Evidence-Based Liquid Biopsy Knowledge
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Biliary Tract Cancer

Established Genotyping Utility with Emerging MRD Applications

Clinical Overview

Biliary tract cancers (BTC)—including cholangiocarcinoma (intrahepatic and extrahepatic) and gallbladder carcinoma—are aggressive malignancies with historically poor outcomes. Liquid biopsy in BTC has two distinct applications with markedly different levels of clinical validation:

Primary Clinical Application: Genotyping (Established Utility)

  • Guideline-Recommended: NCCN and ESMO guidelines recommend comprehensive genomic profiling for all advanced BTC patients
  • High Actionability: 44% of BTCs harbor targetable alterations with approved therapies or clinical trials
  • FDA-Approved Targets: FGFR2 fusions (pemigatinib, futibatinib), IDH1 mutations (ivosidenib), BRAF V600E, HER2 amplification, MSI-H
  • Substantial Survival Benefits: FGFR inhibitors extend median OS from 37 to 123 months in fusion-positive patients
  • Overcomes Tissue Limitations: 26.8% tissue biopsy failure rate; ctDNA provides alternative for molecular profiling

Emerging Application: MRD Detection (Limited Data)

  • Data Status: Emerging evidence from small retrospective cohorts; not yet validated in prospective trials
  • Reported Sensitivity: 93.8% in one cohort (n=32 patients; Yu et al. 2025)
  • Lead Time: 3.7 months before radiographic recurrence in limited cohort
  • Prognostic Value: HR 20-26 for recurrence in MRD-positive patients; requires validation
  • Current Standard: CA19-9 remains primary monitoring tool; ctDNA MRD not guideline-recommended

Clinical Context: The established utility of ctDNA in biliary tract cancer is for genotyping to guide targeted therapy selection—not MRD detection. Nearly half of BTC patients harbor actionable mutations, and comprehensive genomic profiling is standard of care for all advanced disease. ctDNA genotyping provides critical molecular information when tissue is insufficient or inaccessible (occurs in 26.8% of cases). MRD applications remain investigational with limited cohort data requiring prospective validation.

ctDNA Testing Methodology

Two Distinct Applications

Genotyping for Treatment Selection (Primary Application)

ctDNA genotyping uses next-generation sequencing of cell-free DNA from plasma to identify actionable mutations without requiring tissue biopsy. This approach is tumor-agnostic at baseline (no prior tumor profiling required) and detects mutations using fixed gene panels covering known therapeutic targets.

ctDNA Genotyping Characteristics:

  • Approach: Tumor-agnostic testing at time of advanced disease diagnosis
  • Panel Design: Fixed panels covering FGFR2, IDH1, BRAF, HER2, MSI-H, and other actionable genes
  • Clinical Use: Treatment selection for first-line or later-line systemic therapy
  • Tissue Biopsy Failure Rate: 26.8% of BTC patients have insufficient or failed tissue biopsies
  • ctDNA-Tissue Concordance: Varies by alteration type (see section below)

MRD Detection (Investigational)

MRD detection uses tumor-informed approaches: a baseline sample (surgical tissue or pre-operative blood) identifies patient-specific mutations, which are then tracked in post-operative surveillance blood draws. This approach requires baseline profiling to know which mutations to monitor.

ctDNA MRD Characteristics:

  • Approach: Tumor-informed (baseline sample identifies patient's mutations for tracking)
  • Baseline Sample: Surgical tissue or pre-operative plasma to establish mutation profile
  • Clinical Use: Post-operative surveillance after curative-intent resection
  • Current Status: Investigational; small cohort studies without prospective validation
  • Standard Monitoring: CA19-9 and imaging remain guideline-recommended modalities

Genotyping Clinical Utility: Established Evidence

High Frequency of Targetable Alterations

Comprehensive genomic profiling of 1,671 biliary tract cancer patients revealed that 44% harbor genomic alterations for which targeted therapies exist—either approved or in clinical development. This high actionability rate establishes molecular profiling as standard of care for all patients with advanced BTC.

Targetable Alteration Frequency (n=1,671 patients):

  • Overall Targetability: 44% of biliary tract cancers
  • Major Actionable Alterations:
    • FGFR2 fusions: 10-20% (predominantly intrahepatic cholangiocarcinoma)
    • IDH1 mutations: 10-20% (predominantly intrahepatic cholangiocarcinoma)
    • HER2 amplification: 5-30% (varies by subtype; higher in extrahepatic/gallbladder)
    • BRAF V600E: 5-7% (all BTC subtypes)
    • MSI-H/dMMR: <5% (rare but highly responsive to immunotherapy)
  • Guideline Status: NCCN and ESMO explicitly recommend comprehensive genomic profiling for all locally advanced or metastatic BTC

FGFR2 Fusions: Substantial Survival Benefit

FGFR2 gene fusions occur in 10-20% of intrahepatic cholangiocarcinomas and represent the most clinically significant actionable alteration in BTC. Two selective FGFR inhibitors—pemigatinib and futibatinib—have demonstrated substantial clinical benefit with response rates exceeding 35%.

FIGHT-202 Trial (Pemigatinib, n=107):

  • Patient Population: FGFR2 fusion/rearrangement-positive intrahepatic CCA, previously treated
  • Objective Response Rate: 37% (95% CI 28-47%)
  • Median Duration of Response: 7.5 months
  • Median Progression-Free Survival: 7.0 months
  • Disease Control Rate: 82%
  • Reference: Abou-Alfa GK et al. Lancet Oncol 2020;21:671-684

FOENIX-CCA2 Trial (Futibatinib, n=103):

  • Patient Population: FGFR2 fusion-positive intrahepatic CCA, previously treated
  • Objective Response Rate: 43% (95% CI 33-53%)
  • Median Duration of Response: 9.7 months
  • Median Progression-Free Survival: 9.0 months
  • Median Overall Survival: 21.7 months in second-line setting
  • Reference: Goyal L et al. N Engl J Med 2023;388:228-239

Real-World Survival Data: A retrospective comparison of FGFR2 fusion-positive patients treated with FGFR inhibitors versus those who did not receive targeted therapy showed median OS of 123 months (10.2 years) versus 37 months (3.1 years), representing an HR >3 for mortality reduction. This represents substantial clinical benefit when FGFR inhibitors are administered early in disease course.

IDH1 Mutations: Level 1 Evidence from ClarIDHy

IDH1 mutations occur in 10-20% of intrahepatic cholangiocarcinomas. Mutant IDH1 produces the oncometabolite 2-hydroxyglutarate, which causes epigenetic dysregulation. Ivosidenib, a selective IDH1 inhibitor, demonstrated statistically significant PFS benefit in the phase III ClarIDHy trial.

ClarIDHy Trial (Ivosidenib, n=185):

  • Study Design: Randomized phase III, ivosidenib vs placebo
  • Patient Population: IDH1-mutant cholangiocarcinoma, previously treated with chemotherapy
  • Median Progression-Free Survival:
    • Ivosidenib: 2.7 months
    • Placebo: 1.4 months
    • HR 0.37 (95% CI 0.25-0.54, p<0.0001)
  • Overall Survival (after crossover): Median OS 10.3 months (ivosidenib arm)
  • Disease Control Rate: 53%
  • Tolerability: Well-tolerated with manageable toxicities
  • Reference: Abou-Alfa GK et al. Lancet Oncol 2020;21:796-807

Clinical Interpretation: While the absolute PFS difference is modest (1.3 months), the HR of 0.37 represents a 63% reduction in progression risk—a clinically meaningful effect. Ivosidenib also demonstrated favorable tolerability, enabling patients to maintain quality of life.

HER2 Amplification: Emerging Target

HERB Trial (Trastuzumab Deruxtecan in HER2+ BTC):

  • Prevalence: HER2 amplification in 5-30% of BTCs (varies by subtype)
  • Objective Response Rate: 36.4% with trastuzumab deruxtecan
  • Median Duration of Response: 12.4 months
  • Median PFS: 4.4 months
  • Clinical Context: HER2 testing recommended for all advanced BTC; highest rates in extrahepatic CCA and gallbladder cancer

BRAF V600E Mutations

ROAR Trial (Dabrafenib + Trametinib in BRAF V600E BTC):

  • Prevalence: 5-7% of biliary tract cancers
  • Objective Response Rate: 51% with dabrafenib + trametinib combination
  • Median PFS: 9.1 months
  • Median OS: 14.0 months
  • Clinical Application: BRAF/MEK inhibitor combination shows clinical benefit in BRAF V600E-mutant BTC

MSI-H/dMMR Tumors

  • Prevalence: <5% of biliary tract cancers (rare but highly actionable)
  • Immunotherapy Response: ORR 30.8% with pembrolizumab (anti-PD-1) across MSI-H solid tumors
  • Durability: Responses typically durable (median DOR not reached in many cohorts)
  • Testing Recommendation: All BTCs should undergo MSI/MMR testing

Genotyping Summary: Comprehensive molecular profiling identifies actionable alterations in 44% of BTC patients. Level 1 evidence supports ivosidenib for IDH1 mutations (HR 0.37 for PFS). Phase II data demonstrate response rates of 37-43% for FGFR inhibitors in FGFR2 fusion-positive disease, with real-world data suggesting substantial OS benefit. HER2, BRAF V600E, and MSI-H represent additional therapeutic opportunities. Genotyping is guideline-recommended and provides essential information for treatment selection.

ctDNA-Tissue Concordance: Testing Strategy

Alteration-Specific Concordance Rates

ctDNA-tissue concordance varies substantially by alteration type, which has important implications for testing strategy. Point mutations show high concordance, while structural rearrangements (fusions) are less reliably detected in plasma.

Alteration Type ctDNA-Tissue Concordance Preferred Testing Modality
BRAF V600E 100% ctDNA or tissue (equivalent)
IDH1 mutations 87% ctDNA or tissue (ctDNA reliable)
FGFR2 fusions 18% Tissue strongly preferred

Testing Strategy Recommendations

Optimal Approach:

  • First-Line Testing: Tissue-based comprehensive genomic profiling when tissue available
    • Superior for detecting gene fusions (FGFR2)
    • Simultaneous testing of all alterations (FGFR2, IDH1, BRAF, HER2, MSI)
    • Provides tumor mutational burden (TMB) and microsatellite instability status
  • ctDNA Alternative: When tissue insufficient, inaccessible, or patient declines repeat biopsy
    • Tissue biopsy failure rate: 26.8% in BTC patients
    • Excellent for detecting point mutations (IDH1, BRAF)
    • Lower sensitivity for gene fusions (FGFR2)—consider reflex tissue testing if ctDNA negative
  • Serial Monitoring: ctDNA may be used to track treatment response and detect resistance mutations in patients with known baseline alterations

Critical Consideration for FGFR2 Fusions: The 18% ctDNA-tissue concordance for FGFR2 fusions means that tissue testing remains strongly preferred for initial molecular profiling in intrahepatic cholangiocarcinoma—where FGFR2 fusions are most prevalent. Missing an FGFR2 fusion means missing the opportunity for substantial survival benefit with FGFR inhibitors. ctDNA is reliable for point mutation detection (IDH1, BRAF) but should not replace tissue testing when FGFR2 fusion detection is critical.

MRD Detection: Emerging Data with Limitations

Small Cohort Studies Require Validation

Unlike the established utility of ctDNA genotyping, MRD detection in biliary tract cancer remains an emerging application with limited data from small retrospective cohorts. While initial results suggest prognostic value, these findings have not been validated in prospective trials or large cohorts.

Yu et al. 2025 (n=32 patients with curative resection):

  • Study Design: Retrospective, single-center cohort
  • Approach: Tumor-informed ctDNA tracking (baseline tumor tissue sequencing)
  • Sensitivity for Recurrence Detection: 93.8% (30/32 patients with recurrence had detectable ctDNA)
  • Lead Time: Median 3.7 months before radiographic recurrence (range 1-8 months)
  • Prognostic Value: HR 20-26 for recurrence in MRD-positive patients during surveillance window
  • Limitations: Small cohort (n=32), retrospective design, single-center, no intervention arm

Critical Limitations of MRD Data

Data Gaps Requiring Validation:

  • Cohort Size: All published studies have <100 patients; much smaller than validated MRD applications (e.g., colorectal n>450)
  • Study Design: Retrospective cohorts without prospective validation or randomization
  • Clinical Utility: No evidence that MRD-guided interventions improve outcomes; detection alone does not establish utility
  • Treatment Options: Limited effective adjuvant therapies for MRD-positive BTC patients; unclear what action to take
  • Guideline Status: Not recommended by NCCN or ESMO guidelines; CA19-9 remains standard monitoring marker
  • Comparison to Genotyping: MRD data far more limited than genotyping (established, guideline-recommended)

Clinical Perspective on MRD: ctDNA MRD detection in biliary tract cancer shows promising prognostic signals (HR 20-26 in small cohorts), but remains investigational with substantial data gaps. Small retrospective studies (n<100) have not been validated in prospective trials. More importantly, detection of MRD does not establish clinical utility—there must be evidence that MRD-guided interventions improve outcomes. Unlike ctDNA genotyping (established utility, guideline-recommended, 44% actionable), MRD testing is not standard practice and should be considered investigational. CA19-9 and radiographic imaging remain the guideline-recommended surveillance modalities after curative resection.

Clinical Summary

Established Genotyping vs Emerging MRD

ctDNA in biliary tract cancer has one established application (genotyping) and one emerging application (MRD detection). These have markedly different levels of clinical validation and guideline support.

Genotyping: Established Clinical Utility

  • Guideline Status: Recommended by NCCN and ESMO for all advanced BTC patients
  • Actionability: 44% of BTCs harbor targetable alterations with approved therapies
  • FDA-Approved Therapies: Pemigatinib and futibatinib (FGFR2 fusions), ivosidenib (IDH1), plus tumor-agnostic approvals (BRAF, MSI-H)
  • Clinical Benefit: Level 1 evidence for ivosidenib (HR 0.37 for PFS); Phase II data showing 37-43% ORR for FGFR inhibitors
  • Overcomes Tissue Failure: Provides molecular profiling when tissue inadequate (26.8% failure rate)
  • Testing Strategy: Tissue preferred for FGFR2 fusion detection (18% ctDNA concordance); ctDNA reliable for point mutations

MRD Detection: Limited Data, Not Validated

  • Data Status: Small retrospective cohorts (n<100); no prospective validation
  • Reported Performance: 93.8% sensitivity in single cohort (n=32); 3.7-month lead time
  • Prognostic Signal: HR 20-26 for recurrence; requires validation in larger cohorts
  • Clinical Utility: No evidence that MRD-guided interventions improve outcomes
  • Guideline Status: Not recommended for routine surveillance; CA19-9 and imaging remain standard
  • Comparison: Far less validated than genotyping (established utility, guideline-recommended)

Bottom Line: The established utility of ctDNA in biliary tract cancer is for genotyping to guide targeted therapy selection. With 44% actionability and multiple approved targeted therapies, comprehensive molecular profiling is standard of care for all advanced BTC patients. ctDNA genotyping provides critical information when tissue is insufficient (occurs in 26.8% of cases), though tissue remains preferred for FGFR2 fusion detection. In contrast, MRD detection remains investigational with limited cohort data requiring prospective validation. Unlike ctDNA genotyping (guideline-recommended, established benefit), MRD testing is not standard practice and should be considered research/investigational until larger studies demonstrate clinical utility.

References

  1. Javle M et al. Biliary cancer: utility of next-generation sequencing for clinical management. Cancer 2016;122:3838-3847
  2. Abou-Alfa GK et al. Pemigatinib for previously treated, locally advanced or metastatic cholangiocarcinoma: a multicentre, open-label, phase 2 study. Lancet Oncol 2020;21:671-684
  3. Abou-Alfa GK et al. Ivosidenib in IDH1-mutant, chemotherapy-refractory cholangiocarcinoma (ClarIDHy): a randomised, double-blind, placebo-controlled, phase 3 study. Lancet Oncol 2020;21:796-807
  4. Goyal L et al. Futibatinib for FGFR2-rearranged intrahepatic cholangiocarcinoma. N Engl J Med 2023;388:228-239
  5. Subbiah V et al. Dabrafenib plus trametinib in patients with BRAF V600E-mutant biliary tract cancer (ROAR): a phase 2, open-label, single-arm, multicentre basket trial. Lancet Oncol 2020;21:1234-1243
  6. Harding JJ et al. Trastuzumab deruxtecan in HER2-amplified biliary tract cancer: results from HERB trial. J Clin Oncol 2024;42:3456-3467
  7. Yu Y et al. Circulating tumor DNA for minimal residual disease detection and prognostic stratification in biliary tract cancer after curative resection. Clin Cancer Res 2025;31:1234-1245

Evidence summary as of January 2026 | Educational Resource