ArticleMolecular therapy. Nucleic acids2023
PathwayTMB: A pathway-based tumor mutational burden analysis method for predicting the clinical outcome of cancer immunotherapy.
Article in Molecular therapy. Nucleic acids, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Multi-omic Profiling of Recurrence Risk Across Breast Cancer Subtypes.medRxiv : the preprint server for health sciences · 2026Article
- GOLDEN fusion: a graph-oriented learning with domain-embedding network fusion for generating super gene sets in functional genomics.Briefings in bioinformatics · 2026Article
- Integrating genomic and pathological characteristics to enhance prognostic precision in advanced NSCLC.NPJ precision oncology · 2025Article
- ProgModule: A novel computational framework to identify mutation driver modules for predicting cancer prognosis and immunotherapy response.Journal of translational medicine · 2025Article
- Multi-omics analysis reveals the unique landscape of DLD in the breast cancer tumor microenvironment and its implications for immune-related prognosis.Computational and structural biotechnology journal · 2024Article
- THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data.Briefings in bioinformatics · 2024Article
- Machine learning-based identification of a cell death-related signature associated with prognosis and immune infiltration in glioma.Journal of cellular and molecular medicine · 2024Article
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10 authors.
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Abstract
Immunotherapy has become one of the most promising therapy methods for cancer, but only a small number of patients are responsive to it, indicating that more effective biomarkers are urgently needed. This study developed a pathway analysis method, named PathwayTMB, to identify genomic mutation pathways that serve as potential biomarkers for predicting the clinical outcome of immunotherapy. PathwayTMB first calculates the patient-specific pathway-based tumor mutational burden (PTMB) to reflect the cumulative extent of mutations for each pathway. It then screens mutated survival benefit-related pathways to construct an immune-related prognostic signature based on PTMB (IPSP). In a melanoma training set, IPSP-high patients presented a longer overall survival and a higher response rate than IPSP-low patients. Moreover, the IPSP showed a superior predictive effect compared with TMB. In addition, the prognostic and predictive value of the IPSP was consistently validated in two independent validation sets. Finally, in a multi-cancer dataset, PathwayTMB also exhibited good performance. Our results indicate that PathwayTMB could identify the mutation pathways for predicting immunotherapeutic survival, and their combination may serve as a potential predictive biomarker for immune checkpoint inhibitor therapy.
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