ArticleJCO precision oncology2025
AlphaMissense for Identifying Pathogenic Missense Mutations in DNA Damage Repair Genes in Cancer.
Article in JCO precision oncology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Domain-Specific Computational, Functional and Structural Methods Enable Interpretation ofCurrent oncology (Toronto, Ont.) · 2026Article
- Emerging biomarkers in prostate cancer diagnosis and treatment: Insights into genetic, RNA and metabolic markers (Review).International journal of oncology · 2026Review
- Alteplase and Angioedema: Can Clinical Exome Sequencing Redefine the Paradigm?Life (Basel, Switzerland) · 2026Article
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Authors and funding
6 authors.
Funding
Abstract
purposeAlphaMissense is a new artificial intelligence-based approach to predicting the pathogenicity of missense variants. However, whether its predictions can be directly applied to clinical decision making remains unclear. This study aimed to evaluate the accuracy of AlphaMissense predictions for DNA damage repair (DDR) genes using genomic and clinical characteristics.
methodsSequencing data from 56,965 patients with cancer who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing between April 2015 and March 2023 and data from The Cancer Genome Atlas (TCGA)/Pan-Cancer Analysis of Whole Genomes (PCAWG) were analyzed. AlphaMissense pathogenicity was evaluated in six commonly mutated DDR genes. Missense mutations were classified into three categories on the basis of AlphaMissense and OncoKB: known pathogenic, newly identified pathogenic by AlphaMissense, or benign.
resultsIn the MSK-IMPACT cohort, 1,182 (17.5%) of 6,743 unique DDR gene missense mutations were newly identified as pathogenic. In breast, ovarian, pancreatic, and prostate cancers, homologous recombination (HR)-deficiency signatures were more common in tumors with new pathogenic missense mutations in
conclusionOur findings suggest that AlphaMissense can help identify previously unknown pathogenic DDR gene mutations, but its accuracy is gene-dependent. AlphaMissense prediction still requires additional confirmation with clinical and functional validation.
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