Minimal residual disease (MRD) is proposed to drive early recurrence of hepatocellular carcinoma (HCC) after curative treatment, and patients with MRD may benefit from adjuvant treatment. We applied a customized targeted deep sequencing (TDS) to profile tumor genomic alterations in HCC patients undergoing liver transplantation (LT) or hepatectomy, and evaluated their associations with MRD status, recurrence risk, and adjuvant lenvatinib response across multiple independent cohorts. TDS revealed MRD-associated genomic patterns, including increased mutation burden and frequent alterations in TP53 and switch/sucrose non-fermentable (SWI/SNF) genes. Alterations in TP53 and SWI/SNF genes were consistently associated with higher early recurrence rates (48.5 % vs 30.0 %, P = 0.026 for TP53; 56.2 % vs 34.0 %, P = 0.024 for the SWI/SNF genes) and shorter recurrence-free survival (12.2 vs 34.6 months, P = 0.026 for TP53; 9.3 vs 18.6 months, P = 0.018 for the SWI/SNF genes) in the LT cohort, as well as the hepatectomy cohort. Multivariate analysis confirmed these alterations as independent risk factors for MRD. Integrative analysis demonstrated that TP53- and SWI/SNF-altered HCC represent clinically and biologically distinct phenotypes, differing in etiology, differentiation status, mutation burden, and transcriptomic subtypes: TP53 alterations correlated with an epithelial-mesenchymal transition-related subtype, while the SWI/SNF genes alterations related to a MYC-activated subtype. Notably, patients harboring TP53 alterations derived clinical benefit from adjuvant lenvatinib following curative surgery. In conclusion, TDS enables effective identification of MRD-associated genomic alterations and stratifies HCC patients who may benefit from adjuvant lenvatinib, providing a molecular basis for personalized postoperative management.
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