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FGFR2 fusion testing: methodology matters

Molecular profiling is necessary to identify FGFR2 fusions

Read more about The Importance of Molecular Profiling in Cholangiocarcinoma in this white paper by Dr Ghassan Abou-Alfa.

Testing for FGFR2 fusions requires a method that can detect these specific genomic alterations, which are distinct from FGFR2 point mutations.1-3

A variety of molecular profiling methods are now available, with next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) among the most common assays. There are some important differences between the 2 methods.


allows the opportunity, in a molecular target-rich disease like CCA, to analyze a tissue sample for multiple alterations at the same time. Thus, though the specimen size for NGS is initially larger and the turnaround time may be longer, it may preclude the need for further biopsies for purposes of molecular testing.4

FISH tests

are conducted to identify 1 specific, predetermined alteration at a time, so there is a risk of missing other possible alterations.5

FGFR2 fusions have a wide range of fusion partners.1 Therefore, to identify patients with FGFR2 fusions, it is important to select an assay that:


Can detect all FGFR2 fusions, including those with known or unknown fusion partners1,3,6


Reports FGFR2 fusions (vs FGFR2 mutations)1,2

An NGS test that accomplishes these criteria offers the greatest opportunity to identify patients with FGFR2 fusions.


NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) recommend molecular testing for patients with unresectable or metastatic iCCA.7*

*See the Guidelines online at for the full recommendation.

NCCN makes no warranties of any kind whatsoever regarding their content, use, or application and disclaims any responsibility for their application or use in any way. 

NCCN=National Comprehensive Cancer Network. 

Biopsy technique should account for planned molecular profiling as well as diagnostic needs

Compared with the tissue required for a histological diagnosis, additional tissue may be required to satisfy emerging molecular profiling needs in iCCA. Consider creating a molecular profiling plan early on, including tissue requirements for the specific planned biomarker test when determining biopsy technique.

Although more invasive than fine-needle aspiration, core-needle biopsy provides important pathological details about the tumor and typically yields enough tissue to allow for comprehensive molecular profiling.7

Learn more about the differences in biopsy techniques

Core-needle biopsy


  • Acquires more tissue
    • Allows for additional histologic and immunohistochemical testing7
    • Allows for more comprehensive molecular profiling8
  • Acquires more structured tissue
    • Provides information on cytology and
      tissue architecture7


  •  More invasive7

Fine-needle aspiration


  •  Less invasive7
  •  Histological results can be obtained quickly7
  •  May be associated with less complications7


  •  Acquires limited amount of tissue, which does not allow for further testing or comprehensive molecular profiling8

Once the biopsy is performed, the tissue should be processed promptly and prepared according to the specific needs of the molecular profiling assay selected.

References: 1. Lowery MA, Ptashkin R, Jordan E, et al. Clin Cancer Res. 2018;24(17):4154-4161. 2. Silverman IM, Murugesan K, Lihou CF, et al. Presented at: Cholangiocarcinoma Foundation Annual Conference; January 30-February 1, 2019; Salt Lake City, Utah; Poster IC171-19C. 3. Jain A, Borad MJ, Kelley RK, et al. JCO Precis Oncol. 2018:2;1-12. 4. Damodaran S, Berger MF, Roychowdhury S. Am Soc Clin Oncol Educ Book. 2015;e175-e182. 5. Hu L, Ru K, Zhang L, et al. Biomark Res. 2014;2(1):3. 6. Barr FG. Expert Rev Mol Diagn. 2016;16(9):921-923. 7. Referenced with permission from the NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for Hepatobiliary Cancers V.5.2021. © National Comprehensive Cancer Network, Inc. 2021. All rights reserved. Accessed September 21, 2021. To view the most recent and complete version of the guideline, go online to 8. Wee A. J Gastrointest Oncol. 2013;4(1):5-7.