Test Id : NONCR
Neuro-Oncology Gene Panel, Rearrangements Only, Tumor
Useful For
Suggests clinical disorders or settings where the test may be helpful
Identifying rearrangements that may support a diagnosis or help determine prognosis for patients with central nervous system tumors
Identifying rearrangements within genes known to be associated with response or resistance to specific cancer therapies
This test is not intended for use for hematological malignancies.
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 next-generation sequencing to evaluate somatic rearrangements (fusions and abnormal transcript variants) associated with tumors of the central nervous system. This RNA panel includes detection of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal transcript variants. See RNA Targeted Gene Fusions and Abnormal Transcript Variants 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. This test only evaluates targeted rearrangements (fusions and abnormal transcript variants); this test does not detect somatic DNA mutations.
Highlights
This next-generation sequencing tumor profiling assay interrogates targeted rearrangements across 81 genes associated with central nervous system tumors to assess for the presence of somatic rearrangements, such as gene fusions including KIAA1549::BRAF, ZFTA::RELA (previously C11orf95::RELA), and EGFR transcript variants (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.
Method Name
A short description of the method used to perform the test
Targeted 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.
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
BRAF
Brain tumor
Central nervous system (CNS) cancers
EGFR
KIAA1549
Next Gen Sequencing Test
NGS
Oncology panel
RELA
ZFTA
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
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 10% tumor nuclei.
-Preferred amount of tumor area with sufficient percent tumor nuclei: tissue 144 mm(2)
-Minimum amount of tumor area: tissue 36 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 15 unstained slides and must have adequate percent tumor nuclei.
-Tissue fixation: 10% neutral buffered formalin, not decalcified
-For this test, at least 6 mm x 6 mm areas on 4 unstained slides is preferred: this is approximately equivalent to 144 mm(2). The minimum acceptable area is 6 mm x 6 mm on 1 unstained slides: approximately equivalent to 36 mm(2). For specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing.
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 Hematoxylin and eosin-stained and 15 unstained
Collection Instructions:
Submit the followings slides:
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.
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. 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 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
Identifying rearrangements that may support a diagnosis or help determine prognosis for patients with central nervous system tumors
Identifying rearrangements within genes known to be associated with response or resistance to specific cancer therapies
This test is not intended for use for hematological malignancies.
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 next-generation sequencing to evaluate somatic rearrangements (fusions and abnormal transcript variants) associated with tumors of the central nervous system. This RNA panel includes detection of rearrangements in 81 genes, including 104 known gene fusions and 29 known abnormal transcript variants. See RNA Targeted Gene Fusions and Abnormal Transcript Variants 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. This test only evaluates targeted rearrangements (fusions and abnormal transcript variants); this test does not detect somatic DNA mutations.
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 biomarkers, including clinically relevant gene fusions, have been incorporated in the World Health Organization classification of central nervous system (CNS) tumors. Additionally, there are clinically available targeted therapies for patients with certain CNS tumor types harboring specific fusions. This test evaluates targeted regions across 81 genes associated with a variety of adult and pediatric-type CNS tumors for the presence of somatic rearrangements (fusions and abnormal transcript variants) including, but not limited to, KIAA1549::BRAF and ZFTA::RELA (previously C11orf95::RELA) fusions, and EGFR transcript variants (eg, EGFR vIII).
See RNA Targeted Gene Fusions and Abnormal Transcript Variants 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
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 does not include evaluation of somatic DNA mutations.
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.
Variants of uncertain significance may be identified.
A negative result does not rule out the presence of a fusion that may be present below the limits of detection of this assay. The analytical sensitivity of this assay is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content.
Detection of fusion transcripts (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.
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.
The presence or absence of a variant may not be predictive of response to therapy in all patients.
Rare alterations (ie, polymorphisms) may be present that could lead to false-negative or false-positive results.
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 formalin-fixed, paraffin-embedded tissues; other fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure.
Genes may be added or removed based on updated clinical relevance.
Supportive Data
Performance Characteristics
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%.
To ensure accuracy, this test will be performed on cases estimated by a pathologist to have at least 10% tumor cells.
Clinical Reference
Recommendations for in-depth reading of a clinical nature
1. WHO Classification of Tumours Editorial Board: Central Nervous System Tumours. 5th ed. World Health Organization; 2021. WHO Classification of Tumours. Vol 6.
2. Nabors LB, Portnow J, Ammirati M, et al. Central nervous system cancers version 1.2015. J Natl Compr Canc Netw. 2015;13(10);1191-1202
Method Description
Describes how the test is performed and provides a method-specific reference
Polymerase chain reaction amplification-based next-generation sequencing 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 RNA Targeted Gene Fusions and Abnormal Transcript Variants for details regarding the targeted gene regions identified by this test.(Unpublished Mayo method)
A pathology review and macro dissection to enrich for tumor cells is 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.
81456
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 |
|---|---|---|
| NONCR | Neuro-Onc Panel, Fusions Only | 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.
|
|---|---|---|
| 606325 | Result Summary | 50397-9 |
| 606326 | Result | 82939-0 |
| 606327 | Interpretation | 69047-9 |
| 606328 | Additional Information | 48767-8 |
| 606329 | Method | 85069-3 |
| 606330 | Disclaimer | 62364-5 |
| 606331 | Specimen | 31208-2 |
| 606332 | Source | 31208-2 |
| 606454 | Tissue ID | 80398-1 |
| 606333 | Released By | 18771-6 |