Test Catalog

Test Id : MCSTP

MayoComplete Solid Tumor Panel, Next-Generation Sequencing, Tumor

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

Assisting in tumor profiling for diagnosis, predicting prognosis, and identifying targeted therapies for the treatment and management of patients with solid tumors

 

Identifying somatic alterations including single nucleotide variants, small deletions/insertions, gene amplifications, fusions, and splice variants in genes known to be associated with the tumorigenesis of solid tumors

 

Assessment of microsatellite instability and tumor mutational burden status

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 estimate tumor mutational burden (TMB), determine microsatellite instability (MSI) status, and identify somatic sequence variants, gene amplifications, fusions, and specific transcript variants in solid tumors. This panel includes a DNA subpanel for the detection of sequence alterations in 515 genes and amplification of 59 genes as well as an RNA subpanel for the detection of fusions involving 55 genes and specific splice variants involving EGFR, AR, and MET. See Genes Interrogated by MayoComplete Solid Tumor Panel for details regarding genes interrogated by this test.

 

Note: This test is performed to evaluate for somatic (ie, tumor-specific) alterations within the genes listed. Although germline (ie, inherited) alterations may be detected, this test cannot distinguish between germline and somatic alterations with absolute certainty. Follow-up germline testing using whole blood can be performed for confirmation of suspected clinically relevant germline alterations. Germline testing should be performed along with genetic counselling.

Highlights

In addition to single nucleotide variants (SNV) and small insertions/deletions sequence variants, this test also identifies gene amplifications, fusions, and splice variants. Tumor mutational burden (TMB) and microsatellite instability (MSI) status are also determined as part of this test and are often clinically actionable for determining the efficacy of immunotherapy in solid tumors.

 

For each case, a quantitative value for TMB and qualitative assessments for TMB (TMB-Low, TMB-High) and MSI (MSS, MSI-H) are reported.

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 to ensure specimen adequacy.

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 Solid Tumor Panel

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

Cancer NGS Panel

Cancer Panel

Fusion

Fusion panel

Gene fusion

Gene fusion targets

Gene rearrangement

Large Cancer Panel

Large Somatic NGS Cancer Panel

Mayo Clinic Large Cancer Panel

MCSTP

Next Gen Sequencing Test

NGS

Oncology panel

Rearrangement

Sequence variant

Splice variant

Single nucleotide variant

Transcript variant

TSO500

Comprehensive Genomic Profiling

Copy number variant

CNV

Gene amplification

Microsatellite Instability

MSI

Tumor mutational burden

TMB

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 to ensure specimen adequacy.

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 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. However, 40% tumor is preferred.

-Preferred amount of tumor area: 720 mm(2) tissue on up to 20 unstained slides

-Minimum amount of tumor area: 192 mm(2) tissue on up to 20 unstained slides

-Tissue fixation: 10% neutral buffered formalin, not decalcified

-For this test, at least 6mm x 6mm areas on 20 unstained slides is preferred: this is approximately equivalent to 720 mm(2). The minimum acceptable area is 3.1mm x 3.1mm on 20 unstained slides: approximately equivalent to 192 mm(2).

 

Preferred:

Specimen Type: Tissue block

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

 

Acceptable:

Specimen Type: Tissue slide

Slides: 1 stained and 20 unstained

Collection Instructions: Submit 1 hematoxylin and eosin (H and E) stained slide and 20 unstained, nonbaked 5-micron thick sections

Note: The total amount of required tumor can be obtained by scraping up to 20 slides from the same block.

 

Specimen Type: Cytology slides (direct smears or ThinPrep)

Slides: 2 to 6 slides

Collection Instructions: Submit 2 to 6 stained and cover slipped slides with a preferred total of 10,000 nucleated cells or a minimum of at least 6,000 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. An image of the slides will be stored per regulatory requirements.

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

Decalcified specimens
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

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

Assisting in tumor profiling for diagnosis, predicting prognosis, and identifying targeted therapies for the treatment and management of patients with solid tumors

 

Identifying somatic alterations including single nucleotide variants, small deletions/insertions, gene amplifications, fusions, and splice variants in genes known to be associated with the tumorigenesis of solid tumors

 

Assessment of microsatellite instability and tumor mutational burden status

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 estimate tumor mutational burden (TMB), determine microsatellite instability (MSI) status, and identify somatic sequence variants, gene amplifications, fusions, and specific transcript variants in solid tumors. This panel includes a DNA subpanel for the detection of sequence alterations in 515 genes and amplification of 59 genes as well as an RNA subpanel for the detection of fusions involving 55 genes and specific splice variants involving EGFR, AR, and MET. See Genes Interrogated by MayoComplete Solid Tumor Panel for details regarding genes interrogated by this test.

 

Note: This test is performed to evaluate for somatic (ie, tumor-specific) alterations within the genes listed. Although germline (ie, inherited) alterations may be detected, this test cannot distinguish between germline and somatic alterations with absolute certainty. Follow-up germline testing using whole blood can be performed for confirmation of suspected clinically relevant germline alterations. Germline testing should be performed along with genetic counselling.

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 to ensure specimen adequacy.

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 solid tumor malignancies. Molecular genetic profiling is often needed to identify targets amenable to targeted therapies and to minimize treatment costs and therapy-associated risks. Tumor mutational burden (TMB) and microsatellite instability (MSI) status are increasingly important biomarkers for determining effective immunotherapeutic treatment options for patients with solid tumors.(1,2)

 

In addition to providing therapeutic insight, molecular profiling of tumors often provides prognostic and diagnostic information. Next-generation sequencing is an accurate, cost-effective method to identify variants 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 or cytology specimens to assess for Tier I and Tier II variants in 515 genes known to be associated with solid tumors.(3)

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

Next-generation sequencing is performed to estimate tumor mutational burden (TMB) and microsatellite instability (MSI) status, somatic sequence variants, gene amplifications, fusions, and specific transcript variants in solid tumors. This test detects single nucleotide variants and small insertions and deletion within 515 genes, amplification of 59 genes, gene fusions involving 55 genes, and splice variants involving EGFR, AR, and MET.

 

See Genes Interrogated by MayoComplete Solid Tumor Panel for details regarding genes interrogated by this test.

 

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.

 

This test does not differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

 

This test does not detect large structural variants, copy number changes, or insertions, deletions, or duplications greater than approximately 20 base pairs in size.

 

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

 

A negative (ie, wildtype) result does not rule out the presence of an alteration that may be present but below the limits of detection of this assay.

 

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

 

A list of genomic regions in the DNA panel that have insufficient coverage to reliably detect single nucleotide variants and small deletions/insertions are listed in MayoComplete Solid Tumor Panel DNA Panel Excluded DNA Regions.

Supportive Data

Performance Characteristics

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and small deletions-insertions [delins]) is 2% variant allele frequency (VAF) having at least 150X median exon coverage depth. To ensure accuracy, this test will be performed on cases that are estimated by a pathologist to have 20% or more tumor cells, however, for optimal performance of this assay, a tumor purity of 40% is recommended.

 

Verification studies demonstrated concordance between this test and the reference method for detection of SNV and delins in 98.8% (503/509) and 98.6% (294/298) of variants, respectively. Detection accuracy of delins was 99.3% (277/279) in variants 1 to 10 base pairs (bp) in size, 93.3% (14/15) in variants 11 to 20 bp in size, and 75.0% (3/4) in variants greater than 20 bp in size.

 

Gene amplification is identified at a 2.2x fold change based on the normalized read depth over the copy number variant (CNV) target divided by the normalized read depth of the inferred diploid genome. Gene amplification detection is most accurate at 40% or more tumor cells. For gene amplifications, overall sensitivity was 98.7% (81/82), specificity was 92.3% (24/26), and concordance was 95.3% (105/108) during verification studies.

 

Of the 130 microsatellite sites available for evaluation in this assay, at least 20% of sites are required to be unstable to classify the case as MSI-High. Microsatellite instability (MSI) evaluation is most accurate at a tumor purity of 40% or more, although, highly unstable tumors may be detectable at 20% tumor. During verification studies, 100% concordance was observed between this test and orthogonal methods used to detect MSI status.

 

Tumor mutational burden (TMB) was measured as mutations per megabase (Mb) for regions with greater than 50X coverage. When TMB scores were classified as TMB-Low (<10 mut/Mb) or TMB-High (> or =10 mut/Mb), 83% (50/60) concordance was achieved between this test and orthogonal assays detecting TMB status. Of the 10 samples with conflicting qualitative classification (ie, TMB-Low or TMB-High), the TMB quantitative values were near the 10 mut/Mb cutoff (3.9-11.8 mut/Mb). TMB values are most accurate at greater than or equal to 40% tumor purity.

 

Fusions are detected with the presence of 3 or more supporting reads passing pipeline filters and splice variants with 10 or more supporting reads. For fusions and splice variants, overall sensitivity was 98.0% (151/154), specificity was 94.8% (91/96), and overall concordance was 96.8% (242/250). Fusion and splice variant detection are most accurate at greater than or equal to 20% tumor purity.

 

Table 1. Analytical Sensitivity

Variant type

Threshold for positivity

Recommended tumor purity

SNV

> or =2% VAF > or =150X median exon coverage

> or =20%

DELIN

> or =2% VAF, < or =20 bp

> or =20%

Gene amplification

> or =2.2X fold change

> or =40%

MSI status

> or =20% sites unstable= MSI-H

> or =40%

TMB status

> or =10 variants per megabase= TMB-H

> or =40%

Fusion

> or =3 supporting reads

> or =20%

Splice variant

> or =10 supporting reads

> or =20%

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

1. Subbiah V, Solit DB, Chan TA, Kurzrock R: The FDA approval of pembrolizumab for adult and pediatric patients with tumor mutational burden (TMB) > or =10: a decision centered on empowering patients and their physicians. Ann Oncol. 2020 Sep;31(9):1115-1118. doi: 10.1016/j.annonc.2020.07.002

2. 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

3. Li MM, Datto M, Duncavage EJ, et al: Standards and guidelines for the interpretation and reporting of sequence variants in cancer: A joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diag. 2017 Jan;19(1):4-23. doi: 10.1016/j.jmoldx.2016.10.002

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 estimate tumor mutational burden (TMB) and microsatellite instability (MSI) status, somatic sequence variants, gene amplifications, fusions, and specific transcript variants in solid tumors. This test detects single nucleotide variants and small insertions and deletion within 515 genes, amplification of 59 genes, gene fusions involving 55 genes, and splice variants involving EGFR, AR, and MET.(Instruction manual: TruSight Oncology 500 High-Throughput. Illumina; 11/2020)

 

See Genes Interrogated by MayoComplete Solid Tumor Panel for details regarding genes interrogated by this test.

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

Supplemental

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.

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

FFPE tissue: Unused portions of FPPE blocks will be returned. Unused, unstained slides: 5 years; Stained slides: 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

81479 (if appropriate for gov't payors)

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
MCSTP MayoComplete Solid Tumor Panel 73977-1
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.
610425 Result 82939-0
610426 Interpretation 69047-9
610427 Additional Information 48767-8
610428 Clinical Trials 82786-5
610429 Variants of Uncertain Significance 93367-1
610430 Specimen 31208-2
610431 Tissue ID 80398-1
610432 Method 85069-3
610433 Disclaimer 62364-5
610434 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