NeuroPGx is a software for the identification of diplotypes compatible with genotypes at selected SNPs involved in neuropsychiatric drug metabolisms. It helps in pharmacogenomics evaluation of samples, providing information about: (I) the genotypes at evaluated SNPs, (II) the main diplotypes at CYP genes and corresponding metabolization phenotypes, (III) the list of neuropsychiatric drugs with recommended dosage adjustment, (IV) the list of possible (rare) diyplotypes and corresponding metabolization phenotypes.
NeuroPGx is an open-source platform-independent browser-based interface for pharmacogenomics in R. The application is based on the Shiny package and can be run locally or on a server. NeuroPGx was developed using R and Shiny, see papers section for details and citations. Developed by the Genomic Medicine Laboratory at I.R.C.C.S. Santa Lucia Foundation. You can reach us at a.termine@hsantalucia.it. Please use the issue tracker on GitHub to suggest enhancements or report problems.
The automatic identification of diplotypes based on genotypes at selected SNPs is based on CYP genes following CPIC allele definition. All possible diplotypes are evaluated for their enzymatic phenotype based on PharmVar data and the frequency in the reference population.
- Explore: Quickly and easily summarize, visualize, and analyze your data
- Cross-platform: It runs in a browser on every operating system
- Reproducible: Recreate results and share work with others
- Programming: Integrate NeuroPGx's analysis functions with your own R-code
- To set the environment for NeuroPGx local use, R and RStudio must be installed.
- Download R for your operating system (Windows, Linux or macOS) and install using the default settings.
- Download RStudio Free Desktop version and install using the default settings.
- To use the NeuroPGx software, download this repository from here or by clicking the green
Codebutton and selectingDownload ZIP. - Unpack the downloaded ZIP file to your preferred path.
- Open the
app.Rfile using RStudio, then click on the greenrun appbutton at the top-right corner of the central panel window, as shown in the image below.
Your input file can be simply prepared with an Excel spreadsheet. It should have 4 columns: Sample, Gene, rsID, Genotype. Put your samples' ID in the Sample column and fill the Gene and rsID columns with Gene Symbols and dbSNP ids. Please note that you can find the complete list of SNPs in the paper. Genotype column should be filled with genotype information for each sample. A / should be used as separator. Deletions in a SNP can be coded as -/- or A/- while more complex configurations, such as CTT/CTT can be easily reported and are well managed by the NeuroPGx software. NeuroPGx accepts .tsv, .csv and .xlsx files. If you need a more detailed example, we strongly suggest you to check the .xlsx example files provided in the samples folder to simplify your data preparation. Your input file should have the following structure:
| Sample | Gene | rsID | Genotype |
|---|---|---|---|
| Sample1 | CYP2B6 | rs28399499 | T/T |
| Sample1 | CYP2C19 | rs12248560 | C/C |
| Sample1 | CYP2C9 | rs1057910 | A/A |
| Sample1 | CYP2D6 | rs1065852 | G/G |
| Sample1 | CYP3A5 | rs10264272 | C/C |
| Sample2 | CYP2B6 | rs28399499 | T/T |
| Sample2 | CYP2C19 | rs12248560 | C/C |
| Sample2 | CYP2C9 | rs1057910 | A/A |
| Sample2 | CYP2D6 | rs1065852 | G/G |
| Sample2 | CYP3A5 | rs10264272 | C/T |
Please note that we used only one SNP for each Gene to simplify the provided example. You can find a complete set of examples in the samples folder.
NeuroPGx is licensed under the AGPLv3 license. As a summary, the AGPLv3 license requires attribution, including copyright and license information in copies of the software, stating changes if the code is modified, and disclosure of all source code. Details are in the LICENSE file. See our papers section for details and citations.
Precision Medicine into Clinical Practice: A Web-Based Tool Enables Real-Time Pharmacogenetic Assessment of Tailored Treatments in Psychiatric Disorders
Link to paper: https://www.mdpi.com/2075-4426/11/9/851/htm