Exploratory Analysis of Glaucoma-Associated SNPs in a Colombian Cohort Highlights Potential Involvement of Oxidative, Vascular, and Neurodegenerative Pathways

Background/Objectives: Primary open-angle glaucoma (POAG) is a complex multifactorial optic neuropathy involving genetic, vascular, oxidative, inflammatory, and neurodegenerative mechanisms. Despite advances in genome-wide studies, the contribution of genetic variants remains incompletely characterized in underrepresented Latin American populations. This study aimed to characterize the genetic landscape of POAG in a Colombian cohort by identifying previously reported glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers and integrating these findings into biologically relevant pathways. Methods: An exploratory descriptive study was conducted in 21 Colombian patients with confirmed POAG. Whole-exome sequencing (WES) was performed at an average sequencing depth of approximately 100×. Variants were quality-filtered, functionally annotated, and prioritized within 446 POAG-associated genes retrieved from DisGeNET. Previously reported glaucoma-associated variants and rare candidate variants were identified, while pharmacogenomic variants related to latanoprost and timolol response were evaluated using ClinPGx/PharmGKB. Identified genes were classified according to major biological pathways relevant to glaucoma pathophysiology. Results: Of the 446 POAG-associated genes, 381 were detected in the patients’ exomes. A total of 10,220 molecular variants were identified, of which 1,187 synonymous variants were excluded, leaving 9,033 variants for downstream analysis. Among these, 955 were non-synonymous SNVs, including 26 variants previously reported in association with glaucoma and 929 potentially novel coding variants. Previously reported variants included loci in SIX6, LOXL1, CYP1B1, NOS3, and SOD2. Two rare candidate variants (minor allele frequency <1%) were identified in FMNL2 and C3. Pharmacogenomic variants in PTGS1, ADRB1, and ABCC4 with potential implications for response to latanoprost or timolol were also detected. Functional integration highlighted pathways involving oxidative stress, extracellular matrix remodeling, vascular regulation, neurodegeneration, and inflammation. Conclusions: This exploratory analysis identifies known glaucoma-associated variants, rare candidate variants, and pharmacogenomic markers in Colombian patients with POAG. The findings support a multifactorial biological framework involving interconnected oxidative, structural, vascular, neurodegenerative, and inflammatory pathways. The FMNL2 and C3 variants represent candidates for further investigation, while the identified pharmacogenomic variants highlight the potential relevance of genomic profiling for personalized glaucoma management. Larger ancestry-informed case–control studies are required to validate these observations and determine their clinical significance.