1p/19q Deletion 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


1p and 19q deletion by FISH is designed to detect loss of chromosome loci 1p and 19q, which has been seen in oligodendroglial tumors and which has been associated with improved prognosis and response to therapy in patients with primary brain tumors.


A histologic section from the selected tumor block was reviewed by a pathologist to evaluate tumor and normal tissue morphology, and an adjacent paraffin section was used for FISH analysis. Two FISH probe sets are used for the target 1p36 and reference 1q25 loci, and the target 19q13 and reference 19p13 loci. Formalin-fixed, paraffin-embedded tissue on two glass slides 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 two probe sets, one per slide. 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 1p, 1q, 19p and 19q 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 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 1p/19q Deletion 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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