Ultra-Low BCR::ABL1 positivity by digital PCR does not improve post-transplant risk stratification beyond real-time PCR in Ph+ acute lymphoblastic leukemia post-transplant

BACKGROUND: Post-transplant relapse remains a major clinical challenge in Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph + ALL). Real-time quantitative PCR (RQ-PCR) for BCR::ABL1 is the current standard for measurable residual disease (MRD) monitoring, whereas digital PCR (dPCR) offers substantially higher analytical sensitivity. Whether this increased sensitivity translates into additional prognostic value after allogeneic hematopoietic stem cell transplantation (allo-HSCT) remains unclear. METHODS: In this prospective study (NCT06211166), 270 patients with Ph + ALL were longitudinally monitored after allo-HSCT. MRD was assessed in parallel using dPCR, RQ-PCR, and MFC. Based on the first post-transplant MRD detection pattern, patients were categorized into four groups: double-negative (n = 80), dPCR-single-positive (n = 158), RQ-PCR-single-positive (n = 3), and double-positive (n = 29). RESULTS: The dPCR-single-positive pattern was the most prevalent MRD status, accounting for 58.5% of patients. dPCR positivity independently predicted subsequent MFC-MRD conversion (HR 9.56, P = 0.029), with a median lead time of 77 days. In addition, dPCR detected BCR::ABL1 positivity earlier than RQ-PCR, preceding subsequent hematologic relapse by a median of 64.5 and 91.5 days, respectively. However, the cumulative incidence of hematologic relapse (CIR), the primary endpoint of this study, did not differ significantly among the four MRD-defined groups (P = 0.60). Consistently, isolated dPCR positivity was not associated with inferior 2-year leukemia-free survival (LFS; P = 0.30) or overall survival (OS; P = 0.60). CONCLUSIONS: Although dPCR detects molecular disease earlier and anticipates MFC-MRD by 2 months after allo-HSCT in Ph + ALL, isolated ultra-low-level BCR::ABL1 positivity does not impact relapse risk, LFS, or OS. Routine MRD monitoring with RQ-PCR plus MFC remains sufficient for prognostic stratification, while dPCR primarily provides an ultra-early signal to guide timely intervention rather than improving survival prediction.