Comparative Evaluation of Quantitative Real-Time PCR and a Laboratory-Developed Chip-Based Real-Time Digital PCR for JAK2 V617F Allele Burden in Myeloproliferative Neoplasms

Background: Precise quantification of JAK2 V617F variant allele frequency (VAF) is clinically important in Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs). This study evaluated the analytical performance and clinical utility of a laboratory-developed chip-based real-time digital PCR (dPCR) assay for JAK2 V617F and compared it with a commercial quantitative real-time PCR (qPCR) assay. Methods: Residual DNA extracts from 76 JAK2 V617F-positive clinical specimens collected from patients with suspected MPNs were analyzed using both qPCR and dPCR. Analytical performance was assessed according to CLSI-based approaches, including limit of blank (LoB), limit of detection (LoD), precision, linearity, and method comparison. Associations between VAF and hematologic parameters, as well as diagnostic groups, were also examined. Results: Both methods showed a LoB of 0. The LoD was 0.1167% for qPCR and 0.0846% for dPCR, and dPCR demonstrated lower variability than qPCR across high-, intermediate-, and low-concentration samples, with the largest difference observed at low VAF levels. Linearity was excellent for both assays (R2 = 0.988 for qPCR and 0.999 for dPCR), although dPCR showed less low-concentration bias. The two methods were highly correlated (Pearson r = 0.9789, R2 = 0.958), but dPCR yielded slightly higher VAF values overall. VAF was significantly higher in polycythemia vera than in essential thrombocythemia, and both qPCR- and dPCR-based VAFs were positively correlated with white blood cell count. Conclusions: The chip-based laboratory-developed dPCR assay showed high concordance with qPCR while providing lower LoD and better precision at low allele burden. These findings support its potential utility as a sensitive alternative for JAK2 V617F quantification in clinical laboratories, particularly in settings requiring accurate low-level detection and follow-up monitoring.