GP2 ❤️ Open Science 😍
Last Updated: May 2026
This is the online repository for the research project titled "LRRK2 in Focus: A Global Browser Linking Genetic Diversity to Functional Effects". Here we present an interactive web browser with genomic, clinical, and functional data about LRRK2 and its relationship with Parkinson's Disease (PD).
- Data used in the preparation of this article were obtained from the Global Parkinson’s Genetics Program (GP2; https://gp2.org).
- All GP2 data are hosted in collaboration with the Accelerating Medicines Partnership in Parkinson’s disease, and are available via application on the website (https://amp-pd.org/register-for-amp-pd). For up-to-date information on GP2 data acquisition, access, and policies, visit https://gp2.org/. Tier 1 data can be accessed by completing a form on the Accelerating Medicines Partnership in Parkinson’s Disease (AMP®-PD) website (https://amp-pd.org/register-for-amp-pd). Tier 2 data access requires approval and a Data Use Agreement signed by your institution. The GP2 PD case and control data are available via the GP2 website (https://gp2.org; release 11: https://doi.org/10.5281/zenodo.17753486).
- Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.0.0), publicly available on GitHub
THIS_REPO
├── entry.R
├── fetch_data.ipynb
├── global.R
├── ** kinase_activity.tsv
├── ** lrrk2_combined_exome.tsv
├── ** lrrk2_combined_imputed.tsv
├── ** lrrk2_combined_raw.tsv
├── ** lrrk2_combined_wgs.tsv
├── modules
│ ├── annotation_summary_table.R
│ ├── bar_chart.R
│ ├── domain_diagram.R
│ ├── gene_overview.R
│ ├── gene_var_table.R
│ ├── other_resources.R
│ ├── variant_details.R
│ └── world_map.R
├── ** pathogenicity_sources.tsv
├── README.md
├── server.R
├── ui.R
├── util.R
└── www
├── clinvar.png
├── ensembl.png
├── genecards.png
├── gnomad.png
├── gp2_genome_browser.png
├── gp2_gwas_browser.png
├── gp2.png
├── ldlink.png
├── mdsgene.png
├── ncbi.png
├── omim.png
├── uniprot.png
└── world_map.png
**Note: kinase_activity.tsv, pathogenicity_sources.tsv, and lrrk2_combined_[exome/imputed/raw/wgs].tsv are required for the browser but are not hosted in this repository to protect sensitive data. For more details about these files contact the authors: Lara Lange (la.lange@uni-luebeck.de), Spencer Grant (spencer.grant@nih.gov) and Vesna van Midden (vesna.van.midden@gmail.com)
- kinase_activity.tsv includes the columns "Conservation_Score" (Integer between 1-10), "Variant" (ie, A123W), "Mean_pRAB10/RAB10" (Kinase activity measurement), "SD" (Standard deviation), and "Interpretation" ("activating" if that variant is kinase-active, otherwise blank).
- pathogenicity_sources.tsv includes the columns "Variant" (ie, p.A123W) and "Source" (comma-separated list of resources used to determine disease-association).
- lrrk2_combined_[exome/imputed/raw/wgs].tsv are each produced by running fetch_data.ipynb with the GP2 datasets.
- Languages: Python, R, RShiny, bash
| File | Description |
|---|---|
| fetch_data.ipynb | Notebook used to fetch and process GP2 data |
| global.R | Load RShinhy libraries |
| modules/annotation_summary_table.R | Code defining widget for annotation counts across all variants |
| modules/bar_chart.R | Code defining widget for kinase activity bar chart |
| modules/domain_diagram.R | Code defining widget for protein and cDNA diagrams |
| modules/gene_overview.R | Code defining widget for positional metadata for LRRK2 |
| modules/gene_var_table.R | Code defining widget for the main variant data table |
| modules/other_resources.R | Code defining widget for relevant external resources |
| modules/variant_details.R | Code defining widget for variant popup window |
| modules/world_map.R | Code defining widget for world map with variant spectrum donut charts |
| server.R | Main server code for RShiny |
| ui.R | Main UI code for RShiny |
| util.R | Utility functions |
| www/* | .png image files |
| Software | Version(s) | Resource URL | RRID | Notes |
|---|---|---|---|---|
| Python Programming Language | 3.9.19 | http://www.python.org/ | RRID:SCR_008394 | Used for fetching data |
| R Project for Statistical Computing | 4.4.2 | http://www.r-project.org/ | RRID:SCR_001905 | Used to host RShiny |
| RShiny | 1.9.1 | https://shiny.posit.co/ | -- | User interface development |
| PLINK | 2.0 | http://www.nitrc.org/projects/plink | RRID:SCR_001757 | Used for genetic analyses |