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药物基因组学中的人工智能与多组学:精准医学的新时代。

Artificial Intelligence and Multi-Omics in Pharmacogenomics: A New Era of Precision Medicine.

作者信息

Zack Mike, Stupichev Danil N, Moore Alex J, Slobodchikov Ioan D, Sokolov David G, Trifonov Igor F, Gobbs Allan

机构信息

PGxAI Inc., Palo Alto, CA.

出版信息

Mayo Clin Proc Digit Health. 2025 Jun 26;3(3):100246. doi: 10.1016/j.mcpdig.2025.100246. eCollection 2025 Sep.


DOI:10.1016/j.mcpdig.2025.100246
PMID:40881104
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12381589/
Abstract

Pharmacogenomics is entering a transformative phase as high-throughput "omics" techniques become increasingly integrated with state-of-the-art artificial intelligence (AI) methods. Although early successes in single-gene pharmacogenetics reported clear clinical benefits, many drug response phenotypes are governed by intricate networks of genomic variants, epigenetic modifications, and metabolic pathways. Multi-omics approaches address this complexity by capturing genomic, transcriptomic, proteomic, and metabolomic data layers, offering a comprehensive view of patient-specific biology. Advanced AI models, including deep neural networks, graph neural networks, and representation learning techniques, further enhance this landscape by detecting hidden patterns, filling gaps in incomplete data sets, and enabling in silico simulations of treatment responses. Such capabilities not only improve predictive accuracy but also deepen mechanistic insights, revealing how gene-gene and gene-environment interactions shape therapeutic outcomes. At the same time, real-world data from diverse patient populations is broadening the evidence base, underscoring the importance of inclusive datasets and population-specific algorithms to reduce health disparities. Despite challenges related to data harmonization, interpretability, and regulatory oversight, the synergy between multi-omics integration and AI-driven analytics holds relevant promise for revolutionizing clinical decision-making. In this review, we highlighted key technological advances, discussed current limitations, and outlined future directions for translating multi-omics plus AI innovations into routine personalized medicine.

摘要

随着高通量“组学”技术与最先进的人工智能(AI)方法日益融合,药物基因组学正进入一个变革阶段。尽管单基因药物遗传学早期取得的成功报告了明确的临床益处,但许多药物反应表型受基因组变异、表观遗传修饰和代谢途径的复杂网络支配。多组学方法通过捕获基因组、转录组、蛋白质组和代谢组数据层来应对这种复杂性,提供患者特异性生物学的全面视图。先进的人工智能模型,包括深度神经网络、图神经网络和表示学习技术,通过检测隐藏模式、填补不完整数据集中的空白以及实现治疗反应的计算机模拟,进一步提升了这一领域。这些能力不仅提高了预测准确性,还深化了对机制的理解,揭示了基因-基因和基因-环境相互作用如何塑造治疗结果。与此同时,来自不同患者群体的真实世界数据正在拓宽证据基础,强调了包容性数据集和针对特定人群的算法对于减少健康差距的重要性。尽管存在与数据协调、可解释性和监管监督相关的挑战,但多组学整合与人工智能驱动分析之间的协同作用有望彻底改变临床决策。在这篇综述中,我们强调了关键技术进展,讨论了当前的局限性,并概述了将多组学加人工智能创新转化为常规个性化医疗的未来方向。

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本文引用的文献

[1]
Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques.

PLoS Comput Biol. 2025-3-31

[2]
AI Model for Predicting Anti-PD1 Response in Melanoma Using Multi-Omics Biomarkers.

Cancers (Basel). 2025-2-20

[3]
Equitable machine learning counteracts ancestral bias in precision medicine.

Nat Commun. 2025-3-10

[4]
Pharmaco-Multiomics: A New Frontier in Precision Psychiatry.

Int J Mol Sci. 2025-1-26

[5]
The Era of Preemptive Medicine: Developing Medical Digital Twins through Omics, IoT, and AI Integration.

JMA J. 2025-1-15

[6]
Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues.

Hum Genomics. 2025-1-31

[7]
Real-world clinical multi-omics analyses reveal bifurcation of ER-independent and ER-dependent drug resistance to CDK4/6 inhibitors.

Nat Commun. 2025-1-22

[8]
Revolutionizing Personalized Medicine: Synergy with Multi-Omics Data Generation, Main Hurdles, and Future Perspectives.

Biomedicines. 2024-11-30

[9]
The Future of Pharmacogenomics: Integrating Epigenetics, Nutrigenomics, and Beyond.

J Pers Med. 2024-11-27

[10]
PGxQA: A Resource for Evaluating LLM Performance for Pharmacogenomic QA Tasks.

Pac Symp Biocomput. 2025

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