What is the role of the Fluorescence In Situ Hybridization (FISH) test in diagnosing cholangiocarcinoma?

FISH Testing in Cholangiocarcinoma Diagnosis

FISH (Fluorescence In Situ Hybridization) should be used as an adjunctive test to standard brush cytology during ERCP to improve diagnostic sensitivity for cholangiocarcinoma, particularly when initial cytology is negative or equivocal, achieving combined sensitivities of 50-69% while maintaining excellent specificity of 91-100%. 1

How FISH Works

• FISH uses fluorescent-labeled DNA probes targeting chromosomes 3,7,17, and the 9p21 locus to detect chromosomal abnormalities (aneuploidy and polysomy) in cells collected during biliary brushing or EUS-FNA 1
• Malignancy is diagnosed when at least 5 cells show polysomy of 2 or more chromosomes 1
• The test identifies genetic alterations specifically associated with cholangiocarcinoma that may not be visible on routine cytology 1

Performance Characteristics

General Biliary Strictures

• FISH alone: Sensitivity ranges from 31-79%, specificity 92-100% across multiple studies 1
• FISH combined with brush cytology: Overall diagnostic sensitivity increases to 50-69% without compromising specificity or accuracy 1
• When FISH is positive in the setting of negative or atypical cytology, it can identify additional cholangiocarcinoma cases that would otherwise be missed 2

Primary Sclerosing Cholangitis (PSC) Population

• Critical limitation: FISH has suboptimal sensitivity in PSC patients, with pooled sensitivity of only 51% and specificity of 93% for detecting cholangiocarcinoma 1
• Combining FISH polysomy, trisomy, or tetrasomy increases sensitivity to 68% but decreases specificity to 70% 1
• In PSC, FISH should be used selectively in patients with other concerning features (dominant strictures, elevated CA19-9, elevated bilirubin) rather than as a universal screening tool 3

Clinical Algorithm for FISH Use

When to Order FISH

1. Primary indication: Biliary strictures with negative or equivocal (atypical/suspicious) brush cytology during ERCP 1, 4
2. High-risk clinical context: Older age, malignant-appearing strictures on imaging, elevated CA19-9, but inconclusive cytology 1
3. PSC patients: Only when dominant stricture is present plus other concerning features, not routinely 3

Interpreting FISH Results

• Positive FISH (polysomy): Confidently diagnose malignant biliary stricture given appropriate clinical context 1
• Negative FISH: Does not exclude cholangiocarcinoma; consider additional sampling methods 1
• FISH trisomy/tetrasomy alone: Less specific than polysomy; patients have outcomes similar to negative FISH 3

Comparison with Emerging Technologies

• Bile DNA methylation panels (2025 EASL guidelines) achieve superior performance with 100% sensitivity and 90% specificity in PSC-related cholangiocarcinoma, representing a significant advancement over FISH 5
• Single-operator cholangioscopy-guided biopsies show 65% sensitivity and 97% specificity in PSC, potentially superior to FISH in this population 1

Critical Pitfalls to Avoid

• Do not use FISH for gallbladder masses: FISH is validated exclusively for biliary strictures and cholangiocarcinoma, not gallbladder cancer 6
• Do not rely on FISH as standalone screening in PSC: The sensitivity is too low (51%) for routine surveillance; reserve for patients with dominant strictures and other high-risk features 1, 3
• Recognize technical limitations: FISH requires sufficient intact neoplastic cells in the specimen; inadequate brushing samples will yield false negatives 1
• Consider cost and availability: FISH is not universally available and adds significant cost; its use should be determined by local resources and clinical context 1

Practical Implementation

• The Asia-Pacific consensus recommends FISH has an additive role to improve diagnostic performance of standard brush cytology (Evidence Level IIA, Recommendation Grade B) 1
• FISH sensitivity is not affected by the location of biliary strictures (intrahepatic vs. extrahepatic) 1
• In equivocal cytology cases, adding FISH can achieve 100% sensitivity for cholangiocarcinoma detection in some series, though with reduced positive predictive value of 58% 4