Passenger variants as pan-clonal markers of pediatric AML: Implications for molecular MRD

A streamlined, sensitive, and universal molecular method for MRD detection in pediatric AML remains an unmet clinical need. Here, we propose a novel approach based on tracking somatic non-coding passenger variants. Using whole-genome sequencing (WGS) of diagnostic bone marrow DNA, we identify patient-specific somatic passenger variants, which we term "leukemia-specific passenger variants" (LSPVs). Single-cell DNA proteogenomic analyses demonstrate that LSPVs are specific and robust markers of leukemic cells, present across the entire leukemic cell population. Moreover, we show that LSPVs are accurate markers of disease burden, stable from diagnosis to relapse. Importantly, LSPVs can be detected in all patients, suggesting the universal applicability of this approach. Leveraging these findings, we developed DAISY-MRD, a streamlined WGS-based MRD method that does not rely on the presence of specific trackable genetic aberrations and does not require tailored assay design, making it simple, efficient, and feasible in clinical settings.