Beyond Mutation Positivity: Variant Allele Frequency as a Quantitative Biomarker in Precision Oncology

Next-generation sequencing has transformed precision oncology, yet genomic alterations are still largely interpreted as binary events: present or absent, actionable or non-actionable. Variant allele frequency (VAF), defined as the proportion of sequencing reads carrying a specific variant, introduces an additional quantitative dimension to genomic profiling. However, VAF is not a direct measure of tumor clonality, as it is influenced by tumor purity, copy-number alterations, mutation multiplicity, ploidy, sample type, and, in circulating tumor DNA (ctDNA), tumor shedding and disease burden. In this narrative review, we examine the biological and clinical significance of VAF in lung, breast, and colorectal cancers, focusing on its potential prognostic and predictive roles and on its dynamic changes during treatment. Available evidence, largely derived from retrospective and heterogeneous studies, suggests potential associations between VAF and clinical outcomes, particularly in plasma-based analyses. However, these findings primarily support exploratory prognostic associations rather than establishing validated clinical utility, while the ability of VAF to predict the magnitude of benefit from genotype-matched therapies remains insufficiently demonstrated. Longitudinal VAF assessment may offer additional insights into molecular response, residual disease, and treatment-driven clonal evolution, although its independent clinical value requires further prospective validation. Analytical variability, biological confounders, heterogeneous thresholds, and the lack of standardized methodologies further limit clinical interpretation and implementation. Rather than replacing mutation positivity, VAF may therefore represent a complementary quantitative dimension of genomic profiling, potentially contributing to a more refined understanding of tumor heterogeneity and molecular evolution, provided that its clinical validity and utility are established through appropriately designed prospective studies.