In Silico Approach to Predict Indian Pharmacogenomics Variants Based on Analysis of Linkage Disequilibrium (LD) and Expression Quantitative Trait Locus (eQTL)

Abstract

The drug response can vary based on ethnicity as it arises from differences in genetic makeup among the individuals and is associated with drug action, metabolism and action. The efficacy of drugs can be determined by genetic variation and may also lead to adverse effects. The drug responsive variants (Single nucleotide polymorphisms, SNPs) are obtained from pharmacogenomics studies based on the Indian population. We have used GTEx, Top LD, and LDlink computational tools to predict the LD and eQTL score. Furthermore, the Indian allelic frequency is predicted using the IndiGenome database. A total of 11 SNPs (rs1979277, rs3758149, rs1799853, rs9923231, rs2244500, rs4244285, rs10509681, rs1057910, rs749292, rs4775936 and rs700518) has been predicted to have significant LD and eQTL score to associate with the different drugs across the Indian population. The presented data helps in identification of drug target sites in a more appropriate way in the Indian population. Moreover, our findings highlight the importance of ethnicity based drug response and ultimately reduce and avoid the adverse effect of drugs and ensure effective drugtreatment.