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HelpTest ID: 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 the example in this document, 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.
Method Name
Sequence Capture and Targeted Polymerase Chain Reaction (PCR)-Based Next-Generation Sequencing (NGS)
Reporting Name
Neuro-Onc Expanded PanelSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Ambient (preferred) | ||
| Refrigerated | |||
Clinical Information
Molecular biomarkers, including clinically relevant gene mutations (ie, sequence variants) and fusions, have been incorporated in the World Health Organization classification of central nervous system (CNS) tumors. This test evaluates targeted regions across 160 genes associated with a variety of adult and pediatric-type CNS tumors for the presence of somatic mutations and rearrangements (fusions and abnormal transcript variants) including, but not limited to, mutations in IDH1/2, TERT promoter, ATRX, TP53, H3-3A (previously H3F3A), H3C2/H3C3 (previously HIST1H3B/C), BRAF, FGFR1, NF1 and SMARCB1, and KIAA1549::BRAF and ZFTA::RELA (previously C11orf95::RELA) fusions, and EGFR transcript variants (eg, EGFR vIII).
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.
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.
Clinical Reference
1. Schwartzentruber J, Korshunov A, Liu XY, et al: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 2012 Jan;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 Jan;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 Aug;45(8):927-932
4. Brennan CW, Verhaak RG, McKenna A, et al: The somatic genomic landscape of glioblastoma. Cell. 2013 Oct;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 Mar;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 Mar;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 Mar;46(5):444-450
8. Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, et al: Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N Engl J Med. 2015 Jun;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 25;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 Jan;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 Jan;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. WHO Classification of Tumours Editorial Board: Central Nervous System Tumours. 5th ed. World Health Organization; 2021. WHO Classification of Tumours. Vol 6.
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
Day(s) Performed
Monday through Friday
Report Available
12 to 20 daysTest 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
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 |
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