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
Assessing 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, 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.
This test detects BCOR internal tandem duplications of exon 15.
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.
Method Name
A short description of the method used to perform the test
Sequence Capture and Targeted 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
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 Hematology, Oncology, and Hereditary Test Selection 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 360 mm(2)
-Minimum amount of tumor area: tissue 72 mm(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 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: 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 coverslipped 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
Forms
If not ordering electronically, complete, print, and send an 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, 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
Assessing 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, 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.
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 sometimes, there are 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 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 deletion-insertion mutations will be detected in the ALK, APC, BAP1, BCOR, 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 multiexon deletions, duplications, or genomic copy number variants.
Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors including, but not limited to: tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment].(1,2)
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.
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.
Rare polymorphisms may be present that could lead to false-negative or false-positive results.
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 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 to 10 base pair (bp) in size, 95.8% (23/24) in variants 11 to 50 bp in size, and 88.9% (8/9) in variants 51 to 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. Strom SP. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol Med. 2016;13(1):3-11. doi:10.28092/j.issn.2095-3941.2016.0004
2. Spurr L, Li M, Alomran N, et al. Systematic pan-cancer analysis of somatic allele frequency. Sci Rep. 2018;8(1):7735. Published 2018 May 16. doi:10.1038/s41598-018-25462-0
3. US Food and Drug Administration (FDA): Table of Pharmacogenomic Biomarkers in Drug Labeling. FDA; Updated February 10, 2023, Accessed August 1, 2023. Available at www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling
4. Jia Y, Xie Z, Li H. Intergenically spliced chimeric RNAs in cancer. Trends Cancer. 2016;2(9):475-482. doi:10.1016/j.trecan.2016.07.006
5. Jo VY, Fletcher CDM. WHO classification of soft tissue tumours: an update based on the 2013. 4th ed. Pathology. 2014;46(2):95-104. doi:10.1097/PAT.0000000000000050
6. Fletcher CDM. 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
7. 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
8. Podnar J, Deiderick H, Huerta G, Hunicke-Smith S. Next-generation sequencing RNA-seq library construction. Curr Protoc Mol Biol. 2014;106:4.21.1-19. doi:10.1002/0471142727.mb0421s106
9. 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
10. 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
11. 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):227-238e3. doi:10.1016/j.celrep.2018.03.050
12. 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(5):653-663. doi:10.1016/j.jmoldx.2018.05.007
13. 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
14. 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
15. 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;25(13):3753-3758. doi:10.1158/1078-0432.CCR-18-4070
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, 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
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.
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.
81457
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 Information | 48767-8 |
617852 | Specimen | 31208-2 |
617853 | Tissue ID | 80398-1 |
617854 | Method | 85069-3 |
617855 | Disclaimer | 62364-5 |
617856 | Released By | 18771-6 |