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HelpTest Code BRFKT BRAF and KIT Mutation Analysis, Next-Generation Sequencing, Tumor
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 216 mm(2)
-Minimum amount of tumor area: tissue 36 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 Tissue Requirement for Solid Tumor Next-Generation Sequencing. In this document, the sizes are given as 4 mm x 4 mm x 10 slides as preferred: approximate/equivalent to 144 mm(2) and the minimum as 3 mm x 1 mm x 10 slides: approximate/equivalent to 36 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 slides
Slides: 1 Stained and 10 unstained
Collection Instructions: Submit 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 10 slides from the same block.
Additional Information: Unused unstained slides will not be returned.
Specimen Type: Cytology slides (direct smears or ThinPrep)
Slides: 1 to 3 Slides
Collection Instructions: Submit 1 to 3 slides stained and coverslipped with a preferred total of 5000 nucleated cells, or a minimum of at least 3000 nucleated cells.
Note: Glass coverslips are preferred; plastic coverslips are acceptable but will result in longer turnaround times.
Additional Information: Cytology slides will not be returned.
Useful For
Identifying specific mutations within the BRAF and KIT genes that predict response to therapy
Genetics Test Information
This test uses targeted next-generation sequencing to evaluate for somatic mutations within the BRAF and KIT genes. See Targeted Genes and Methodology Details for BRAF/KIT Mutation Analysis for details regarding the targeted gene regions evaluated by this test.
This test is performed to evaluate for somatic mutations within solid tumor samples. It does not assess for germline alterations within the BRAF and KIT genes.
Additional Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| SLIRV | Slide Review in MG | No | Yes |
Testing Algorithm
When this test is ordered, slide review will always be performed at an additional charge.
Special Instructions
Method Name
Sequence Capture and Targeted Next-Generation Sequencing (NGS)
Reporting Name
BRAF/KIT Mutation Analysis, TumorSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time | Special Container |
|---|---|---|---|
| Varies | Ambient (preferred) | ||
| Refrigerated | |||
Reject Due To
| Specimens that have been decalcified (all methods) Specimens that have not been formalin-fixed, paraffin-embedded, except for cytology slides Extracted nucleic acid (DNA/RNA) |
Reject |
Clinical Information
The signaling pathways stimulated by the KIT protein control many important cellular processes, such as cell growth and division (proliferation), survival, and movement (migration). KIT protein signaling is important for the development and function of certain cell types, including early blood cells (hematopoietic stem cells), mast cells, cells in the gastrointestinal tract, and melanocytes. BRAF is a member of the mitogen-activated protein/extracellular signal-regulated (MAP/ERK) kinase pathway, which plays a role in cell proliferation and differentiation. Dysregulation of this pathway is a key factor in tumor progression.
Targeted therapies directed to pathways involving KIT and BRAF have demonstrated some success with increases both in progression-free and overall survival in patients with melanoma. Effectiveness of these therapies, however, depends in part on the mutation status of the pathway components.
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.
Cautions
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.
DNA variants of uncertain significance may be identified.
A negative result does not rule out the presence of a variant that may be present but 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.
Point mutations and small deletion-insertion mutations will be detected in the BRAF and KIT genes only. This test may detect single exon deletions but does not detect multiexon deletions, duplications, or genomic copy number variants.
Variant allele frequency (VAF) is the percentage of sequencing reads supporting a specific variant divided by the total sequencing reads at that position. In somatic testing, VAF should be interpreted in the context of several factors including, but not limited to: tumor purity/heterogeneity/copy number status (ploidy, gains/losses, loss of heterozygosity) and sequencing artifact/misalignment.(1,2)
Rare polymorphisms may be present that could lead to false-negative or false-positive results.
The presence or absence of a variant may not be predictive of response to therapy in all patients.
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 cytology slides and formalin-fixed, paraffin-embedded tissues; other types of fixatives are discouraged. Improper treatment of tissues, such as decalcification, may cause polymerase chain reaction failure.
Method Description
Next-generation sequencing is performed to evaluate the presence of a mutation in all coding regions of the BRAF and KIT genes. See Targeted Genes and Methodology Details for BRAF/KIT Mutation Analysis for details regarding the targeted gene regions evaluated by this test.(Unpublished Mayo method)
A pathology review and macro dissection to enrich for tumor cells are performed prior to slide scraping.
Day(s) Performed
Monday through Friday
Report Available
12 to 20 daysPerforming Laboratory
Mayo Clinic Laboratories in Rochester
Test 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
88381-Microdissection, manual
81406
81479
81479 (if appropriate for government payers)
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| BRFKT | BRAF/KIT Mutation Analysis, Tumor | 36908-2 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 617945 | Result | 82939-0 |
| 617946 | Interpretation | 69047-9 |
| 617947 | Additional Information | 48767-8 |
| 617948 | Specimen | 31208-2 |
| 617949 | Tissue ID | 80398-1 |
| 617950 | Method | 85069-3 |
| 617951 | Disclaimer | 62364-5 |
| 617952 | Released By | 18771-6 |