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Test Code NONCR Neuro-Oncology Gene Panel, Rearrangements Only, Tumor


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


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.


Useful For

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

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. 

Additional Tests

Test ID Reporting Name Available Separately Always Performed
SLIRV Slide Review in MG No, (Bill Only) Yes

Testing Algorithm

When this test is ordered, slide review will always be performed at an additional charge.

Method Name

Targeted Polymerase Chain Reaction (PCR)-Based Next-Generation Sequencing (NGS)

Reporting Name

Neuro-Onc Panel, Fusions Only

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

Specimens that have been decalcified (all methods)
Specimens that have not been formalin-fixed, paraffin-embedded
Extracted nucleic acid (DNA/RNA)		 Reject

Clinical Information

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

An interpretive report will be provided.

Interpretation

The interpretation of molecular biomarker analysis includes an overview of the results and the associated diagnostic, prognostic, and therapeutic implications.

Cautions

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

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

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.

Day(s) Performed

Monday through Friday

Report Available

12 to 20 days

Specimen Retention Time

FFPE tissue block: Unused portions of blocks will be returned 10 to 14 days after testing is complete; FFPE tissue slides: Unused slides are stored indefinitely and not returned

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

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

81456

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NONCR Neuro-Onc Panel, Fusions Only 73977-1

 

Result ID Test Result Name Result LOINC Value
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

NY State Approved

Yes