RShiny web application for navigating genome-wide association study (GWAS) results and their functional and regulatory annotation to guide gene prioritization.
The KidneyGPS is available at https://kidneygps.ur.de/gps/. It summarizes information on association and annotation of variants and genes mapping to 424 genetic loci identified for glomerular filtration rate based on a GWAS meta-analysis of UK Biobank and CKDGen consortium data (n=1,201,909) [Stanzick et al. Nat. Commun. 2021]. Variants and genes were anotated using various data sources that are described in detail on the website.
KidneyGPS depends on the following other R packages: data.table, shiny, shinyBS, DT, shinyjs, shinyWidgets, htmltools
- Version 2.3 (current version)
- Integration of eGFR association statistics separated by diabetes status for all credible set variants.
- Version 2.2
- Re-organisation of the GPS tab with extendend filter options.
- Version 2.1
- separated drug information by indication for kidney diseases according to the ICD-11 codes.
- Version 2.0
- reanalysis of the 424 loci regarding stability of independent signals. 594 stable independent signals were identified using stepwise conditioning with GCTA. Credible sets were re-calculated for these signals resulting in 35,885 credible set variants.
- Version 1.3.1
- additional summary numbers in "GPS tab" below GPS table; in minor fixes
- Version 1.3
- Integrated drugability data from Therapeutic Target Database
- Version 1.2
- additional evidence for human phenotypes, GWAS evidence from Gorski et al. and Winkler et al.
- Version 1.1
- updated eQTL data
- Verion 1.0
- based on results published in Stanzick et al. Nat. Commun. 2021
If you are using the app, please cite Stanzick et al. Nat Commun 2021.
Please contact kira.stanzick@ukr.de if you need assistance.