Cell-free DNA Whole Genome Sequencing for Non-Invasive Minimal Residual Disease Detection in Multiple Myeloma
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Minimal residual disease (MRD) monitoring in multiple myeloma (MM) relies on invasive bone marrow (BM) biopsies, which often yield insufficient tumor material. We performed whole genome sequencing of cell-free DNA from 163 plasma samples from 51 patients to develop a non-invasive MRD classifier. BM WGS identified a median of 2,502 clonal mutations, enabling cfDNA tracking at levels comparable to BM-based MRD testing. The cfDNA classifier achieved a mean AUC of 0.86 against multiparameter flow cytometry and targeted immunoglobulin sequencing (clonoSEQ), and MRD negativity after one year of maintenance was strongly associated with two-year relapse-free survival probability (Hazard Ratio = 24), with cfDNA changes preceding clinical progression by a median of 12.6 months. To establish a BM-agnostic mode, a plasma-only classifier trained on baseline cfDNA established a mean AUC of 0.79 compared to BM clinical testing and stratified relapse risk (HR = 4.18), enabling MRD detection in patients with suboptimal BM samples. Longitudinal cfDNA profiles detected subclonal evolution in half of profiled patients. Cell-free DNA whole genome sequencing provides a sensitive, scalable, and clinically informative platform for non-invasive MRD monitoring in MM.
Statement of Translational Significance
Currently, myeloma MRD assays require invasive, painful bone marrow sampling and fail to account for spatial heterogeneity. High-depth, cell-free whole genome sequencing tracks thousands of personalized mutations in blood, identifying molecular relapse a median of 12.6-19 months before clinical progression and showing a stronger association with progression-free survival than standard bone-marrow tests (hazard ratio = 24 for BM-informed mutation lists). This scalable, comprehensive approach enables dynamic multiple myeloma monitoring and risk-adapted treatment.
Summary Paragraph
Minimal residual disease (MRD) monitoring is one of the strongest predictors of progression-free and overall survival in multiple myeloma (MM); as such, clinicians currently rely on invasive bone-marrow sampling that patients tolerate poorly for serial assessment. We show that longitudinal whole-genome sequencing of plasma cell-free DNA, guided by personalized mutation catalogs from diagnostic bone marrow, detects residual tumor DNA at ultra-low levels. This approach tracked disease dynamics across serial samples, achieved strong concordance with standard clinical MRD assays, accurately predicted progression-free survival, and detected subclonal evolution driving relapse. While developed initially using bone marrow reference, we found that cell-free DNA collected at baseline provided comparable mutational information to serve as a reference for subsequent MRD blood draws. This plasma-only classifier requires no marrow input, identified persistent disease when diagnostic marrow was insufficient for referencing, stratified relapse risk, and detected rising MRD probabilities a median of 19 months before progression. Together, these results establish cell-free DNA whole genome sequencing as a minimally invasive platform for comprehensive genomic surveillance in MM, reducing dependence on painful repeat marrow biopsies and enabling earlier, risk-adapted intervention. More broadly, this strategy can extend to diverse cancers to guide personalized therapy and identify relapse earlier.
