26294 Neuro-Oncology Expanded Gene Panel with Rearrangement, Tumor (NONCP)

​ATRX, BRAF, Brain tumor, Central nervous system (CNS) cancers, EGFR, H3F3A, HIST1H3B, HIST1H3C, IDH1, IDH2, Next Gen Sequencing Test, NGS, Oncology panel, RELA, SMARCA4, SMARB1, TERT, H3-3A, H3C2, H3C3, MSI, Microsatellite Instability

NeuroOnc Exp GenPa Tum (NONCP)

TI NONCPSO

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.

Necessary Information:

Pathology report (final or preliminary) at minimum containing the following information must accompany specimen in order 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 in Special Instructions on Mayo Labs website. For this test, 6mm x 6mm x 10 slides is preferred: approximate/equivalent to 360 mm(2) with the minimum acceptable of 4mm x 4mm x 10 slides: approximate/equivalent to 144mm(2). 

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 variant or fusion that may be present below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 5% mutant allele frequency with a minimum coverage of 500X in a sample with 20% or more tumor content. The analytical sensitivity for fusions is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content.

Point mutations and small insertion/deletion mutations will be detected in 89 genes. This test may detect single exon deletions but does not detect multi-exon deletions, duplications, or genomic copy number variants in any of the genes tested

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. Refer to the Targeted DNA Gene Regions Interrogated by Neuro-Oncology Panel for the most up to date list of genes included in this test.

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.

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