GP2 ❤️ Open Science 😍
Last Updated: January 2026
This repository accompanies the manuscript "Genome-Wide Association and Population-Tailored Polygenic Risk for Parkinson's Disease in Taiwan." It contains analysis scripts and summary resources for the first and largest genome-wide investigation of Parkinson's disease in Taiwanese populations.
Genotype imputation was performed using the Taiwan Biobank Imputation Server, leveraging a population-specific whole-genome reference panel to optimize variant coverage and accuracy.
- All data used in this repository were generated using GP2-funded resources from the East Asian Parkinson's Disease Genomics Consortium (EAPDGC), as part of the Global Parkinson's Genetics Program (GP2).
- Access to the individual-level data used in this article is coordinated by the corresponding authors and governed by the GP2 Tier 2 data access policy.
- Data access may be granted upon reasonable request, subject to approval and a Data Use Agreement signed by the applicant's institution.
If you use this repository or find it helpful for your research, please cite the corresponding manuscript:
Genome-Wide Association and Population-Tailored Polygenic Risk for Parkinson's Disease in Taiwan [Authors, Global Parkinson's Genetics Program (GP2), 2025] (DOI: 10.5281/zenodo.18232864)
analyses/– scripts used throughout the project
├── analyses
│ ├── 01_QC_PCA.R
│ ├── 02_GWAS.R
│ ├── 03_manhattan.R
│ ├── 04_regional_plot.R
│ ├── 05_SNCA_conditional.R
│ ├── 06_haplotype.R
│ ├── 07a_1000G_TW_projection.R
│ ├── 07b_1000G_TW_LRRK2_PCA.R
│ ├── 08_LRRK2.R
│ ├── 09_beta_comparison.R
│ └── 10_PRS.R
├── LICENSE
└── README.md
Primary language: R
| Script | Description |
|---|---|
01_QC_PCA.R |
Genotyping QC and principal component analysis. Input genotypes are PLINK files converted from IDAT via Illumina GenomeStudio. |
02_GWAS.R |
Genome-wide association analysis using imputed data and PLINK 2.0. |
03_manhattan.R |
Generation of Manhattan plots for GWAS results. |
04_regional_plot.R |
LocusZoom-style regional association plots for key loci. |
05_SNCA_conditional.R |
Conditional association analyses at the SNCA locus and regional plots. |
06_haplotype.R |
Haplotype estimation and visualization for SNCA and LRRK2. |
07a_1000G_TW_projection.R |
PCA-based ancestry projection using 1000 Genomes and the Taiwan cohort. |
07b_1000G_TW_LRRK2_PCA.R |
East Asian + Taiwan PCA with LRRK2 variant carriers highlighted. |
08_LRRK2.R |
Case–control and age-at-onset analyses stratified by LRRK2 Asian variants. |
09_beta_comparison.R |
Effect size comparison with prior PD GWAS (e.g., Nalls 2019, Foo 2020) and beta–beta plots. |
10_PRS.R |
Construction and evaluation of polygenic risk scores (AUC, ROC, deciles). |
| Software | Version(s) | Resource URL | RRID | Notes |
|---|---|---|---|---|
| GenomeStudio | 2.0 | https://www.illumina.com/products/by-type/informatics-products/microarray-software/genomestudio.html | RRID:SCR_010973 | Convert IDAT intensity files to PLINK-formatted genotype data |
| PLINK | 2.0 | https://www.cog-genomics.org/plink/2.0/ | RRID:SCR_001757 | GWAS, scoring (PRS), and basic genotype processing |
| PLINK | 1.9 | https://www.cog-genomics.org/plink/ | RRID:SCR_001757 | LD calculations, pruning, IBD, and legacy QC steps |
| R | 4.3 | https://www.r-project.org/ | RRID:SCR_001905 | Downstream analyses and visualization. Key packages: dplyr, tidyr, data.table, ggplot2, haplo.stats, geneHapR, pROC, patchwork |
For questions, please open an issue or contact the corresponding author.