Virtual Pharmacist: A Platform for Pharmacogenomics

Abstract

We present Virtual Pharmacist, a web-based platform that takes common types of high-throughput data, namely microarray SNP genotyping data, FASTQ and Variant Call Format (VCF) files as inputs, and reports potential drug responses in terms of efficacy, dosage and toxicity at one glance. Batch submission facilitates multivariate analysis or data mining of targeted groups. Individual analysis consists of a report that is readily comprehensible to patients and practioners who have basic knowledge in pharmacology, a table that summarizes variants and potential affected drug response according to the US Food and Drug Administration pharmacogenomic biomarker labeled drug list and PharmGKB, and visualization of a gene-drug-target network. Group analysis provides the distribution of the variants and potential affected drug response of a target group, a sample-gene variant count table, and a sample-drug count table. Our analysis of genomes from the 1000 Genome Project underlines the potentially differential drug responses among different human populations. Even within the same population, the findings from Watson’s genome highlight the importance of personalized medicine. Virtual Pharmacist can be accessed freely at http://www.sustc-genome.org.cn/vp or installed as a local web server. The codes and documentation are available at the GitHub repository (https://github.com/VirtualPharmacist/vp). Administrators can download the source codes to customize access settings for further development.

Further Investigation of the Role of ACYP2 and WFS1 Pharmacogenomic Variants in the Development of Cisplatin-Induced Ototoxicity in Testicular Cancer Patients

“…There is large variability among studies investigating the genetics of CIO with respect to phenotype definitions, treatment protocols, and patient demographics (29). Furthermore, examination of clinically relevant pharmacogenetic variants and drug-gene interaction networks has reported that cisplatin traits are affected by multiple genetic variations (30), providing further evidence for the polygenic nature of CIO (7). If CIO pharmacogenomic variants are to impact the lives of patients, future research will need to focus on uncovering the factors that contribute to differences and similarities in genetic susceptibility across cohorts of patients.…”

Pharmacogenetic Variation in Over 100 Genes in Patients Receiving Acenocumarol

“…Our results offer an initial insight to the use of a genomic approach in pharmacogenetics showing that the advent of next generation sequencing may offer an alternative to identify and utilize individual variation to potentially explain a pharmacological relevant phenotype (Cheng et al, 2015 ). Future endeavors should focus on confirming these observations in a larger population.…”

Systematic Review and Meta‐analysis of the Influence of Genetic Variation on Ototoxicity in Platinum‐Based Chemotherapy

“…Further research should involve appropriate replication studies, considering the factors discussed above regarding interstudy heterogeneity, to confirm consistent associations with specific polymorphisms to eventually influence clinical decisions. 24,64,79,86 Research via GWAS and next-generation sequencing is needed to look into the polygenic nature of PBC-induced ototoxicity 12,25,40,87 to identify additional variants and evaluate cumulative risk scores. 4,34 Lastly, increasing the diversity of populations studied will improve the curation of associated variants and improve the relevance of genomic medicine to additional populations worldwide, 88 with the eventual goal of identifying patients at high risk of ototoxicity who will benefit from less ototoxic chemotherapy regimens or the use of novel otoprotective agents.…”