Detecting time-varying genetic effects in Alzheimer's disease using a longitudinal genome-wide association studies model

Abstract

INTRODUCTION: The development and progression of Alzheimer's disease (AD) is a complex process, during which genetic influences on phenotypes may also change. Incorporating longitudinal phenotypes in genome-wide association studies (GWAS) could unmask these genetic loci. METHODS: We conducted a longitudinal GWAS using a varying coefficient test to identify age-dependent single nucleotide polymorphisms (SNPs) in AD. Data from 1877 Alzheimer's Neuroimaging Data Initiative participants, including impairment status and amyloid positron emission tomography (PET) scan standardized uptake value ratio (SUVR) scores, were analyzed using a retrospective varying coefficient mixed model association test (RVMMAT). RESULTS: RVMMAT identified 244 SNPs with significant time-varying effects on AD impairment status, with 12 SNPs on chromosome 19 validated using National Alzheimer's Coordinating Center data. Age-stratified analyses showed these SNPs’ effects peaked between 70 and 80 years. Additionally, 73 SNPs were linked to longitudinal amyloid accumulation changes. Pathway analyses implicated immune and neuroinflammation-related disruptions. DISCUSSION: Our findings demonstrate that longitudinal GWAS models can uncover time-varying genetic signals in AD. Highlights: Identify time-varying genetic effects using a longitudinal GWAS model in AD. Illustrate age-dependent genetic effects on both diagnoses and amyloid accumulation. Replicate time-varying effect of APOE in a second dataset.