Salivary Digital PCR With Epigenetic Cell Counting Correction as a Feasible Non-Invasive Platform for Longitudinal JAK2V617F Monitoring in Myeloproliferative Neoplasms

Abstract Intensive longitudinal monitoring of somatic mutation variant allele frequency (VAF) is needed to characterize clonal dynamics during therapy in myeloproliferative neoplasms (MPN). Salivary digital PCR, corrected for buccal epithelial DNA contamination by epigenetic cell counting (ECC), has not been formally benchmarked against whole blood and plasma cell-free DNA (cfDNA) as a quantitative monitoring platform. We evaluated concordance of JAK2 V617F VAF across four simultaneously collected biospecimens (whole blood, ACK-lysed white blood cells, saliva, plasma cfDNA) in 12 prospective IFNα-treated MPN patients monitored weekly over 12 months. Feasibility of mail-based at-home collection was assessed by sample return rate and DNA yield. ECC-corrected salivary VAF achieved r = 0.990 concordance with whole blood ( n = 33), approaching the agreement between two blood-derived sources ( r = 0.988, n = 69) and substantially outperforming cfDNA ( r = 0.817, n = 40). Overall, there was a 90% sample return rate and 96% of participant-months met the 5 ng/µL DNA threshold for digital PCR. These findings establish proof of concept for ECC-corrected salivary digital PCR as a feasible and analytically rigorous non-invasive platform for longitudinal mutation monitoring that outperforms cfDNA. The 90% sample return rate and 96% DNA adequacy over 12 months support the use of this approach in larger decentralized studies, though formal validation in adequately powered cohorts will be required before clinical deployment.