Single-molecule cfDNA sequencing establishes clinical utility for ecDNA monitoring and multimodal liquid biopsy analysis

Cell-free DNA (cfDNA) profiling enables minimally invasive cancer detection and monitoring. We present SIMMA, a low-input single-molecule sequencing approach that enables multimodal whole-genome and high-depth targeted sequencing of the same cfDNA sample for both tumour-agnostic and tumour-informed liquid biopsy analysis. Across 792 plasma and cerebrospinal fluid cfDNA samples from 277 paediatric patients with diverse brain and extracranial tumours, SIMMA enabled tumour diagnosis, detection of driver mutations, and reconstruction of extrachromosomal DNA (ecDNA) months before clinical relapse. Using conformal prediction trained on genome-wide fragmentomics, genomic and epigenomic data, SIMMA predicts disease burden as a continuous variable and provides well-calibrated uncertainty estimates for each sample, achieving a limit of detection of [~]100 ppm from low-pass whole-genome sequencing data. In summary, SIMMA establishes the clinical utility of multimodal cfDNA profiling with uncertainty quantification for individual patients and unlocks the potential of ecDNA as a liquid biopsy biomarker for disease detection and monitoring across diverse aggressive malignancies.