Genomic architecture of FGFR2 fusions in cholangiocarcinoma and its implication for molecular testing

Abstract

Background Cholangiocarcinoma (CCA) is a primary malignancy of the biliary tract with a dismal prognosis. Recently, several actionable genetic aberrations were identified with significant enrichment in intrahepatic CCA, including FGFR2 gene fusions with a prevalence of 10–15%. Recent clinical data demonstrate that these fusions are druggable in a second-line setting in advanced/metastatic disease and the efficacy in earlier lines of therapy is being evaluated in ongoing clinical trials. This scenario warrants standardised molecular profiling of these tumours. Methods A detailed analysis of the original genetic data from the FIGHT-202 trial, on which the approval of Pemigatinib was based, was conducted. Results Comparing different detection approaches and displaying representative cases, we described the genetic landscape and architecture of FGFR2 fusions in iCCA and show biological and technical aspects to be considered for their detection. We elaborated parameters, including a suggestion for annotation, that should be stated in a molecular diagnostic FGFR2 report to allow a complete understanding of the analysis performed and the information provided. Conclusion This study provides a detailed presentation and dissection of the technical and biological aspects regarding FGFR2 fusion detection, which aims to support molecular pathologists, pathologists and clinicians in diagnostics, reporting of the results and decision-making.

First proficiency testing for NGS‐based and combined NGS‐ and FISH‐based detection of FGFR2 fusions in intrahepatic cholangiocarcinoma

“…In this study, we report the results of a multi‐centre round robin test of FGFR2 fusion testing in cholangiocarcinoma by targeted NGS‐based RNA analysis and FISH. Complementing our in silico data [ 14 ], the wet‐lab data derived from this study significantly contribute to implementing and optimising FGFR2 fusion testing in a diagnostic setting.…”

“…In this study, we report the results of a multi-centre round robin test of FGFR2 fusion testing in cholangiocarcinoma by targeted NGS-based RNA analysis and FISH. Complementing our in silico data [14], the wetlab data derived from this study significantly contribute to implementing and optimising FGFR2 fusion testing in a diagnostic setting. The detection of full-length transcripts by RNAsequencing in FFPE material is technically challenging due to the prominent degradation of RNA in FFPE 105 NGS proficiency testing for FGFR2 fusions in iCCC samples.…”

“…An FGFR2 :: ATE1 fusion was previously detected in one case of uterine corpus endometrial carcinoma in the TCGA dataset [ 21 ] but with other exons fused. As described elsewhere [ 14 ], the gene locus of ATE1 is directly downstream of the FGFR2 gene locus. This rearrangement leads to a fusion of FGFR2 and ATE1 where the fluorochrome‐labelled probes are located further upstream of both FGFR2 and ATE1 .…”

“…The detection of full-length transcripts by RNAsequencing in FFPE material is technically challenging due to the prominent degradation of RNA in FFPE 105 NGS proficiency testing for FGFR2 fusions in iCCC samples. Additionally, the genomic architecture of FGFR2 gene fusions [14] including the diversity of different fusion partners and involved exons needs to be appropriately reflected in a diagnostic test setting. While all methods may be used in routine diagnostics, their ability to detect complex genetic events differs and knowledge of these differences is required for interpretation and reporting of test results.…”

“…While the biological underpinnings are clear and clinical exploitability was demonstrated, data on the performance of assays currently used to detect FGFR2 fusions are far less clear. Extending our comprehensive in silico [ 14 ] analysis using genomic data from FIGHT‐202 [ 9 ], we here report results from a multi‐centric round robin test comparing several RNA‐based next‐generation sequencing (NGS) assays as well as fluorescence in situ hybridisation (FISH) and derive testing recommendations.…”