Monitoring of Measurable Residual Disease Using Circulating DNA after Allogeneic Hematopoietic Cell Transplantation

Simple Summary The major cause of treatment failure after allogeneic stem cell transplantation (allo-HSCT) is due to relapse of the underlying disease. Novel methods and strategies are needed to detect early relapse after allo-HSCT. The present study reports the clinical utility of monitoring measurable residual disease (MRD) and mixed chimerism (MC) by droplet-digital PCR in circulating cell-free DNA (cfDNA) in 62 patients with myeloid malignancies undergoing allo-HSCT. MC in circulating cfDNA at an optimal threshold of 18% discriminated patients with hematological relapse from patients in complete remission after allo-HSCT. Most of the mutations identified using a targeted next-generation sequencing (NGS) panel were detected in cfDNA at relapse and were suitable for the monitoring of MRD. In several cases, mutations were detected earlier in cfDNA than in peripheral blood mononuclear cells. In conclusion, longitudinal analysis of cfDNA for MRD and MC can be used as a complementary tool for early detection of relapse in patients after allo-HSCT and could be used to guide clinical interventions. Relapse of the underlying disease is a frequent complication after allogeneic hematopoietic stem cell transplantation (allo-HSCT). In this study, we describe the clinical utility of measurable residual disease (MRD) and mixed chimerism (MC) assessment in circulating cell-free DNA (cfDNA) analysis to detect earlier relapse in patients with hematological malignancies after allo-HSCT. A total of 326 plasma and peripheral blood mononuclear cell (PBMCs) samples obtained from 62 patients with myeloid malignancies were analyzed by droplet-digital PCR (median follow-up: 827 days). Comparison of MC in patients at relapse and in complete remission identified an optimal discriminating threshold of 18% of recipient-derived cfDNA. After performing a targeted next-generation sequencing (NGS) panel, 136 mutations in 58 patients were detected. In a total of 119 paired samples, the putative mutations were detected in both cfDNA and PBMCs in 73 samples (61.3%). In 45 samples (37.8%) they were detected only in cfDNA, and in only one patient (0.9%) were they detected solely in DNA from PBMCs. Hence, in 6 out of 23 patients (26%) with relapse after allo-HSCT, MRD positivity was detected earlier in cfDNA (mean 397 days) than in DNA derived from PBMCs (mean 451 days). In summary, monitoring of MRD and MC in cfDNA might be useful for earlier relapse detection in patients with myeloid malignancies after allo-HSCT.