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LRRK2 in Focus: A Global Browser Linking Genetic Diversity to Functional Effects

GP2 ❤️ Open Science 😍

License: MIT DOI

Last Updated: May 2026

Summary

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 Statement

  • 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

Helpful Links

Repository Orientation

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.

Analysis Scripts

  • 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

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