Next generation sequencing-based measurable residual disease detection predicts outcomes in patients with acute myeloid leukemia undergoing allogeneic stem cell transplantation

Sensitive, scalable and affordable measurable residual disease (MRD) assays are needed to guide treatment decisions in acute myeloid leukemia (AML), particularly around allogeneic hematopoietic stem cell transplantation (allo-SCT). Next-generation sequencing (NGS)-based MRD assays offer broad applicability and high sensitivity, but remain too costly for routine use in resource-limited environments. We developed a cost-efficient, sensitive NGS MRD assay utilizing single-molecule molecular inversion probes (smMIPs) targeting 92 genomic loci in 33 AML driver genes and applied it to 93 AML patients in remission prior to allo-SCT. MRD positivity, defined as the presence of ≥ 1 non-DTA (DNMT3A, TET2, ASXL1) gene variant with ≥ 0.5% variant allele frequency (VAF), was associated with significantly shorter post-transplantation overall survival (OS; p < 0.001). In multivariable analysis, NGS-based MRD detection remained an independent predictor of inferior OS (hazard ratio 4.58; p = 0.002). Conditioning intensity did not associate with outcome of MRD-positive patients in this retrospective cohort. Mutations at diagnosis and pretransplantation showed variable concordance across genes, and consistently lower VAFs at the later timepoint. In three patients, multiple low-VAF clustered variants in RUNX1 and TET2 were detected pre-transplantation, potentially indicating treatment-induced mutagenesis. These findings demonstrate that a broadly applicable, smMIP-based NGS MRD assay can provide clinically relevant risk stratification before allo-SCT in AML, while its low library preparation costs of approximately 8€ per sample may facilitate wide implementation in routine practice and allow more patients to receive MRD-directed therapeutic interventions.