AD-GCN: A novel graph convolutional network integrating multi-omics data for enhanced Alzheimer’s disease diagnosis

Alzheimer's disease (AD) etiology is complex, influenced by demographic risk factors such as age, sex, and educational level, alongside multi-omics factors derived from genomics, transcriptomics, and epigenomics. Advancements in multi-omics technology present both challenges and opportunities for AD diagnosis, enabling a more comprehensive understanding of the complex interactions among contributing factors, with the goal of improving diagnostic accuracy. To address this challenge, we propose a novel feature fusion approach in this study, AD-GCN, which integrates multi-omics data and their interaction networks to achieve more precise diagnosis and analysis of AD. In this study, we applied polygenic risk score and random forest algorithms for feature selection on genetic variation and methylation data. We then developed an AD-GCN for both multi-omics and single-omics classification tasks and compared its performance with that of machine learning ensemble methods. The experimental results demonstrated that multi-omics classification significantly outperformed single-omics classification, with AD-GCN surpassing the machine-learning ensembles. These findings highlight AD-GCN's strong potential to enhance AD diagnosis and improve accuracy in differentiating disease stages by integrating interactions across omics data, laying a solid foundation for the development of more precise and personalized AD diagnostic models.