Abstract 1916: Oncogenic fusion detection for leukemia patients using droplet digital PCR

Abstract Accurate quantification of residual disease burden in acute myeloid leukemia (AML) patients is of paramount importance for treatment decision-making and long-term survival. Currently, measurable residual disease (MRD) detection is assessed using multiparameter flow cytometry, RT-qPCR or sequencing. Unfortunately, these techniques are limited by high costs, utility in only a subset of patients, and slow turnaround. In half of leukemia patients, gene fusions drive their disease. Despite oncogenic fusions representing the ideal biomarker for MRD monitoring in these patients, molecular assays to detect these fusions are available in only a limited subset of cases (e.g. BCR-ABL, RUNX1-RUNX1T1). This is largely due to qPCR-based assays not being scalable to cover all the potential fusions, reliance on standard curves, and relative quantification. To address this unmet need, we have developed a sensitive, specific, rapid and scalable droplet-digital PCR (ddPCR)-based assay for personalized gene fusion detection. This assay uses fusion break-point information obtained from clinical sequencing to inform a personalized ddPCR assay targeting each individual’s disease-defining fusion. As proof of principle, we applied our assay to KMT2A fusion detection. We selected KMT2A fusions because they are challenging to target for MRD detection given the diverse spectrum of fusion partners and the clinical need to assess response to therapy with novel Menin inhibitors that target these fusions. In this proof-of-principle study at Washington University, we banked serial specimens from 19 patients with KMT2A fusion driven acute leukemia. From sequencing obtained at diagnosis, we determined each patient’s fusion breakpoint and designed their personalized fusion detection assay. In diagnostic specimens, these assays reliably detected each patient’s oncogenic fusion. We subsequently banked 1-17 serial peripheral blood or bone marrow specimens per patients for longitudinal monitoring. For four patients with treatment failure, we were able to detect persistent/increasing fusion abundance in the peripheral blood up to 100 days before detection by standard of care bone marrow assessment. For the remainder of patients who achieved a remission, we observed clearance of their fusions to a limit of detection of 1:100, 000. This study highlights the utility of our approach for sensitive, personalized fusion MRD detection. This assay has the potential to change the paradigm for MRD monitoring in acute leukemia from discrete testing of bone marrow samples at the end of induction or consolidation to serial peripheral blood monitoring throughout treatment. This is possible because our assay is inexpensive, rapid to turnaround, and highly sensitive in peripheral blood. Long-term this could improve real-time disease burden assessment to improve treatment decision-making and outcomes for patients with any fusion driven leukemia. Citation Format: Hannah C. Davis, Ellie R. Wilson, Xiaojuan Cao, Maggie J. Cox, Francesca Ferraro, David H. Spencer, Stephen T. Oh, Grant A. Challen, Andrew L. Young. Oncogenic fusion detection for leukemia patients using droplet digital PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1916.