Cell-free DNA measurable residual disease as a predictor of postallogeneic hematopoietic cell transplant outcomes.

The measurable residual disease (MRD) assessment provides an attractive predictor of alloHCT outcomes. Cell-free DNA (cfDNA) has been applied to diagnosis, early detection, and disease burden monitoring in various tumors but its utility as an MRD test in myeloid malignancies has not been systematically evaluated. We sought to determine the differential sensitivity between bone marrow (BM) and cfDNA MRD and to assess the effect of cfDNA MRD on alloHCT outcomes. The technical and clinical validation cohort including 82 patients participating in clinical trials (BMT CTN-0201 and 0402) were utilized. Ultra-deep error-corrected targeted sequencing was performed on plasma and bone marrow-derived DNA. We demonstrated that 94.6% (range 93.9-95.3%) of cfDNA was derived from hematopoietic tissue. The mutant allele fraction was congruent between BM and cfDNA (rho = 0.8, p<0.0001), however, cfDNA appeared to be more sensitive in detecting clones with variant allele frequency (VAF) <0.26%. CfDNA-MRD clearance by day 90 post-alloHCT (D90) was associated with improved relapse-free survival (RFS, median survival not reached vs 5.5 months, p <0.0001) and overall survival (OS, median survival not reached vs 7.3 months, p < 0.0001) when compared to patients with persistent MRD. Irrespective of pre-alloHCT MRD, D90 cfDNA MRD was associated with inferior 2-year OS (16.7% vs. 84.8%, p <0.0001) and RFS (16.7% vs. 80.7%, p <0.0001). CfDNA appears to be an accurate, minimally invasive alternative to BM aspirates in MRD assessment and confers important prognostic implications in patients with myeloid malignancies undergoing alloHCT.