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Test Code NONCP Neuro-Oncology Expanded Gene Panel with Rearrangement, 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 20% tumor nuclei.

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

-Minimum amount of tumor area: tissue 72 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 specimen preparation guidance, see Tissue Requirement for Solid Tumor Next-Generation Sequencing. For this test, 6 mm x 6 mm x 10 slides are preferred: approximate/equivalent to 360 mm(2); with the minimum acceptable of 4 mm x 4 mm x 10 slides: approximate/equivalent to 144 mm(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:

1. 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.

2. Unused unstained slides will not be returned.


Forms

If not ordering electronically, complete, print, and send an Oncology Test Request (T729) with the specimen.

Useful For

Identifying mutations and rearrangements that may support a diagnosis or help determine prognosis for patients with CNS tumors

 

Identifying specific mutations and 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 for microsatellite instability (MSI) status, somatic mutations, and rearrangements (fusions and abnormal transcript variants) involving 160 genes associated with tumors of the central nervous system. This panel includes a DNA subpanel for the detection of sequence alterations in 89 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 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 counseling.

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.

Reporting Name

Neuro-Onc Expanded Panel

Specimen Type

Varies

Specimen Minimum Volume

See Specimen Required

Specimen Stability Information

Specimen Type Temperature Time Special Container
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

Reference Values

An interpretive report will be provided.

Supportive Data

Performance Characteristics

The limit of detection for calling a somatic variant (single nucleotide variants [SNV] and deletions-insertions [delins]) is 5% variant allele frequency (VAF) and having 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) of variants, respectively. Concordance for the detection of delins was 98.9% (186/188) in variants 1 to 10 base pairs (bp) in size, 95.8% (23/24) in variants 11 to 50 bp in size, and 88.9% (8/9) in variants 51 to 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 status was observed between this test and the reference method.

 

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 20% tumor cells.

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

CPT Code Information

81455

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NONCP Neuro-Onc Expanded Panel 73977-1

 

Result ID Test Result Name Result LOINC Value
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