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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


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

5. Diagnosis, potential diagnosis, or differential diagnosis



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. Tissue blocks are preferred over tissue slides.

 

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

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.


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 within 89 genes associated with tumors of the central nervous system, gene fusions within 1445 genes, known abnormal transcript variants in the MET and EGFR genes, and BCOR exon 15 internal tandem duplications. See Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel and Targeted Gene Fusions for the Neuro-Oncology Expanded Panel 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.

 

Standalone orderable tests will only be used if the specimen received is insufficient for both portions of testing. Appropriate test code will be added per the direction of testing prioritization.

 

This test includes DNA mutation and RNA fusion analyses. A reflex test is added only when there is insufficient specimen for both test components. Indicate the preferred prioritization of testing on paperwork. If the specimen is insufficient for all portions of testing, the lab will use this prioritization to select the appropriate reflex test ID, reducing communication delays. If additional tests are ordered on same specimen, include them in the prioritization preferences.

Reporting Name

Neuro-Onc Expanded Panel

Specimen Type

Varies

Specimen 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

DNA validation studies demonstrated concordance between this test and the reference method for detection of SNV and deletions-insertions (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.

 

RNA validation studies demonstrated concordance between this test and the reference method for detection of gene fusions is 96.6% (256/265). No gene fusions were detected in 14 normal tissues, and no gene fusions were detected in the negative control sample (100% specificity).

 

To ensure this assay detects variants based on established sensitivity, 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

Tissue blocks: Unused portions of blocks will be returned; Tissue slides: Unused slides are stored for at least 5 years; Extracted DNA/RNA: 3 months

Performing Laboratory

Mayo Clinic Laboratories in Rochester

CPT Code Information

 

81455

81456

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

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
NONCM Neuro-Onc Panel, Mutations Only Yes No
MCRSP MayoComplete Targeted RNAseq Panel Yes No