Abstract
Isolated extramedullary manifestations (IEM) of acute myeloid leukemia (AML) are recurrent events, especially following allogeneic hematopoietic cell transplantation (alloHCT). To date, measurable residual disease (MRD) assessment for this difficult-to-treat patient cohort has not been established. In this study, we evaluated highly sensitive next-generation sequencing (NGS) of IEM-AML tumor and compared it with cell-free DNA (cfDNA) from plasma, as well as highly sensitive NGS analysis of bone marrow mononuclear cells (BMMC) and peripheral blood mononuclear cells (PBMC), in a cohort of 15 IEM-AML patients with 19 IEM-AML episodes. cfDNA demonstrated a superior representation of IEM-AML tumor mutations compared to BMMC or PBMC, with a median variant allele frequency (VAF) of 0.8% and a mutation detection rate of 62% (37 of 60 mutations), compared to a median VAF of 0.05% and detection rate of 27%, respectively (16 of 60 mutations, p < 0.01). Among 44 mutations identified in 14 IEM-AML relapse tumors, 30 mutations (68%) were known from initial diagnosis. Using diagnostic mutations from initial diagnosis for MRD analysis and detection of IEM-AML relapse, 16 of 17 IEM-AML relapse episodes were detected via cfDNA, whereas only 7 of 17 were identified using conventional analysis of BMMC or PBMC. Our findings demonstrate that cfDNA analysis from plasma effectively captures the molecular profile of IEM-AML. More than one-third of clinically relevant mutations were exclusively detected through cfDNA and were missed by conventional NGS-MRD of BMMC or PBMC. These results suggest that MRD monitoring using cfDNA offers a more comprehensive and sensitive approach to detecting IEM-AML relapse compared to standard methods.