Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring

Circulating tumor DNA (ctDNA) is increasingly investigated in lymphomas because it enables non-invasive molecular profiling, longitudinal assessment of clonal evolution, and quantification of minimal residual disease (MRD), which reflects residual tumor burden and treatment response and serves as a clinically validated prognostic biomarker. The clinical utilities of ctDNA include supporting diagnosis, enabling early detection of relapse, and resolving ambiguous imaging findings. Current approaches for ctDNA assessment in lymphomas include droplet digital PCR, immunoglobulin clonotype sequencing, hybrid-capture next-generation sequencing with unique molecular identifiers or duplex barcoding, and phased sequencing. Establishing ctDNA as a clinical-grade assay requires rigorous quality control and standardization across all technical steps, from blood collection and plasma processing to cfDNA extraction, quantification, and analytically validated genotyping and MRD measurement. Large prospective trials and international standardization efforts are underway to define ctDNA-based MRD assessment as a reproducible and clinically actionable tool in lymphoma care. In this review, we outline key pre-analytical and analytical workflows for ctDNA assessment in lymphomas and discuss unresolved challenges and future directions in the field.