Allele frequencies of pharmacogenetic biomarkers and genomic ancestry in a sample of the Cuban population

Abstract Objectives A growing set of drugs includes a pharmacogenetic biomarker as a requirement before prescription. This study aims to determine the frequency of allelic variants with functional repercussions in clinically relevant pharmacogenes and its relation with genomic ancestry in Cuban individuals. Methods 10 single nucleotide variants (SNVs) across eight genes, included in the list of genetic variants required for the prescription of warfarin, tacrolimus, azathioprine, simvastatin, carbamazepine, abacavir and clopidogrel were analyzed. From genotyping in 948 Cuban individuals, population frequencies and Hardy–Weinberg equilibrium assessment were determined using PLINK v1.9. As a result of the ADMIXTURE analysis, previously performed on this sample, the relationship with the individual proportion of contribution of European, African, Native American and Asian ancestry was evaluated. Results Minor allele frequencies (MAFs) ranged from 0.0216 to 0.2781. Hardy–Weinberg equilibrium (HWE) deviations in three variants ( CYP2C9 rs1799853, HLA-A rs1061235 , SLCO1B1 rs4149056) were identified. Among individuals presenting the SNVs CYP2C9 rs1799853, CYP4F2 rs2108622, SLCO1B1 rs4149056, HLA-B rs2395029, the average European ancestry was higher; in contrast, individuals with the variant CYP3A5 rs10264272 presented higher African ancestry. Conclusions The variability in the analysis of each included allele, is representative of the genetic heterogeneity of the Cuban population and provides a remarkable example of diversity among populations.