Cell-free DNA analysis for cancer management: Technologies, features, and clinical translation

Abstract

The rising incidence and mortality of malignant tumors worldwide call for more effective early cancer screening strategies. Liquid biopsy, particularly the analysis of plasma cell-free DNA (cfDNA), has emerged as a promising non-invasive approach with high sensitivity. cfDNA carries a wealth of tumor-derived molecular information, enabling comprehensive profiling of cancer-associated alterations. In this review, we first summarize seven major cfDNA detection technologies: polymerase chain reaction (PCR)-based assays, bisulfite sequencing, metagenomic sequencing, nanopore sequencing, whole-exome sequencing (WES), whole-genome sequencing (WGS), and CRISPR-based methods. We then describe eleven representative cfDNA features, including fragmentomics, transcription start site (TSS) nucleosome coverage, promoter fragmentation entropy (PFE), DNA methylation, transcription factor (TF) footprints, histone modification patterns, gene mutations, copy number variations (CNVs), T-cell receptor (TCR) repertoires, microbiome signatures, and end-motif patterns. Collectively, these features offer new opportunities for early cancer detection, recurrence monitoring, and therapeutic response assessment. We focus on the technologies and analytical methodologies underlying cfDNA detection, discuss their current and emerging applications in oncology, and highlight recent advances in cfDNA-based approaches. We also critically evaluate the advantages and challenges of clinical implementation and propose future directions for optimizing cfDNA-driven cancer screening strategies.

Keywords

Cell-free DNA / Liquid biopsy / Cancer screening / Multidimensional feature / Clinical application

References

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