Test Catalog

Test Id : MCGST

MayoComplete Gastrointestinal Stromal Tumor (GIST) Panel, Next-Generation Sequencing, Tumor

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

Establishing diagnosis and identifying targeted therapies for patients with gastrointestinal stromal tumors

 

Assessment of microsatellite instability

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 KIT, PDGFRA, APC, BRAF, HRAS, KRAS, NF1, NRAS, PIK3CA, SETD2, and TP53 genes and to determine microsatellite instability status. See Targeted Genes and Methodology Details for MayoComplete Gastrointestinal Stromal Tumor 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

Evaluates formalin-fixed, paraffin-embedded tumor or cytology slides from patients with gastrointestinal stromal tumors for gene mutations to identify candidates for targeted therapy.

 

Microsatellite instability (MSI) status is also 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)

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 GIST Panel

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

BRAF

Gastrointestinal Stromal Tumor

GIST

GST11

GST12

GST13

GST14

GST17

GST18

GST9

KIT

KRAS

Microsatellite Instability

MSI

Next Gen Sequencing Test

NGS

Oncology panel

PIK3CA

PDGFRA

TP53

Tumor panel

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 216mm(2)

-Minimum amount of tumor area: tissue 36mm(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 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 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.

Note: The total amount of required tumor nuclei can be obtained by scraping up to 10 slides from the same block.

Additional Information: Unused unstained slides will not be returned.

 

Specimen Type: Cytology slides (direct smears or ThinPrep)

Slides: 1 to 3 Slides

Collection Instructions: Submit 1 to 3 slides stained and cover slipped 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

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 slides
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

Establishing diagnosis and identifying targeted therapies for patients with gastrointestinal stromal tumors

 

Assessment of microsatellite instability

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 KIT, PDGFRA, APC, BRAF, HRAS, KRAS, NF1, NRAS, PIK3CA, SETD2, and TP53 genes and to determine microsatellite instability status. See Targeted Genes and Methodology Details for MayoComplete Gastrointestinal Stromal Tumor 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

Targeted cancer therapies are defined as antibody or small molecule drugs that block the growth and spread of cancer by interfering with specific cell molecules involved in tumor growth and progression. Multiple targeted therapies have been approved by the US Food and Drug Administration for treatment of specific cancers. Molecular genetic profiling is often needed to identify targets amenable to targeted therapies and to minimize treatment costs and therapy-associated risks. Microsatellite instability status is an important biomarker for determining effective immunotherapeutic treatment options for patients with solid tumors.

 

Next-generation sequencing is an accurate, cost-effective method to identify mutations across numerous genes known to be associated with response or resistance to specific targeted therapies. This test is a single assay that uses formalin-fixed paraffin-embedded tissue to assess for common mutations in the following genes known to be associated with gastrointestinal stromal tumors (GIST): APC, BRAF, HRAS, KIT, KRAS, NF1, NRAS, PDGFRA, PIK3CA, SETD2, and TP53. The results of this test can be useful for assessing prognosis and guiding treatment of individuals with GIST.

 

See Targeted Genes and Methodology Details for MayoComplete Gastrointestinal Stromal Tumor 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.

 

DNA variants of uncertain significance may be identified.

 

A negative result does not rule out the presence of a variant 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 APC, BRAF, HRAS, KIT, KRAS, NF1, NRAS, PDGFRA, PIK3CA, SETD2, and TP53 genes. This test may detect large single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants in any of the genes tested.

 

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

 

The presence or absence of a variant 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 if there is 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), respectively. Concordance for the detection of delins was 98.9% (186/188) in variants 1-10 base pairs (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 assessment was observed between this test and the reference method.

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

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

2. El-Menyar A, Mekkodathil A, Al-Thani H: Diagnosis and management of gastrointestinal stromal tumors: an up-to-date literature review. J Can Res Ther. 2017 Oct-Dec;13(6):889-900. doi: 10.4103/0973-1482.177499

3. 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 status and evaluate the presence of a mutation in all coding regions of the APC, BRAF, HRAS, KIT, KRAS, NF1, NRAS, PDGFRA, PIK3CA, SETD2, and TP53 genes. See Targeted Genes and Methodology Details for MayoComplete Gastrointestinal Stromal Tumor Panel for details regarding the targeted gene regions evaluated by this test.(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 10-14 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
81445

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
MCGST MayoComplete GIST Panel In Process
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.
617873 Result 82939-0
617874 Interpretation 69047-9
617875 Additional Info 48767-8
617876 Specimen 31208-2
617877 Tissue ID 80398-1
617878 Method 85069-3
617879 Disclaimer 62364-5
617880 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