ALK Rearrangement by FISH (for Lung Cancer)

Performing Lab: 
UCSF Clinical Cancer Genomics Lab
CPT Code: 

Specimen Type
Formalin-fixed, paraffin-embedded tissue on three (3) 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


ALK Rearrangement by FISH is designed to detect loss rearrangement (breakapart) of the ALK gene.  In lung cancer, ALK rearrangement correlates with EML4-ALK gene fusion, and it has been observed in approximately 5% of lung cancers, predominantly adenocarcinomas or mixed carcinomas with an adenocarcinoma component.  It is very infrequent in other histological subtypes.  Advanced lung cancer patients with ALK rearrangement have shown therapeutic response to the ALK inhibitor crizotinib.  ALK rearrangement has also been observed as a frequent event in inflammatory myofibroblastic tumors (IMT) and may be helpful in the diagnosis of IMT. 


The ALK gene rearrangement by FISH assay is designed to identify ALK gene rearrangement on chromosome 2p23. It utilizes a Vysis LSI ALK (2p23) Dual Color Break Apart Rearrangement Probe set. The probe set includes two FISH probes. The first probe flanks the 3' (telomeric) side of the ALK gene, producing an orange signal while the second probe flanks the 5' (centromeric) side of the ALK 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 fusion and break-apart 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. For inflammatory myofibroblastic tumors, the absence if ALK rearrangement does not rule out the diagnosis.

This test utilizes a laboratory modification of the procedure for the Vysis ALK Break Apart FISH Probe Kit, which is FDA-approved for the detection of ALK gene rearrangement via fluorescence in situ hybridization (FISH) in formalin-fixed paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) tissue specimens. Modifications were validated by the UCSF Clinical Cancer Genomics Laboratory to confirm performance characteristics, in compliance with current guidelines for clinical implementation. This test has not been cleared or approved by the U.S. Food and Drug Administration. The test was validated by the UCSF Clinical Cancer Genomics Laboratory (CCGL) to confirm performance characteristics, in compliance with current guidelines for clinical implementation


Blocks selected for ALK 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 APeX
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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