Virtual Pharmacist: A Platform for Pharmacogenomics.
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.
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Ronghai
R
Cheng
Division of Genomics and Bioinformatics, The Chinese University of Hong Kong, Hong Kong, China.
Ross Ka-Kit
RK
Leung
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Yao
Y
Chen
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Yidan
Y
Pan
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Yin
Y
Tong
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Zhoufang
Z
Li
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Luwen
L
Ning
Departments of Surgery, Stanford University, Stanford, California, United States of America.
Xuefeng B
XB
Ling
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
Jiankui
J
He
D057225:Data Mining; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D020407:Internet; D015999:Multivariate Analysis; D010597:Pharmacogenetics; D057285:Precision Medicine; D055553:Prescription Drugs / Q000009:adverse effects / Q000493:pharmacokinetics / Q000627:therapeutic use*; D014584:User-Computer Interface
D055553:Prescription Drugs