MRDagent: Iterative and Adaptive Parameter Optimisation for stable ctDNA-Based MRD Detection in Heterogeneous Samples

Motivation Minimal residual disease (MRD) as critical biomarker for cancer prognosis and management, plays a crucial role in improving patient outcomes. However, detecting minimal residual disease (MRD) via next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) variant calling remains unstable due to the extremely low variant allele frequency (VAF) and significant inter- and intra-sample heterogeneity. Although parameter optimization can theoretically enhance variants detection performance, achieving stable MRD detection remains challenging due to three key factors: (i) the necessity for individualized parameter tuning across numerous heterogeneous genomic intervals within each sample, (ii) the tightly interdependent parameter requirements across different stages of variant detection workflows, and (iii) the limitations of current automated parameter optimization methods. Results In this study, we propose MRDagent, a novel variant detection tool designed specifically for MRD detection. MRDagent incorporates an iterative and self-adaptive optimisation framework capable of handling unknown objectives, varying constraints, and highly coupled parameters across stages. A key innovation of MRDagent is the integration of a convolutional neural network (CNN)-based meta-model, trained on historical data to enable rapid parameter prediction. This significantly enhances computational efficiency and generalisation performance. Extensive evaluations on simulated and real-world datasets demonstrate MRDagent’s superior and stable performance, providing an efficient, reliable solution for MRD detection in clinical and high-throughput research applications. Availability MRDagent is freely available at https://github.com/aAT0047/MRDagent.git.The corresponding dataset and software archive are available at Zenodo: https://doi.org/10.5281/zenodo.15458496. Supplementary information Supplementary data are available at Bioinformatics online.