BRAF Rearrangement by FISH

Performing Lab: 
UCSF Clinical Cancer Genomics Lab
CPT Code: 

Specimen Type
Formalin-fixed, paraffin-embedded tissue on six (6) unstained slides (5 microns thick) on charged glass. One adjacent hematoxylin and eosin stained (H&E) slide should also be included. Slides should be labeled with pathology case number and block identification. Cytology smears may also be used for testing if there is sufficient tumor present. Contact the laboratory at 415.502.3252 or [email protected] if testing on a cytology smear is desired.
Methodology: Fluorescence in-situ hybridization (FISH)
Turnaround Time: 7-14 days


BRAF rearrangement by FISH is designed to detect BRAF-KIAA1549 rearrangement, BRAF rearrangement is a common occurrence in pilocytic astrocytoma, occurring in approximately 60-70% of those tumors.  Most commonly, there is a tandem duplication of chromosome 7q34, resulting in fusion of the 3' BRAF catalytic domain to the KIAA1549 gene.  However, other BRAF rearrangements have been observed.  Less commonly, BRAF fusion has been identified in other low-grade gliomas, including tumors with mixed glial and gangliocytic differentiation.


The BRAF Rearrangement Testing by FISH assay is designed to identify BRAF gene rearrangement on chromosome 7q34. It utilizes the Empire Genomics BRAF Break Apart Fish Probe (BRAFBA-20-ORGR). The probe set includes two FISH probes. The first probe flanks the 3' side of the BRAF gene, producing an orange signal while the second probe flanks the 5' side of the BRAF gene, producing a green signal. Formalin-fixed, paraffin-embedded tissue on one glass slide is de-paraffinized and then treated with pepsin to digest tissue proteins and allow for probes to reach target DNA. The DNA is then heat denatured and subsequently allowed to hybridize with the probe set. After hybridization, the slides are washed to remove any of the excess unbound probes and the nuclei are counterstained with DAPI (4,6 diamidino-2-phenylidole). Enumeration of the cells with extra orange signals, or separate orange and green signals is conducted by microscopic examination of cell nuclei using a fluorescence microscope equipped with appropriate excitation and emission filters.


The clinical interpretation of this test should be evaluated within the context of the patient's medical history, other diagnostic tests, and the histologic and immunohistochemical features of the tumor.

The BRAF Rearrangement Testing by FISH assay is not an FDA approved test. The test was validated by the UCSF Clinical Cancer Genomics Laboratory to confirm performance characteristics, in compliance with current guidelines for clinical implementation. The laboratory is CLIA certified to perform high complexity testing.


Blocks selected for BRAF Rearrangement Testing must contain tumor tissue. The assay is optimized for formalin-fixed tissue; tissue processed with other fixatives will not be rejected, but may not provide interpretable results. Decalcified specimens are usually unsuitable for FISH testing but an attempt at hybridization will be performed. An adjacent H&E-stained slide must be included. Contact the laboratory at 415.502.3252 or [email protected] if the specimen suitability is uncertain. Label slides with pathology case number and block identification.

Specimen rejection criteria include: All required slides not included. Insufficient tumor tissue present on slide as determined by pathologist. Outside slides not labeled or not accompanied by printed copy of test order.


UCSF Clinicians — this test can be ordered through Pathology
Outside Physicians — this test can be ordered with the CCGL Requisition Form

For all specimens, an interpretation of this test by a laboratory physician will automatically be performed and billed for separately.

CCGL Test Order Submission

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