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HelpTest 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
A 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 Requirements for Solid Tumor Next-Generation Sequencing. In this document, the sizes are given as 6 mm x 6 mm x 10 slides as preferred: approximate/equivalent to 360 mm(2) and the minimum as 4 mm x 4 mm x 10 slides: approximate/equivalent to 144 mm(2).
Preferred: Submit 2, if available, of the following specimens.
Acceptable: Submit at least one of the following specimens.
Specimen Type: Tissue block
Collection Instructions: Submit a formalin-fixed, paraffin-embedded tissue block with acceptable amount of tumor tissue.
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
10 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.
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 central nervous system 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 alterations and somatic mutations 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.
Special Instructions
Reporting Name
Neuro-Onc Expanded PanelSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Ambient (preferred) | |
| Refrigerated | ||
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.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 daysSpecimen Retention Time
Tissue blocks: Unused portions of blocks will be returned; Tissue slides: Unused slides are stored for at least 5 years; Extracted DNA/RNA: 3 monthsPerforming 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 |