Test Catalog

Test Id : NONCP

Neuro-Oncology Expanded Gene Panel with Rearrangement, Tumor

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

Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS)

 

Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS

 

Identifying specific mutations and rearrangements within genes known to be associated with response or resistance to specific cancer therapies

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 and rearrangements (fusions and abnormal transcript variants) involving 187 genes associated with tumors of the central nervous system. This panel includes a DNA subpanel for the detection of sequence alterations in 118 genes and an RNA subpanel for the detection of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal transcript variants. See Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel and RNA Targeted Gene Fusions and Abnormal Transcript Variants in Special Instructions for details regarding the targeted gene regions identified by this test.

 

Of note, this test is performed to evaluate for somatic (ie, tumor-specific) mutations 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 non-neoplastic (normal) tissue can be performed for confirmation of suspected clinically relevant germline alterations. Germline testing should be performed along with genetic counselling.

Highlights

This next-generation sequencing tumor profiling assay interrogates targeted gene regions and rearrangements across 187 genes associated with central nervous system tumors to assess for the presence of somatic mutations and rearrangements, including mutations in IDH1/2, TERT, ATRX, TP53, H3F3A, HIST1H3B/C, BRAF, SMARCB1, and SMARCA4, and rearrangements involving RELA, BRAF, and EGFR (eg, EGFR vIII).

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 (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

Neuro-Onc Expanded Panel

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

ATRX

BRAF

Brain tumor

Central nervous system (CNS) cancers

EGFR

H3F3A

HIST1H3B

HIST1H3C

IDH1

IDH2

Next Gen Sequencing Test

NGS

Oncology panel

RELA

SMARCA4

SMARB1

TERT

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 30% tumor nuclei.

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

-Minimum amount of tumor area: tissue 144 mm(2)

-If ordered in conjunction with CMAPT / Chromosomal Microarray, Tumor, Formalin-Fixed Paraffin-Embedded, the preferred amount of tissue is 430 mm(2), the minimum amount is 180 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. For this test, 6mm x 6mm x 10 slides is preferred: approximate/equivalent to 360 mm(2) with the minimum acceptable of 4mm x 4mm x 10 slides: approximate/equivalent to 144mm(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 slide

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: If the amount of tissue available is close to the minimum required, the ordering provider may be asked to prioritize between the DNA and RNA components of the assay.

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

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 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)
Frozen
Refrigerated

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

Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS)

 

Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS

 

Identifying specific mutations and rearrangements within genes known to be associated with response or resistance to specific cancer therapies

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 and rearrangements (fusions and abnormal transcript variants) involving 187 genes associated with tumors of the central nervous system. This panel includes a DNA subpanel for the detection of sequence alterations in 118 genes and an RNA subpanel for the detection of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal transcript variants. See Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel and RNA Targeted Gene Fusions and Abnormal Transcript Variants in Special Instructions for details regarding the targeted gene regions identified by this test.

 

Of note, this test is performed to evaluate for somatic (ie, tumor-specific) mutations 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 non-neoplastic (normal) tissue 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.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Molecular analysis of biomarkers is increasingly being used in oncology practice to support and guide diagnosis, prognosis, and therapeutic management. Molecular profiling has been incorporated in the World Health Organization classification of central nervous system (CNS) tumors and allows for robust delineation of diagnostic groups characterized by distinct molecular profiles with superior prognostic significance than histopathological classification alone. This test interrogates targeted regions across 187 genes associated with a variety of adult and pediatric CNS tumors to assess for the presence of somatic mutations and rearrangements, including mutations in IDH1/2, TERT, ATRX, TP53, H3F3A, HIST1H3B/C, BRAF, SMARCB1, and SMARCA4, and rearrangements involving RELA, BRAF, and EGFR (eg, EGFR vIII).

 

See Targeted Gene Regions Interrogated by Neuro-Oncology 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 test is not designed to 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 (wild-type) result does not rule out the presence of a mutation or rearrangement that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100 times in a sample with 30% or greater tumor content, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content. 

 

This test does not detect large single or multiexon deletions or duplications or genomic copy number alterations

 

Rare polymorphisms may be present that could lead to false-negative or false-positive results. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion of the findings. Misinterpretation of results may occur if the information provided is inaccurate or incomplete.

 

Genes may be added or removed based on updated clinical relevance. Please refer to the Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel in Special Instructions for the most up to date list of genes included in this test.

Supportive Data

Detection of somatic mutations (DNA): The DNA mutation portion of the assay has been shown to detect more than 97% of single base substitutions, insertions, and deletions within the reportable range of this assay.

 

Detection of fusion transcripts (RNA): The RNA fusion portion of the test exhibited 94.2% sensitivity (49/52) in detecting fusion transcripts (confirmed detection by reverse transcriptase polymerase chain reaction or chromosomal microarray). No fusion transcripts were detected in 25 unique samples (100% specificity compared to chromosomal microarray) resulting in an overall concordance of 96.1%.

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

1. Schwartzentruber J, Korshunov A, Liu XY, et al: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012;482(7384):226-231

2. Zhang J, Wu G, Miller CP, et al: Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet. 2013;45(6):602-612

3. Jones DT, Hutter B, Jager N, et al: Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet. 2013;45(8):927-932

4. Brennan CW, Verhaak RG, McKenna A, et al: The somatic genomic landscape of glioblastoma. Cell. 2013;155(2):462-477

5. Brastianos PK, Horowitz PM, Santagata S, et al: Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations. Nat Genet. 2013;45(3):285-289

6. Clark VE, Erson-Omay EZ, Serin A, et al: Genomic analysis of non-NF2 meningiomas reveals mutations in TRAF7, KLF4, AKT1, and SMO. Science. 2013;339(6123):1077-1080

7. Wu G, Diaz AK, Paugh BS, et al: The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma. Nat Genet. 2014;46(5):444-450

8. Cancer Genome Atlas Research N, Brat DJ, Verhaak RG, et al: Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med. 2015;372(26):2481-2498

9. Eckel-Passow JE, Lachance DH, Molinaro AM, et al: Glioma groups based on 1p/19q, IDH, and TERT promoter mutations in tumors. N Engl J Med. 2015;372(26):2499-2508

10. Ceccarelli M, Barthel FP, Malta TM, et al: Molecular profiling reveals biologically discrete subsets and pathways of progression in diffuse glioma. Cell. 2016;164(3):550-563

11. Pajtler KW, Mack SC, Ramaswamy V, et al: The current consensus on the clinical management of intracranial ependymoma and its distinct molecular variants. Acta Neuropathol 2017;133(1):5-12

12. Northcott PA, Buchhalter I, Morrissy AS, et al: The whole-genome landscape of medulloblastoma subtypes. Nature. 2017;547(7663):311-317

13. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, eds: WHO Classification of Tumours of the Central Nervous System. Revised 4th ed. IARC; 2016

14. Nabors LB, Portnow J, Ammirati M, et al: Central nervous system cancers version 1.2015. J Natl Compr Canc Netw. 2015 Oct;13(10);1191-1202

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 (NGS) is performed to test for the presence of a mutation in approximately 95% of exonic regions and exon/intron boundaries of 118 targeted genes. NGS is performed to test for the presence of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal gene transcript variants. See Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel and RNA Targeted Gene Fusions and Abnormal Transcript Variants 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.

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

Unused portions of blocks will be returned. 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

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
NONCP Neuro-Onc Expanded Panel 38179-8
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.
603048 Result Summary 50397-9
603049 Result 82939-0
603050 Interpretation 69047-9
603051 Additional Information 48767-8
603052 Specimen 31208-2
603053 Source 31208-2
603054 Tissue ID 80398-1
603055 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