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

Neuro-Oncology Expanded Gene Panel with Rearrangement, Tumor (NONCP)
Test Code: NONCPSO
Synonyms/Keywords

​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

Useful For

Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS)

Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS

Identifying specific mutations and rearrangements within genes known to be associated with response or resistance to specific cancer therapies

Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)
​Tissue Block​FFPE Block with acceptable amount of tumor tissue​Slides:  1 H & E, 15 unstained
Collection Processing Instructions

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 30% tumor nuclei.

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

-Minimum amount of tumor area: tissue 144 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 10 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). 

Specimen Stability Information
Specimen TypeTemperature
​Varies ​ ​​Ambient (preferred)
​Frozen
​Refrigerated
Rejection Criteria
Specimens that have been decalcified (all methods). Specimens that have not been formalin-fixed, paraffin-embedded.
Interference

This test is not designed to differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

DNA variants of uncertain significance may be identified.

A negative (wild-type) result does not rule out the presence of a mutation or rearrangement that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100 times in a sample with 30% or greater tumor content, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content. 

This test does not detect large single or multiexon deletions or duplications or genomic copy number alterations

Rare polymorphisms may be present that could lead to false-negative or false-positive results. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion of the findings. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. 

Performing Laboratory Information
Performing LocationDay(s) Test PerformedAnalytical TimeMethodology/Instrumentation
​Mayo Clinic Laboratories​Monday through Friday; Varies​12-20 daysPolymerase Chain Reaction (PCR)-Based Next-Generation Sequencing (NGS)​
Reference Lab
Reference Range Information
Performing LocationReference Range
​Mayo Clinic Laboratories​An interpretive report will be provided.
Interpretation

​An interpretive report will be provided.

Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
​81455​1
​88381​1
Synonyms/Keywords

​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

Ordering Applications
Ordering ApplicationDescription
If the ordering application you are looking for is not listed, contact your local laboratory for assistance.
Specimen Requirements
Specimen TypePreferred Container/TubeAcceptable Container/TubeSpecimen VolumeSpecimen Minimum Volume
(allows for 1 repeat)
Pediatric Minimum Volume
(no repeat)
​Tissue Block​FFPE Block with acceptable amount of tumor tissue​Slides:  1 H & E, 15 unstained
Collection Processing

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 30% tumor nuclei.

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

-Minimum amount of tumor area: tissue 144 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 10 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). 

Specimen Stability Information
Specimen TypeTemperature
​Varies ​ ​​Ambient (preferred)
​Frozen
​Refrigerated
Rejection Criteria
Specimens that have been decalcified (all methods). Specimens that have not been formalin-fixed, paraffin-embedded.
Interference

This test is not designed to differentiate between somatic and germline alterations. Additional testing may be necessary to clarify the significance of results if there is a potential hereditary risk.

DNA variants of uncertain significance may be identified.

A negative (wild-type) result does not rule out the presence of a mutation or rearrangement that may be present but below the limits of detection of this assay. The analytical sensitivity of this assay for sequence reportable alterations is 15% mutant allele frequency with a minimum coverage of 100 times in a sample with 30% or greater tumor content, and for rearrangements is a minimum coverage of 10 targeted fusion reads with 5 unique fusion molecules in a sample with 10% or greater tumor content. 

This test does not detect large single or multiexon deletions or duplications or genomic copy number alterations

Rare polymorphisms may be present that could lead to false-negative or false-positive results. Test results should be interpreted in the context of clinical findings, tumor sampling, and other laboratory data. If results obtained do not match other clinical or laboratory findings, contact the laboratory for discussion of the findings. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. 

Useful For

Identifying mutations and rearrangements that may support a diagnosis for patients with tumors of the central nervous system (CNS)

Identifying mutations and rearrangements that may help determine prognosis for patients with tumors of the CNS

Identifying specific mutations and rearrangements within genes known to be associated with response or resistance to specific cancer therapies

Reference Range Information
Performing LocationReference Range
​Mayo Clinic Laboratories​An interpretive report will be provided.
Interpretation

​An interpretive report will be provided.

For more information visit:
Performing Laboratory Information
Performing LocationDay(s) Test PerformedAnalytical TimeMethodology/Instrumentation
​Mayo Clinic Laboratories​Monday through Friday; Varies​12-20 daysPolymerase Chain Reaction (PCR)-Based Next-Generation Sequencing (NGS)​
Reference Lab
For billing questions, see Contacts
Outreach CPTs
CPTModifier
(if needed)
QuantityDescriptionComments
​81455​1
​88381​1
For most current information refer to the Marshfield Laboratory online reference manual.