Population-Scale Pharmacogenomic Profiling in the Western Balkan Populations

Background: Pharmacogenomic variation contributes to interindividual differences in drug response, yet population-specific pharmacogenomic profiles remain insufficiently characterized in the Western Balkans (WB). This study aimed to comprehensively characterize pharmacogenomic variability in the WB populations using whole-genome sequencing (WGS), assess population differences in pharmacogenomic profiles, evaluate concordance among star allele calling tools, and identify rare and previously unreported variants in pharmacogenes. Methods: WGS data from 250 healthy individuals from five WB populations were analyzed across 88 pharmacogenes. Star alleles were assigned using Aldy4, PharmCAT, PyPGx, and Stargazer. Principal component analysis (PCA) was used to assess population structure, and pharmacogenomic allele and phenotype frequencies were compared within five European subpopulations. Unreported pharmacovariants were annotated using Ensembl VEP, gnomAD, ClinVar, and ClinPGx, with functional impact assessed using multiple in silico prediction tools. Results: A total of 357 star alleles were identified, with high tool concordance except for complex genes such as CYP2D6. WB populations clustered within the European genetic space, with limited subpopulation differentiation. Significant differences were observed within WB and compared with European populations, including clinically relevant genes CYP2B6, CYP2C19, RYR1, and VKORC1. Among 33 clinically relevant pharmacogenes, 22,638 SNVs were identified, including six previously unreported variants. Conclusions: The WB populations show substantial pharmacogenomic similarity to other European populations, while also exhibiting clinically relevant population-specific differences. Comprehensive WGS-based profiling revealed both established and previously unreported pharmacogenomic variation, highlighting the importance of including underrepresented populations in precision medicine research.