Identifying FGFR2 fusions/rearrangements in cholangiocarcinoma patients using a novel cfDNA algorithm for treatment with RLY-4008, a highly selective irreversible FGFR2 inhibitor

Background: FGFR2 fusions/rearrangements (f/r) are a critical therapeutic target in cholangiocarcinoma (CCA). Genomic profiling based on tumor tissue is standard for CCA patients but can be challenging due to the limited specimens often obtained during diagnostic biopsies and the aggressive nature of the disease prompting clinicians to forego repeat biopsies to rapidly initiate therapy. Cell-free DNA (cfDNA) may offer a noninvasive approach to overcome these tissue limitations, however, there are technical challenges detecting the long tail of unique FGFR2 fusion partners. We assessed the utility of a de novo FGFR2 f/r calling algorithm in identifying these alterations. Methods: Patients with unresectable or metastatic CCA identified with an FGFR2 f/r by local tissue or plasma testing were enrolled in the first-in-human study of RLY-4008, a highly selective FGFR2 irreversible inhibitor (NCT04526106). Pre-treatment samples were evaluated centrally by next generation sequencing (NGS) in tumor tissue and by Guardant360®CDx (G360) in cfDNA. A novel research-use only de novo f/r calling algorithm (fusion partner agnostic) was applied to the G360 test to broaden the capability of detecting FGFR2 f/r. The objective was to evaluate the feasibility (failure rate) and the sensitivity (percent positive agreement [PPA]) of the novel cfDNA f/r-calling algorithm to compare to the local and central tissue assessments for identifying FGFR2 f/r. Results: Forty-eight CCA patients with FGFR2 f/r per local testing had available tumor tissue and plasma for central testing. All of these patients had FGFR2 f/r initially identified based on tumor tissue. FGFR2 f/r included 10 FGFR2-BICC1 fusions and 38 non-FGFR2-BICC1 fusions. Implementation of the de novo f/r calling algorithm increased the f/r calling of G360 from 30 to 38. Undetectable circulating tumor DNA occurred in one patient (2%). The PPA of research-use G360 with local results was 81% (38/47). Central tissue NGS also confirmed 38 f/r with a PPA of 93% (38/41) while failure due to low DNA yield or insufficient tumor content occurred in seven patients (15%). Agreement of FGFR2 f/r calling between the central tissue NGS and research-use G360 was 84% (31/37). Conclusions: In this study, FGFR2 f/r detection using a novel fusion partner-agnostic cfDNA approach has an acceptable performance and is a feasible noninvasive option for screening CCA patients. These encouraging results suggest a utility of cfDNA in FGFR2 f/r profiling, which will be prospectively validated in the RLY-4008-101 pivotal study. Conflict of interest: Ownership: CF: Relay Therapeutics. OSK: Relay Therapeutics. Advisory Board: PC: OSE Immunotherapeutics. LG: (DSMB) AstraZeneca (SAC) Alentis Therapeutics AG, Black Diamond, H3Biomedicine, Incyte Corporation, QED Therapeutics, Servier, Sirtex Medical, Taiho, Transthera, Kinnate. SK: Exelixis, Guardant Health, Tempus. CYAL: Incyte, Transthera, QED Therapeutics. DYO: AstraZeneca, Novartis, Genentech/Roche, Merck Serono, Bayer, Taiho, ASLAN, Halozyme, Zymeworks, BMS/Celgene, BeiGene, Basilea, Turning Point, Yuhan, Arcus Biosciences, IQVIA. MPS: AstraZeneca, GE. AMS: Relay Therapeutics, Mersana. Board of Directors: n/a. Corporate-sponsored Research: MB: Relay Therapeutics. JC: (all institutional funding) Bayer, GlaxoSmithKline, Janssen, Lilly, AstraZeneca, Roche/Genentech, Merck/Serono, Toray Industries, Novartis, Plexxikon, Bristol Myers Squibb, Taiho, Transgene, Innate Pharma, Loxo, Blueprint Medicines, Celgene, Abbvie, Merck Sharp & Dohme. ED: Relay Therapeutics Lilly, Pfizer, Incyte, AstraZeneca, SMP Oncolog, Zymeworks, NGM Biopharmaceuticals, Ipsen, Syneos Health. LG: (all institutional funding) Adaptimmune, Bayer, Eisai, Merck, Macrogenics, Genentech, Novartis, Incyte, Eli Lilly, Loxo Oncology, Relay Therapeutics, QED Therapeutics, Servier, Taiho, LEAP Therapeutics, Bristol Meyers Squibb, Nucana. VM: (all institutional funding/PI) AbbVie, AceaBio, Adaptimmune, ADC Therapeutics, Aduro, Agenus, Amcure, Amgen, Astellas, AstraZeneca, Bayer, Beigene, BioInvent International AB, BMS, Boehringer, Boheringer, Boston, Celgene, Daichii Sankyo, DEBIOPHARM, Eisai, e-Terapeutics, Exelisis, Forma Therapeutics, Genmab, GSK, Harpoon, Hutchison, Immutep, Incyte, Inovio, Iovance, Janssen, Kyowa Kirin, Lilly, Loxo, MedSir, Menarini, Merck, Merus, Millennium, MSD, Nanobiotix, Nektar, Novartis, Odonate Therapeutics, Pfizer, Pharma Mar, PharmaMar, Principia, PsiOxus, Puma, Regeneron, Rigontec, Roche, Sanofi, Sierra Oncology, Synthon, Taiho, Takeda, Tesaro, Transgene, Turning Point Therapeutics, Upshersmith. DYO: (all institutional funding) AstraZeneca, Novartis, Array, Eli Lilly, Servier, BeiGene, MSD, Handok. AMS: (all institutional) AstraZeneca, ArQule, BeiGene/Springworks, Black Diamond Therapeutics, Elevation Oncology, Kura, Lilly, Merus, Northern Biologics, Pfizer, PMV Pharma, Relay Therapeutics, Repare Therapeutics, Revolution Medicine, Surface Oncology. ViS: Relay Therapeutics. Other Substantive Relationships: PC: (honoraria) ITeos Therapeutics, Amgen, Janssen (travel) Netris Pharma, Amgen, Merck Sharp & Dohme, Roche, Merck Serono, AstraZeneca/MedImmune. ED: (consulting fees) QED, Taiho, Helsinn, Incyte, Basilea, SMP Oncology, G1 Therapeutics (honoraria) Pfizer. CF: (employment) Relay Therapeutics. LG: (consulting fees) Alentis Therapeutics, Genentech, Exelixis, Incyte Corporation, QED Therapeutics, Servier, Sirtex Medical, and Taiho. VM: (consulting fees) Roche, Bayer, Pieris, BMS, Janssen, Basilea, Regeneron/Sanofi, Nanobiotix. MPS: (consulting fees) AstraZeneca, Incyte (honoraria) Roche (travel) Incyte, BMS, AstraZeneca (medical writing support) Roche. OSK: (employment) Relay Therapeutics. DT: (honoraria) Ipsen, Eisai, BMS, Roche (consulting fees) Novartis, Celgene, SIRTEX, Eisai, Ipsen, Bayer, BMS (travel) AstraZeneca.