Concordance of Flow Cytometry and Real-Time Quantitative Polymerase Chain Reaction for Measurable Residual Disease Detection in Childhood B-Cell Acute Lymphoblastic Leukemia: A Real-Life Data Analysis

Objective: Measurable residual disease (MRD) is the cornerstone of risk-adapted therapy in childhood B-cell acute lymphoblastic leukemia (B-ALL). In Türkiye, MRD assessment relies on flow cytometry (FCM), whereas molecular MRD is not routinely available. We aimed to evaluate the concordance between an experienced FCM laboratory and an international EuroMRD reference real-time quantitative polymerase chain reaction (RQ-PCR) laboratory and its potential impact on treatment. Patients, Materials and Methods: In this real-world study, 85 paired bone marrow samples from 46 children with B-ALL were analyzed simultaneously for MRD by FCM and RQ-PCR. MRD positivity was defined as ≥1×10⁻⁴. Qualitative agreement was evaluated by concordance and Cohen's kappa coefficient. Diagnostic performance of FCM was evaluated using RQ-PCR as the reference method. Results: Qualitative concordance between FCM and RQ-PCR was 87.1%, indicating moderate agreement (κ=0.64, 95% CI 0.45-0.83). Concordance was 83% at the end of induction (EOI) (κ=0.58) and 93% at the end of consolidation (EOC) (κ=0.71). FCM showed excellent specificity (96.8%), but modest sensitivity (60.9%). Reliance on FCM alone would have altered MRD-guided treatment allocation in 17% of patients at EOI and 7% at EOC, mainly because of false-negative results. Conclusion: FCM-MRD performed in an experienced laboratory demonstrated moderate agreement with an international EuroMRD reference laboratory but failed to detect some RQ-PCR-MRD positivite cases, potentially affecting treatment decisions. These findings highlight the need for continuous quality assurance, national reference laboratories, dedicated MRD laboratory teams with long-term continuity, and complementary use of molecular MRD techniques alongside FCM to standardize MRD assessment.