained, nonbaked slides with 5-micron thick sections of the tumor tissue.

Note: The total amount of required tumor nuclei can be obtained by scraping up to 15 slides from the same block.

Additional Information: Unused unstained slides will not be returned.

 

Specimen Type: Cytology slides (direct smears or ThinPrep)

Slides: 2 to 4 Slides

Collection Instructions: Submit 2 to 4 slides stained and cover slipped with a preferred total of 10,000 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

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

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded, except for cytology slide
Extracted nucleic acid (DNA/RNA)
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

Useful For
Suggests clinical disorders or settings where the test may be helpful

Primarily for identifying mutations that help in the diagnosis of specific soft tissue and bone tumors (sarcoma)

 

Secondarily for identifying mutations that have therapeutic or prognostic significance

 

Assessment of microsatellite instability for immunotherapy decisions

Genetics Test Information
Provides information that may help with selection of the correct genetic test or proper submission of the test request

This test uses targeted next-generation sequencing to evaluate for somatic mutations within the ALK, APC, BAP1, BCOR (exon 15), BRAF, CDKN2A, CTNNB1, DICER1, EED, EGFR, FGFR4, GNA11, GNA14, GNAQ, GNAS, H3-3A, H3-3B, KIT, MDM2, MED12, MYOD1, NF1, PDGFRA, PDGFRB, PTPRD, ROS1, SMARCB1, SUZ12, TERT-promoter, TP53, and TSC2 genes. In addition, this test evaluates 138 gene targets for the presence of somatic gene fusions. It also assesses for microsatellite instability status and BCOR internal tandem duplications. See Targeted Genes and Methodology Details for MayoComplete Sarcoma Panels and Targeted Genes Fusions and Methodology Details for MayoComplete Sarcoma Panel for details regarding the targeted gene regions evaluated by this test.

 

This test is performed to evaluate for somatic mutations within solid tumor samples. It does not assess for germline alterations within the genes listed.

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. Microsatellite instability status is an increasingly important biomarker for determining effective immunotherapeutic treatment options for patients with solid tumors.

 

This next-generation sequencing assay interrogates targeted regions for the presence of somatic mutations, chromosomal translocations, interstitial deletions, and inversions that lead to gene fusions that are common in various sarcomas.

 

See Targeted Genes and Methodology Details for MayoComplete Sarcoma Panels and Targeted Genes Fusions and Methodology Details for MayoComplete Sarcoma Panel for details regarding the targeted gene regions evaluated 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 test cannot differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

 

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, that interfere with obtaining a high-quality RNA specimen despite rapid preservation.

 

DNA variants and fusions of uncertain significance may be identified.

 

A negative result does not rule out the presence of a variant or fusion that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X in a sample with 20% or more tumor content.

 

Point mutations and small insertion/deletion mutations will be detected in the ALK, APC, BAP1, BCOR (exon 15), BRAF, CDKN2A, CTNNB1, DICER1, EED, EGFR, FGFR4, GNA11, GNA14, GNAQ, GNAS, H3-3A, H3-3B, KIT, MDM2, MED12, MYOD1, NF1, PDGFRA, PDGFRB, PTPRD, ROS1, SMARCB1, SUZ12, TERT-promoter, TP53, and TSC2 genes. This test may detect single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants in any of the genes tested.

 

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 gene fusion target list of interest.

 

Rare alterations (ie, polymorphisms) may be present that could lead to false-negative or false-positive results.

 

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.

 

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

 

Test results should be interpreted in the context of clinical, tumor sampling, histopathological, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion. Misinterpretation of results may occur if the information provided is inaccurate and/or incomplete.

 

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.

Supportive Data

Performance Characteristics

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delins, formerly indels]) is 5% variant allele frequency and having at least 500x deduplicated coverage.

 

Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins is 99.7% (699/701) and 96.6% (226/234) of variants, respectively. Concordance for the detection of delins was 98.9% (186/188) in variants 1-10 base pair (bp) in size, 95.8% (23/24) in variants 11-50 bp in size, and 88.9% (8/9) in variants 51-200 bp in size.

 

Microsatellite instability (MSI) evaluation is accurate at a tumor purity of at least 10% for colorectal tumors and 20% for other tumor types. During verification studies, 98% (200/204) concordance for MSI status was observed between this test and the reference method.

 

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

 

To ensure accuracy, this test will be performed on cases that are estimated by a pathologist to have at least 20% tumor cells.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. US Food and Drug Administration (FDA): Table of Pharmacogenomic Biomarkers in Drug Labeling. FDA; Updated March 29, 2022, Accessed August 3, 2022. Available at www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling

2. 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

3. Jo VY, Fletcher CD: WHO classification of soft tissue tumours: an update based on the 2013 (4th) edition. Pathology. 2014 Feb;46(2):95-104. doi: 10.1097/PAT.0000000000000050

4. 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

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

6. Podnar J, Deiderick H, Huerta G, Hunicke-Smith S: Next-generation sequencing RNA-seq library construction. Curr Protoc Mol Biol. 2014 Apr 14;106:4.21.1-19. doi: 10.1002/0471142727.mb0421s106

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

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

9. Gao Q, Liang WW, Foltz SM, et al: Driver fusions and their implications in the development and treatment of human cancers. Cell Rep 2018 Apr 3;23(1):227-238e3. doi: 10.1016/j.celrep.2018.03.050

10. 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

11. 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

12. 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

13. Marcus L, Lemery SJ, Keegan P, Pazdur R: FDA Approval Summary: Pembrolizumab for the treatment of microsatellite instability-high solid tumors. Clin Cancer Res. 2019 Jul 1;25(13):3753-3758. doi: 10.1158/1078-0432.CCR-18-4070

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

Next-generation sequencing is performed to determine microsatellite instability (MSI) status and evaluate the presence of a mutation in targeted regions of the ALK, APC, BAP1, BCOR (exon 15), BRAF, CDKN2A, CTNNB1, DICER1, EED, EGFR, FGFR4, GNA11, GNA14, GNAQ, GNAS, H3-3A, H3-3B, KIT, MDM2, MED12, MYOD1, NF1, PDGFRA, PDGFRB, PTPRD, ROS1, SMARCB1, SUZ12, TERT-promoter, TP53, and TSC2 genes. RNA-based next-generation sequencing is performed to test for the presence of rearrangements involving targeted regions of 138 fusion. See Targeted Genes and Methodology Details for MayoComplete Sarcoma Panels and Targeted Genes Fusions and Methodology Details for MayoComplete Sarcoma Panel for details regarding the targeted gene regions evaluated by this test. genes.(Unpublished Mayo method)

 

A pathology review and macro dissection to enrich for tumor cells are performed prior to slide scraping

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.

12 to 20 days

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

FFPE tissue block: Unused portions of blocks will be returned within 10 to14 days after testing is complete; FFPE tissue/cytology slides: Unused tissue slides are stored indefinitely; Digital images are obtained and stored for all slides used in testing.

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.

88381–Microdissection, manual

81455

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
MCSRC MayoComplete Sarcoma 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.
617849 Result 82939-0
617850 Interpretation 69047-9
617851 Additional Info 48767-8
617852 Specimen 31208-2
617853 Tissue ID 80398-1
617854 Method 85069-3
617855 Disclaimer 62364-5
617856 Released By 18771-6

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

Test Update Resources

Change Type Effective Date
New Test 2022-10-24