Tumour heterogeneity, encompassing genetic, epigenetic, and microenvironmental diversity, remains a fundamental obstacle in precision oncology. Traditional bulk sequencing captures only averaged molecular profiles, thereby masking rare yet functionally critical subpopulations that drive malignant progression and therapeutic resistance. Recently, the emergence of single-cell sequencing technologies has overcome the limitations of bulk approaches, enabling high-resolution analyses of the genome, transcriptome, epigenome and proteome at the single-cell level. These advances have enabled detailed mapping of tumour ecosystems, identification of key cellular subtypes, reconstruction of evolutionary trajectories and elucidation of intercellular communication networks within the tumour microenvironment. Accumulating evidence demonstrates that single-cell technologies elucidate fundamental aspects of tumour biology and reveal potential diagnostic and therapeutic targets. This review systematically summarises the recent advances and applications of single-cell sequencing in the field of precision oncology, with particular emphasis on its applications in mechanistic discovery, diagnosis, therapy, and prognosis. Furthermore, we discuss current challenges related to technology, data analysis, and clinical translation, and outline future research directions. In summary, single-cell sequencing has profoundly reshaped our understanding of tumour biology and is propelling oncology into a new era of precision, prediction, and personalisation.
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2026 The Author(s). Clinical and Translational Discovery published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.
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