Test Catalog

Test ID: FGFR2    
FGFR2 (10q26.1) Rearrangement, FISH, Tissue

Useful For Suggests clinical disorders or settings where the test may be helpful

Providing prognostic information and guiding treatment for patients with cholangiocarcinomas and other tumor types including bladder, thyroid, oral cavity, and brain

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

This test does not include a pathology consult. If a pathology consultation is requested, PATHC / Pathology Consultation should be ordered and the appropriate FISH test will be ordered and performed at an additional charge.


This test includes a charge for application of the first probe set (2 FISH probes) and professional interpretation of results. Additional charges will be incurred for all reflex probes performed. Analysis charges will be incurred based on the number of cells analyzed per probe set. If no cells are available for analysis, no analysis charges will be incurred.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Cholangiocarcinoma is a malignancy arising from the biliary tract epithelium. These tumors are often clinically advanced at the time of presentation and the prognosis is very poor with a short overall survival. Treatment is generally limited to surgical resection, which is associated with a high degree of morbidity, and palliative chemotherapy regimens. Therefore, additional treatment options are eagerly sought.


Rearrangement of the FGFR2 gene region has been identified in a subset of cholangiocarcinomas. These rearrangements result in overexpression of FGFR2, which offers the possibility of using targeted FGFR2-inhibitor therapy for treatment. FGFR2 rearrangement has been identified in a number of other cancers including those of the bladder, thyroid, oral cavity, and brain. In the future, it is likely that the presence of FGFR2 rearrangements will be exploited in the treatment of these cancers as well.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Interpretation Provides information to assist in interpretation of the test results

A positive result is detected when the percent of cells with an abnormality exceeds the normal cutoff for the probe set.


A positive result suggests rearrangement of the FGFR2 locus and a tumor that may be responsive to targeted FGFR2-inhibitor therapy.


A negative result suggests no rearrangement of the FGFR2 gene region at 10q26.1.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This test is not approved by the US Food and Drug Administration, and it is best used as an adjunct to existing clinical and pathologic information.

Fixatives other than formalin (eg, Prefer, Bouin) may not be successful for FISH assays; however, nonformalin fixed samples will not be rejected.

Paraffin-embedded tissues that have been decalcified are generally unsuccessful for FISH analysis. The pathologist reviewing the hematoxylin and eosin-stained slide may find it necessary to cancel testing.

Supportive Data

FISH analysis was performed on 38 paraffin-embedded tissue samples and 25 noncancerous lymph node control specimens. Rearrangement of FGFR2 was identified in 13 cholangiocarcinoma tumors. The normal controls were used to generate a normal cutoff for this assay.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Mitesh BJ, Champion MD, Egan JB, et al: Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma. PLOS Genetics 2014 Feb;10(2):e1004135

2. Graham RP, Barr Fritcher EG, Pestova E, et al: Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma. Hum Pathol 2014 Aug;45(8):1630-1638

3. Arai Y, Totoki Y, Hosoda F, et al: Fibroblast growth factor receptor 2 tyrosine kinase fusions define a unique molecular subtype of cholangiocarcinoma. Hepatology 2014;59:1427-1434

4. Wu YM, Su F, Kalyana-Sundaram S, et al: Identification of targetable FGFR gene fusions in diverse cancers. Cancer Discov June 2013;3(6):636-647