Integration of multi-omics approaches in exploring intra-tumoral heterogeneity

Intra-tumoral heterogeneity (ITH) is common in malignant tumors and arises from dynamic variations across genetic, epigenetic, transcriptomic, proteomic, metabolic, and microenvironmental factors. This complexity drives tumor evolution and treatment resistance, undermining the accuracy of clinical diagnosis, prognosis, and treatment planning. Despite recent advances in multi-omics technologies that enable comprehensive mapping of ITH across molecular layers, major challenges remain in clinical translation. This review outlines the principles and clinical applications of eight major omics modalities in the context of ITH: genomics, single-cell genomics, transcriptomics, epigenomics, proteomics, radiomics, microbiome, and metabolomics. We highlight the unique contributions of each omics platform to tumor profiling and emphasize how their integration enhances biological interpretation, patient stratification, and biomarker discovery. Furthermore, we will focus more extensively on the limitations of applying these approaches to ITH analysis. Instead of providing an exhaustive catalog, this review highlights major controversies, technical hurdles, and conceptual gaps that impede the clinical translation of multi-omics-based ITH analysis, with the aim of addressing ITH-related clinical challenges.