Integrative multi-omics approaches identify molecular pathways and improve Alzheimer's disease risk prediction.

INTRODUCTION: Alzheimer's disease (AD) is a complex neurodegenerative disorder with heterogeneous genetic and molecular underpinnings. Polygenic scores (PGS) capture little of this complexity. METHODS: We conducted genome-, transcriptome-, and proteome-wide association studies (G/T/PWAS) on 15,480 individuals from the Alzheimer's Disease Sequencing Project R4 (ADSP) to identify AD-associated signals, followed by pathway enrichment analysis. Integrative risk models (IRMs) were developed using genetically regulated components of gene and protein expression and clinical covariates. Elastic-net logistic regression and random forest classifiers were evaluated using standard metrics and compared against baseline PGS. RESULTS: Known and novel signals were identified via G/T/PWAS. Enrichment analyses highlighted cholesterol and immune signaling pathways. The best-performing IRM, random forest with transcriptomic and covariate features, achieved area under the receiver operating characteristic (AUROC) of 0.703 and area under the precision-recall curve (AUPRC) of 0.622, significantly outperforming PGS and baseline models. DISCUSSION: Integrating univariate discovery approaches with multivariate modeling enhances AD risk prediction and offers novel insights into underlying biological processes. HIGHLIGHTS: Identified novel contributions to Alzheimer's disease (AD) from a multi-omics perspective. Integrated genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and proteome-wide association studies (PWAS) in a unified association study framework. Developed a method for predicting heritable risk of late-onset AD. Demonstrated that ancestry-aware modeling improves AD risk prediction accuracy.