In 2020, the U.S. FDA approved the marketing of pemigatinib, the first targeted cholangiocarcinoma drug for FGFR2 fusions or other rearrangement types (FDA-approved assay), for the treatment of adult patients with locally advanced or metastatic cholangiocarcinoma (CCA) harboring FGFR2 gene fusions. There are numerous FGFR2 fusion partner genes in cholangiocarcinoma, involving 19 genes, which are simple and intuitive to design as breakout probes. However, it should be noted that four genes in 10q26, where FGFR2 is located, are in close proximity, within 6 Mb, so that the red and green genes detected by the FGFR2 breakthrough probe may be indistinguishable from each other, and may be misclassified as negative. When encountering the red-green spacing, NGS method should be used to verify each other.