Exploration of Targeted Anti-tumor Therapy

Table 2. Selected trials evaluating liquid biopsy in blood in BTCs

Year	Authors	Trial type	Population	Assay	Concordance rate liquid/tissue	Notable results
Localized BTCs
2023	Yoo et al. [58]	Randomized phase II	101 patients R0/R1 resected eCCA and regional lymph-node metastases, randomized to gemcitabine-cisplatin versus capecitabine	Signatera, tumor-informed assay	No comparison to tissue	Patients with positive ctDNA before adjuvant chemotherapy had shorter RFS than those with negative ctDNA
Metastatic BTCs
2019	Mody et al. [61]	Retrospective study	124 patients Locally advanced or metastatic BTC (≈ 70% intrahepatic; early-onset < 50 vs. ≥ 50 years)	Guardant^®	No comparison to tissue	Blood-based liquid biopsy can be used for molecular characterization and can identify clinically relevant alterations including 5% IDH1 and 7% FGFR2 mutations
2019	Ettrich et al. [62]	Retrospective study	32 patients Unresectable locally advanced or metastatic cholangiocarcinoma (UICC stage III/IV; gallbladder cancer excluded), all indicated for palliative chemotherapy	QIAamp Circulating Nucleic Acid Kit for ctDNA extraction NGS of 15 gene panel, selected frequently mutated genes	No comparison to tissue	Variant allele frequency correlates with tumor load and PFS 63% of therapy-naive patients experienced changes in their mutational profiles during chemotherapy Patients with mutations via blood-based liquid biopsy in BAP1, PBRM1, KRAS, or TP53 show a trend toward shorter PFS
2020	Lamarca et al. [63]	Post hoc analysis of patient data collected as part of the prospective ABC-01, -02, and -03	534 patients From the ABC-01/-02/-trial 109 (20.4%) had iCCA; 86 (78.9%) primarily metastatic; 52 (47.7%) with liver-only disease; 66 (60.6%) of these iCCA patients were treated with cisplatin plus gemcitabine	FoundationOne Liquid^® Oncomine	IDH1 mutation: 100% FGFR2 fusion: 100% FGFR2 mutation: 100%	High concordance with tissue analysis 40% targetable alterations detected: IDH1 mutations: 19% FGFR2 alterations: 10% (5% fusions, 5% mutations) ctDNA before palliative treatment not linked to PFS or OS
2020	Aguado et al. [64]	ctDNA analysis of the randomized phase III trial ClarIDHy	186 patients Previously treated, advanced iCCA	ctDNA/digital PCR	IDH1: 92% concordance between plasma ctDNA and tissue samples	mIDH1 detection in plasma ctDNA and tumor tissue was concordant in 92% of samples (193/210) Among ivosidenib-treated patients, IDH1 mutation clearance occurred in 10/36 (28%) with PFS ≥ 2.7 months versus 0/40 with PFS < 2.7 months No IDH1 mutation clearance was observed in any placebo-treated patients (n = 49), regardless of outcome
2021	Chen et al. [65]	Retrospective study	150 patients Metastatic BTCs	QIAamp Circulating Nucleic Acid Kit for cfDNA extraction	TP53: 35.1% in ctDNA vs. 40.4% in tissue samples KRAS: 20.1% in ctDNA vs. 22.6% in tissue samples	94.8% of patients showed at least one change detected in their ctDNA Median maximum somatic allele frequency was 6.47% (0.1–34.8%) Higher tumor mutation burden: patients with mutations in LRP1B, TP53, or ERBB family genes had significantly higher tumor mutation burden
2021	Okamura et al. [72]	Observational genomic profiling study conducted under the UCSD-PREDICT prospective protocol (NCT02478931)	121 patients Pathologically confirmed BTCs	Guardant^®	Overall population: TP53: 68% KRAS: 80% PIK3CA: 90% Metastatic site vs. Primary tumor: TP53: 78% vs. 65% KRAS: 100% vs. 74% PIK3CA: 100% vs. 87%	Common genetic alterations: ctDNA: TP53 (38%), KRAS (28%), PIK3CA (14%) Tissue-DNA: TP53 (44%), CDKN2A/B (33%), KRAS (29%) Clinical outcomes: Matched therapy: longer PFS (HR 0.60, P = 0.047) and higher disease control (61% vs. 35%, P = 0.04) Unmatched therapy: shorter PFS and lower disease control
2021	Yang et al. [73]	Multicohort observational analysis	187 patients ICI cohort 1 (n = 43): PD-1 inhibitor + lenvatinib ICI cohort 2 (n = 108): other ICI-based regimens Non-ICI cohort (n = 36): non-ICI therapies	MagMAX cfDNA isolation Kit; TIANamp genomic DNA Kit	No comparison to tissue	CNV detection by liquid biopsy can predict response to immunotherapy Lower CNV risk scores were associated with higher clinical benefit rates in both ICI cohorts Patients with low CNV risk scores exhibited lower rates of PD and higher rates of SD and PR Higher disease control rate was observed in low CNV risk groups compared to high-risk groups Elevated CNV risk scores were linked to increased PD rates in both ICI cohorts
2022	Berchuck et al. [68]	Retrospective, multi-institutional study	1,671 patients Advanced BTCs	Guardant^®	IDH1: 87% concordance between cfDNA and tissue samples BRAF V600E: 100% concordance FGFR2 fusions: 18% concordance	Targetable alterations detected in 44% of patients
2025	Hwang et al. [67]	Retrospective single-center study	102 patients Systemic treatment-naive advanced BTCs (49% iCCA, 26.5% eCCA, 24.5% gallbladder cancer)	Oncomine Comprehensive Assay and AlphaLiquid^®100 panels	IDH1 mutations: sensitivity: 100%; PPV: 71.4% PIK3CA mutations: sensitivity: 100%; PPV: 83.3% BRCA1/2 mutations: sensitivity: 100%; PPV: 77.8% MET amplifications: sensitivity: 100%; PPV: 100% MSI-high: sensitivity: 100%; PPV: 100% ERBB2 amplifications: sensitivity: 40.0%; PPV: 100%	ctDNA identified targetable alterations in 34.3% of patients, including FGFR2 fusions, IDH1 mutations, MSI, ERBB2 amplifications, PIK3CA mutations, BRCA1/2 mutations, and MET amplification A novel FGFR2-TNS1 fusion was detected via ctDNA analysis The highest ctDNA variant allele frequency is associated with chemotherapy outcome
Evaluation of resistance mechanisms during treatment
2017	Goyal et al. [74]	Prospective translational analysis within the context of the BGJ398 phase II trial	9 patients, 4 of them included in the BGJ398 trial FGFR2 fusion-positive iCCA	Guardant^®	No comparison to tissue	All 3 FGFR2 fusion-positive iCCA patients developed secondary FGFR2 kinase-domain mutations upon progression 2 patients exhibited multiple distinct FGFR2 mutations, indicating polyclonal resistance

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BRAF: v-Raf murine sarcoma viral oncogene homolog B; BRCA1/2: breast cancer 1/2; BTCs: biliary tract cancers; cfDNA: cell-free DNA; CNV: copy number variation; ctDNA: circulating tumor DNA; eCCA: extrahepatic cholangiocarcinoma; FGFR2: fibroblast growth factor receptor 2; HR: hazard ratio; iCCA: intrahepatic cholangiocarcinoma; ICI: immune checkpoint inhibitor; IDH1: isocitrate dehydrogenase 1; MSI: microsatellite instability; NGS: next-generation sequencing; OS: overall survival; PCR: polymerase chain reaction; PD: progressive disease; PD-1: programmed cell death 1; PFS: progression-free survival; PPV: positive predictive value; PR: partial response; RFS: recurrence-free survival; SD: stable disease

Declarations

Author contributions

JG: Conceptualization, Investigation, Writing—original draft, Writing—review & editing. HM: Conceptualization, Investigation, Writing—original draft, Validation, Writing—review & editing, Supervision. All authors read and approved the submitted version.

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The authors declare that they have no conflicts of interest.

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References

Banales JM, Marin JJG, Lamarca A, Rodrigues PM, Khan SA, Roberts LR, et al. Cholangiocarcinoma 2020: the next horizon in mechanisms and management. Nat Rev Gastroenterol Hepatol. 2020;17:557–88. [DOI] [PubMed] [PMC]

Banales JM, Cardinale V, Carpino G, Marzioni M, Andersen JB, Invernizzi P, et al. Cholangiocarcinoma: current knowledge and future perspectives consensus statement from the European Network for the Study of Cholangiocarcinoma (ENS-CCA). Nat Rev Gastroenterol Hepatol. 2016;13:261–80. [DOI] [PubMed]

Qurashi M, Vithayathil M, Khan SA. Epidemiology of cholangiocarcinoma. Eur J Surg Oncol. 2025;51:107064. [DOI] [PubMed]

Valle JW, Lamarca A, Goyal L, Barriuso J, Zhu AX. New Horizons for Precision Medicine in Biliary Tract Cancers. Cancer Discov. 2017;7:943–62. [DOI] [PubMed] [PMC]

Oh DY, Ruth He A, Qin S, Chen LT, Okusaka T, Vogel A, et al. Durvalumab plus Gemcitabine and Cisplatin in Advanced Biliary Tract Cancer. NEJM Evid. 2022;1:EVIDoa2200015. [DOI] [PubMed]

Kelley RK, Ueno M, Yoo C, Finn RS, Furuse J, Ren Z, et al.; KEYNOTE-966 Investigators. Pembrolizumab in combination with gemcitabine and cisplatin compared with gemcitabine and cisplatin alone for patients with advanced biliary tract cancer (KEYNOTE-966): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet. 2023;401:1853–65. [DOI] [PubMed]

Pellino A, Loupakis F, Cadamuro M, Dadduzio V, Fassan M, Guido M, et al. Precision medicine in cholangiocarcinoma. Transl Gastroenterol Hepatol. 2018;3:40. [DOI] [PubMed] [PMC]

Javle MM, Murugesan K, Shroff RT, Borad MJ, Abdel-Wahab R, Schrock AB, et al. Profiling of 3,634 cholangiocarcinomas (CCA) to identify genomic alterations (GA), tumor mutational burden (TMB), and genomic loss of heterozygosity (gLOH). JCO. 2019;37:4087. [DOI]

Drilon A. TRK inhibitors in TRK fusion-positive cancers. Ann Oncol. 2019;30:viii23–30. [DOI] [PubMed]

10.

Zheng Y, Qin Y, Gong W, Li H, Li B, Wang Y, et al. Specific genomic alterations and prognostic analysis of perihilar cholangiocarcinoma and distal cholangiocarcinoma. J Gastrointest Oncol. 2021;12:2631–42. [DOI] [PubMed] [PMC]

11.

Vogel A, Bridgewater J, Edeline J, Kelley RK, Klümpen HJ, Malka D, et al.; ESMO Guidelines Committee. Biliary tract cancer: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up. Ann Oncol. 2023;34:127–40. [DOI] [PubMed]

12.

Bonneville R, Krook MA, Kautto EA, Miya J, Wing MR, Chen HZ, et al. Landscape of Microsatellite Instability Across 39 Cancer Types. JCO Precis Oncol. 2017;2017:PO.17.00073. [DOI] [PubMed] [PMC]

13.

Lee V, Murphy A, Le DT, Diaz LA Jr. Mismatch Repair Deficiency and Response to Immune Checkpoint Blockade. Oncologist. 2016;21:1200–11. [DOI] [PubMed] [PMC]

14.

Lee PC, Hendifar A, Osipov A, Cho M, Li D, Gong J. Targeting the Fibroblast Growth Factor Receptor (FGFR) in Advanced Cholangiocarcinoma: Clinical Trial Progress and Future Considerations. Cancers (Basel). 2021;13:1706. [DOI] [PubMed] [PMC]

15.

Katoh M. Fibroblast growth factor receptors as treatment targets in clinical oncology. Nat Rev Clin Oncol. 2019;16:105–22. [DOI] [PubMed]

16.

Krook MA, Reeser JW, Ernst G, Barker H, Wilberding M, Li G, et al. Fibroblast growth factor receptors in cancer: genetic alterations, diagnostics, therapeutic targets and mechanisms of resistance. Br J Cancer. 2021;124:880–92. [DOI] [PubMed] [PMC]

17.

Abou-Alfa GK, Sahai V, Hollebecque A, Vaccaro G, Melisi D, Al-Rajabi R, et al. Pemigatinib for previously treated, locally advanced or metastatic cholangiocarcinoma: a multicentre, open-label, phase 2 study. Lancet Oncol. 2020;21:671–84. [DOI] [PubMed] [PMC]

18.

Javle M, Roychowdhury S, Kelley RK, Sadeghi S, Macarulla T, Weiss KH, et al. Infigratinib (BGJ398) in previously treated patients with advanced or metastatic cholangiocarcinoma with FGFR2 fusions or rearrangements: mature results from a multicentre, open-label, single-arm, phase 2 study. Lancet Gastroenterol Hepatol. 2021;6:803–15. [DOI] [PubMed]

19.

WITHDRAWN: FDA grants accelerated approval to infigratinib for metastatic cholangiocarcinoma [Internet]. FDA [cited 2025 Apr 15]. Available from: https://www.fda.gov/drugs/resources-information-approved-drugs/withdrawn-fda-grants-accelerated-approval-infigratinib-metastatic-cholangiocarcinoma

20.

Macarulla T, Mizuno T, Brandi G, Li J, Chen M-H, Kang JH, et al. FOENIX-CCA4: A phase 2 study of futibatinib 20 mg and 16 mg in patients with advanced cholangiocarcinoma (CCA) and fibroblast growth factor receptor 2 (FGFR2) fusions/rearrangements. JCO. 2024;42:TPS572. [DOI]

21.

Borad MJ, Schram AM, Kim RD, Kamath SD, Sahai V, Dotan E, et al. Updated dose escalation results for ReFocus, a first-in-human study of highly selective FGFR2 inhibitor RLY-4008 in cholangiocarcinoma and other solid tumors. JCO. 2023;41:4009. [DOI]

22.

Droz Dit Busset M, Shaib WL, Mody K, Personeni N, Damjanov N, Harris WP, et al. 47P Derazantinib for patients with intrahepatic cholangiocarcinoma harboring FGFR2 fusions/rearrangements: Primary results from the phase II study FIDES-01. Ann Oncol. 2021;32:S376. [DOI]

23.

Pant S, Schuler M, Iyer G, Witt O, Doi T, Qin S, et al.; RAGNAR Investigators. Erdafitinib in patients with advanced solid tumours with FGFR alterations (RAGNAR): an international, single-arm, phase 2 study. Lancet Oncol. 2023;24:925–35. [DOI] [PubMed] [PMC]

24.

Waitkus MS, Diplas BH, Yan H. Biological Role and Therapeutic Potential of IDH Mutations in Cancer. Cancer Cell. 2018;34:186–95. [DOI] [PubMed] [PMC]

25.

Zhu AX, Macarulla T, Javle MM, Kelley RK, Lubner SJ, Adeva J, et al. Final Overall Survival Efficacy Results of Ivosidenib for Patients With Advanced Cholangiocarcinoma With IDH1 Mutation: The Phase 3 Randomized Clinical ClarIDHy Trial. JAMA Oncol. 2021;7:1669–77. [DOI] [PubMed] [PMC]

26.

Jones RL, Macarulla T, Charlson JA, Van Tine BA, Goyal L, Italiano A, et al. A phase Ib/II study of olutasidenib in patients with relapsed/refractory IDH1 mutant solid tumors: Safety and efficacy as single agent. JCO. 2020;38:e16643. [DOI]

27.

Rodon J, Goyal L, Mercade TM, Ikeda M, Kondo S, Oh DY, et al. Abstract CT098: A first-in-human phase 1 study of LY3410738, a covalent inhibitor of mutant IDH, in advanced IDH-mutant cholangiocarcinoma and other solid tumors. Cancer Res. 2023;83:CT098. [DOI]

28.

Harding JJ, Lowery MA, Shih AH, Schvartzman JM, Hou S, Famulare C, et al. Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition. Cancer Discov. 2018;8:1540–7. [DOI] [PubMed] [PMC]

29.

Yang X, Wu H. RAS signaling in carcinogenesis, cancer therapy and resistance mechanisms. J Hematol Oncol. 2024;17:108. [DOI]

30.

Robertson S, Hyder O, Dodson R, Nayar SK, Poling J, Beierl K, et al. The frequency of KRAS and BRAF mutations in intrahepatic cholangiocarcinomas and their correlation with clinical outcome. Hum Pathol. 2013;44:2768–73. [DOI] [PubMed] [PMC]

31.

Tannapfel A, Sommerer F, Benicke M, Katalinic A, Uhlmann D, Witzigmann H, et al. Mutations of the BRAF gene in cholangiocarcinoma but not in hepatocellular carcinoma. Gut. 2003;52:706–12. [DOI] [PubMed] [PMC]

32.

Wang W, Lian B, Xu C, Wang Q, Li Z, Zheng N, et al. Expert consensus on the diagnosis and treatment of solid tumors with BRAF mutations. Innovation (Camb). 2024;5:100661. [DOI] [PubMed] [PMC]

33.

Subbiah V, Lassen U, Élez E, Italiano A, Curigliano G, Javle M, et al. Dabrafenib plus trametinib in patients with BRAF^V600E-mutated biliary tract cancer (ROAR): a phase 2, open-label, single-arm, multicentre basket trial. Lancet Oncol. 2020;21:1234–43. [DOI] [PubMed]

34.

Ko AH, Zalupski M, Al-Rajabi RMT, Matin K, Cohen DJ, Krishnamurthi SS, et al. A phase 2 basket trial of ulixertinib (BVD-523) in combination with hydroxychloroquine in patients with advanced gastrointestinal malignancies harboring MAPK pathway mutations (BVD-523-HCQ). JCO. 2023;41:TPS4174. [DOI]

35.

Doherty MK, Tam VC, McNamara MG, Jang R, Hedley D, Chen E, et al. Randomised, Phase II study of selumetinib, an oral inhibitor of MEK, in combination with cisplatin and gemcitabine chemotherapy for patients with advanced biliary tract cancer. Br J Cancer. 2022;127:1473–8. [DOI] [PubMed] [PMC]

36.

Tomuleasa C, Tigu AB, Munteanu R, Moldovan CS, Kegyes D, Onaciu A, et al. Therapeutic advances of targeting receptor tyrosine kinases in cancer. Signal Transduct Target Ther. 2024;9:201. [DOI] [PubMed] [PMC]

37.

Javle M, Borad MJ, Azad NS, Kurzrock R, Abou-Alfa GK, George B, et al. Pertuzumab and trastuzumab for HER2-positive, metastatic biliary tract cancer (MyPathway): a multicentre, open-label, phase 2a, multiple basket study. Lancet Oncol. 2021;22:1290–300. [DOI] [PubMed]

38.

Ohba A, Morizane C, Ueno M, Kobayashi S, Kawamoto Y, Komatsu Y, et al. Multicenter phase II trial of trastuzumab deruxtecan for HER2-positive unresectable or recurrent biliary tract cancer: HERB trial. Future Oncol. 2022;18:2351–60. [DOI] [PubMed]

39.

Meric-Bernstam F, Makker V, Oaknin A, Oh DY, Banerjee S, González-Martín A, et al. Efficacy and Safety of Trastuzumab Deruxtecan in Patients With HER2-Expressing Solid Tumors: Primary Results From the DESTINY-PanTumor02 Phase II Trial. J Clin Oncol. 2024;42:47–58. [DOI] [PubMed] [PMC]

40.

Harding JJ, Fan J, Oh DY, Choi HJ, Kim JW, Chang HM, et al. Zanidatamab for HER2-amplified, unresectable, locally advanced or metastatic biliary tract cancer (HERIZON-BTC-01): a multicentre, single-arm, phase 2b study. Lancet Oncol. 2023;24:772–82. [DOI] [PubMed]

41.

Piha-Paul SA, Azaro A, Arkenau HT, Oh DY, Galsky MD, Pal SK, et al. A first-in-human phase I study of TAS0728, an oral covalent binding inhibitor of HER2, in patients with advanced solid tumors with HER2 or HER3 aberrations. Invest New Drugs. 2021;39:1324–34. [DOI] [PubMed] [PMC]

42.

Chen X, Guo F, Zhang X, Qiu J, Zheng T, Qiu H, et al. A single-arm, open-label, phase II study investigating anti-HER2 ADC plus anti-PD-1 antibody in patients with unresectable locally advanced or metastatic BTC with HER2 overexpression. JCO. 2023;41:TPS619. [DOI]

43.

Ten Haaft BH, Pedregal M, Prato J, Klümpen HJ, Moreno V, Lamarca A. Revolutionizing anti-HER2 therapies for extrahepatic cholangiocarcinoma and gallbladder cancer: Current advancements and future perspectives. Eur J Cancer. 2024;199:113564. [DOI] [PubMed]

44.

Marabelle A, Le DT, Ascierto PA, Di Giacomo AM, De Jesus-Acosta A, Delord JP, et al. Efficacy of Pembrolizumab in Patients With Noncolorectal High Microsatellite Instability/Mismatch Repair-Deficient Cancer: Results From the Phase II KEYNOTE-158 Study. J Clin Oncol. 2020;38:1–10. [DOI] [PubMed] [PMC]

45.

FDA Converts to Full Approval Indication for KEYTRUDA® (pembrolizumab) for Certain Adult and Pediatric Patients With Advanced Microsatellite Instability-High (MSI-H) or Mismatch Repair Deficient (dMMR) Solid Tumors [Internet]. Rahway: Merck & Co., Inc.; c2025 [cited 2025 Feb 22]. Available from: https://www.merck.com/news/fda-converts-to-full-approval-indication-for-keytruda-pembrolizumab-for-certain-adult-and-pediatric-patients-with-advanced-microsatellite-instability-high-msi-h-or-mismatch-repair-deficient/

46.

Huang EJ, Reichardt LF. Neurotrophins: roles in neuronal development and function. Annu Rev Neurosci. 2001;24:677–736. [DOI] [PubMed] [PMC]

47.

Thiele CJ, Li Z, McKee AE. On Trk—the TrkB signal transduction pathway is an increasingly important target in cancer biology. Clin Cancer Res. 2009;15:5962–7. [DOI] [PubMed] [PMC]

48.

Amatu A, Sartore-Bianchi A, Bencardino K, Pizzutilo EG, Tosi F, Siena S. Tropomyosin receptor kinase (TRK) biology and the role of NTRK gene fusions in cancer. Ann Oncol. 2019;30:viii5–15. [DOI] [PubMed] [PMC]

49.

Hong DS, DuBois SG, Kummar S, Farago AF, Albert CM, Rohrberg KS, et al. Larotrectinib in patients with TRK fusion-positive solid tumours: a pooled analysis of three phase 1/2 clinical trials. Lancet Oncol. 2020;21:531–540. [DOI] [PubMed] [PMC]

50.

FDA approves entrectinib for NTRK solid tumors and ROS‑1 NSCLC [Internet]. [cited 2025 Jan 25]. Available from: https://www.fda.gov/drugs/resources-information-approved-drugs/fda-approves-entrectinib-ntrk-solid-tumors-and-ros-1-nsclc

51.

Spizzo G, Puccini A, Xiu J, Goldberg RM, Grothey A, Shields AF, et al. Molecular profile of BRCA-mutated biliary tract cancers. ESMO Open. 2020;5:e000682. [DOI] [PubMed] [PMC]

52.

Trikudanathan G, Navaneethan U, Njei B, Vargo JJ, Parsi MA. Diagnostic yield of bile duct brushings for cholangiocarcinoma in primary sclerosing cholangitis: a systematic review and meta-analysis. Gastrointest Endosc. 2014;79:783–9. [DOI] [PubMed]

53.

Rompianesi G, Di Martino M, Gordon-Weeks A, Montalti R, Troisi R. Liquid biopsy in cholangiocarcinoma: Current status and future perspectives. World J Gastrointest Oncol. 2021;13:332–50. [DOI] [PubMed] [PMC]

54.

Ilyas SI, Affo S, Goyal L, Lamarca A, Sapisochin G, Yang JD, et al. Cholangiocarcinoma - novel biological insights and therapeutic strategies. Nat Rev Clin Oncol. 2023;20:470–86. [DOI] [PubMed] [PMC]

55.

Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011;11:426–37. [DOI] [PubMed]

56.

Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 2016;164:57–68. [DOI] [PubMed] [PMC]

57.

Reck M, Gale D, Zhu Z, Harpole D, Taube J, Mitsudomi T, et al. LBA49 Associations of ctDNA clearance (CL) during neoadjuvant Tx with pathological response and event-free survival (EFS) in pts with resectable NSCLC (R-NSCLC): Expanded analyses from AEGEAN. Ann Oncol. 2024;35:S1239. [DOI]

58.

Yoo C, Laliotis G, Jeong H, Jeong JH, Kim K-P, Lee S, et al. Utility of circulating tumor DNA (ctDNA) as a predictive biomarker for disease monitoring in patients (pts) with cholangiocarcinoma (CCA) before and during adjuvant chemotherapy (ACT): Sub-analysis of the randomized phase 2 STAMP trial. JCO. 2023;41:4123. [DOI]

59.

Yu J, Avriett TA, Ray CM, Kim RD. Circulating tumor DNA analysis guiding adjuvant treatment in resected stage III cholangiocarcinoma: a case report. J Gastrointest Oncol. 2024;15:485–90. [DOI] [PubMed] [PMC]

60.

Monroe G, Malla M. Post-operative Surveillance and Management of Intrahepatic Cholangiocarcinoma Using Circulating Tumor DNA: A Case Report. Cureus. 2024;16:e55914. [DOI] [PubMed] [PMC]

61.

Mody K, Kasi PM, Yang J, Surapaneni PK, Bekaii-Saab T, Ahn DH, et al. Circulating Tumor DNA Profiling of Advanced Biliary Tract Cancers. JCO Precis Oncol. 2019;3:1–9. [DOI] [PubMed]

62.

Ettrich TJ, Schwerdel D, Dolnik A, Beuter F, Blätte TJ, Schmidt SA, et al. Genotyping of circulating tumor DNA in cholangiocarcinoma reveals diagnostic and prognostic information. Sci Rep. 2019;9:13261. [DOI] [PubMed] [PMC]

63.

Lamarca A, Ross P, Wasan HS, Hubner RA, McNamara MG, Lopes A, et al. Advanced Intrahepatic Cholangiocarcinoma: Post Hoc Analysis of the ABC-01, -02, and -03 Clinical Trials. J Natl Cancer Inst. 2020;112:200–10. [DOI] [PubMed]

64.

Aguado E, Abou-Alfa GK, Zhu AX, Macarulla T, Fan B, Nejad P, et al. IDH1 mutation detection in plasma circulating tumor DNA (ctDNA) and association with clinical response in patients with advanced intrahepatic cholangiocarcinoma (IHC) from the phase III ClarIDHy study. JCO. 2020;38:4576. [DOI]

65.

Chen C, Wang T, Yang M, Song J, Huang M, Bai Y, et al. Genomic Profiling of Blood-Derived Circulating Tumor DNA from Patients with Advanced Biliary Tract Cancer. Pathol Oncol Res. 2021;27:1609879. [DOI] [PubMed] [PMC]

66.

Mahipal A, Clemens KM, Liao J, Weipert CM, Bucheit L, Khushman MM. Real-world testing, treatment patterns, and outcomes following liquid biopsy in advanced cholangiocarcinoma. JCO. 2024;42:455. [DOI]

67.

Hwang S, Woo S, Kang B, Kang H, Kim JS, Lee SH, et al. Concordance of ctDNA and tissue genomic profiling in advanced biliary tract cancer. J Hepatol. 2025;82:649–57. [DOI] [PubMed]

68.

Berchuck JE, Facchinetti F, DiToro DF, Baiev I, Majeed U, Reyes S, et al. The clinical landscape of cell-free DNA alterations in 1671 patients with advanced biliary tract cancer. Ann Oncol. 2022;33:1269–83. [DOI] [PubMed]

69.

Silverman IM, Hollebecque A, Friboulet L, Owens S, Newton RC, Zhen H, et al. Clinicogenomic Analysis of FGFR2-Rearranged Cholangiocarcinoma Identifies Correlates of Response and Mechanisms of Resistance to Pemigatinib. Cancer Discov. 2021;11:326–39. [DOI] [PubMed]

70.

Neumann O, Burn TC, Allgäuer M, Ball M, Kirchner M, Albrecht T, et al. Genomic architecture of FGFR2 fusions in cholangiocarcinoma and its implication for molecular testing. Br J Cancer. 2022;127:1540–9. [DOI] [PubMed] [PMC]

71.

Larson MH, Pan W, Kim HJ, Mauntz RE, Stuart SM, Pimentel M, et al. A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection. Nat Commun. 2021;12:2357. [DOI] [PubMed] [PMC]

72.

Okamura R, Kurzrock R, Mallory RJ, Fanta PT, Burgoyne AM, Clary BM, et al. Comprehensive genomic landscape and precision therapeutic approach in biliary tract cancers. Int J Cancer. 2021;148:702–12. [DOI] [PubMed] [PMC]

73.

Yang X, Hu Y, Yang K, Wang D, Lin J, Long J, et al. Cell-free DNA copy number variations predict efficacy of immune checkpoint inhibitor-based therapy in hepatobiliary cancers. J Immunother Cancer. 2021;9:e001942. [DOI] [PubMed] [PMC]

74.

Goyal L, Saha SK, Liu LY, Siravegna G, Leshchiner I, Ahronian LG, et al. Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma. Cancer Discov. 2017;7:252–63. [DOI] [PubMed] [PMC]

75.

Goyal L, Shi L, Liu LY, Fece de la Cruz F, Lennerz JK, Raghavan S, et al. TAS-120 Overcomes Resistance to ATP-Competitive FGFR Inhibitors in Patients with FGFR2 Fusion-Positive Intrahepatic Cholangiocarcinoma. Cancer Discov. 2019;9:1064–79. [DOI] [PubMed] [PMC]

76.

Goyal L, DiToro D, Facchinetti F, Martin EE, Peng P, Baiev I, et al. A model for decoding resistance in precision oncology: acquired resistance to FGFR inhibitors in cholangiocarcinoma. Ann Oncol. 2025;36:426–43. [DOI] [PubMed]

77.

Driescher C, Fuchs K, Haeberle L, Goering W, Frohn L, Opitz FV, et al. Bile-Based Cell-Free DNA Analysis Is a Reliable Diagnostic Tool in Pancreatobiliary Cancer. Cancers (Basel). 2020;13:39. [DOI] [PubMed] [PMC]

78.

Shen N, Zhang D, Yin L, Qiu Y, Liu J, Yu W, et al. Bile cellfree DNA as a novel and powerful liquid biopsy for detecting somatic variants in biliary tract cancer. Oncol Rep. 2019;42:549–60. [DOI] [PubMed] [PMC]

79.

Li Z, Liu Y, Fu J, Mugaanyi J, Yan J, Lu C, et al. Bile is a reliable and valuable source to study cfDNA in biliary tract cancers. Front Oncol. 2022;12:961939. [DOI] [PubMed] [PMC]

80.

Han JY, Ahn KS, Kim TS, Kim YH, Cho KB, Shin DW, et al. Liquid Biopsy from Bile-Circulating Tumor DNA in Patients with Biliary Tract Cancer. Cancers (Basel). 2021;13:4581. [DOI] [PubMed] [PMC]

81.

Arechederra M, Rullán M, Amat I, Oyon D, Zabalza L, Elizalde M, et al. Next-generation sequencing of bile cell-free DNA for the early detection of patients with malignant biliary strictures. Gut. 2022;71:1141–51. [DOI] [PubMed] [PMC]

82.

Javle MM, Rimassa L, Goyal L, Mahipal A, Fountzilas C, Liao CY, et al. First-308: Phase III study of tinengotinib versus physician’s choice in patients with FGFR-altered, chemotherapy- and FGFR inhibitor–refractory/relapsed cholangiocarcinoma. JCO. 2024;42:TPS575. [DOI]