Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy

The adoption of liquid biopsy approaches in clinical practice has triggered a significant paradigm shift in the diagnostic, prognostic, and predictive outcomes for cancer patients. Circulating tumor DNA (ctDNA) is considered a valuable biomarker for monitoring tumor burden and its mutational dynamics. In this context, not all cell-free DNA (cfDNA) molecules are derived from tumor cells. Furthermore, due to tumor heterogeneity, not all ctDNA molecules contain cancer-associated alleles, complicating the direct quantification of the circulating tumor allele fraction (cTF) within the total cfDNA. Cancer arises from the accumulation of multiple genetic and epigenetic changes. Each of these molecular features can be exploited as the basis of methodological strategies used in ctDNA quantification. Different layers of omics data, from genomics, evaluating mutational analysis of somatic single-nucleotide variants and copy number alterations, to epigenomics, primarily consisting of the evaluation of methylation profiles and fragmentation patterns, can be used for this purpose. Some of these approaches can be effective in a multi-modal manner. To date, the quantification approaches for estimating cTF vary enormously, making direct comparisons and an assessment of their translational value challenging. Moreover, the lack of regulatory approval for many of these assays is a critical barrier to their widespread clinical adoption. This review explores the different omics approaches described for ctDNA quantification, outlining strengths and limitations, and highlighting their valuable applications in clinical settings.