Large-Scale Data Analysis of Post-Traumatic Stress Disorder (PTSD) Through GWAS Fine-Mapping and Systems Biology

Background/Objectives: Post-Traumatic Stress Disorder (PTSD) is a complex psychiatric condition with a strong polygenic and stress-related biological basis. Although Genome-Wide Association Studies (GWAS) have acknowledged abundant risk variants, translating these findings into biologically meaningful candidates remains challenging. This study introduces an integrative computational approach from raw file preparation by python-coded application into downstream in-depth silico analyses designed to systematically refine GWAS signals for PTSD using fine-mapping, linkage disequilibrium (LD), and haplotype analyses. Methods: GWAS source file for PTSD was obtained from the GWAS Catalog (EFO_0001358) and analyzed using a custom Python pipeline integrating data harmonization, genome-wide visualization, LD estimation via 1000 Genomes reference panels, approximate Bayesian fine-mapping, and Haploview-inspired haplotype inference. SNPs were filtered based on statistical significance, LD structure, and posterior inclusion probability. Downstream systems’ biology analyses included protein–protein interaction modeling and pharmacogenomics (PGx) annotations. Results: From the primary GWAS dataset, 100 top-ranked SNPs were selected, leading to the identification of 58 significant loci. LD and haplotype analyses refined these signals to 93 candidate SNPs (66 genes). Following the exclusion of non-protein-coding genes, 45 genes remained, and network-based prioritization generated a final list of 20 biologically connected and pharmacogenetically relevant genes associated with PTSD. Conclusions: This integrative approach provided a robust and reproducible framework for GWAS fine-mapping and variant prioritization, effectively reducing large-scale GWAS outputs to biologically interpretable PTSD risk loci and genes.