Identification of novel GWAS genetic risk variants for Parkinson’s disease in East Asian populations
GP2 ❤️ Open Science 😍
Last Updated: March 2026
This is the online repository for the short report titled "Identification of novel GWAS genetic risk variants for Parkinson’s disease in East Asian populations".
- 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. In this analysis we used GP2 Tier 2 Release 11 data (10.5281/zenodo.17753486).
- Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.0.0), publicly available on GitHub
- Summary statistics from the Million Veteran's Program were made available through a collaboration, apply for access here: https://www.mvp.va.gov/pwa/mvp-data-available-research
- Analyses conducted on the UKBiobank were performed on the DNANexus platform, apply for access here: https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access
- The
analyses/directory includes all analyses discussed in the manuscript
├── LICENSE.txt
├── README.md
└── analyses
├── GP2_EAS_QC_association.sh
├── Meta_EAS.Rmd
└── METAL.ipynb
- Languages: python3, bash, and R
| Directory | Notebooks | Description |
|---|---|---|
| analysis/ | GP2_EAS_QC_association.sh | Analysis description |
| analysis/ | Meta_EAS.Rmd | Analysis description |
| analysis/ | METAL.ipynb | Analysis description |
| Software | Version(s) | Resource URL | RRID | Notes | |
|---|---|---|---|---|---|
| Python Programming Language | 3.9 and 3.10 | http://www.python.org/ | RRID:SCR_008394 | pandas; numpy; seaborn; matplotlib; statsmodel; used for general data wrangling/plotting/analyses | |
| R Project for Statistical Computing | 4.2 | http://www.r-project.org/ | RRID:SCR_001905 | tidyverse; dplyr; tidyr; ggplot; data.table; used for general data wrangling/plotting/analyses | |
| PLINK | 2.0 and 1.9 | http://www.nitrc.org/projects/plink | RRID:SCR_001757 | used for genetic analyses | |
| ANNOVAR | 2020-06-08 | http://www.openbioinformatics.org/annovar/ | RRID:SCR_012821 | Genetic annotation software | |
| METAL | 2020-05-05 | http://csg.sph.umich.edu//abecasis/Metal/ | RRID:SCR_002013 | used for averaging effect allele frequency in meta-analyses | |
| Functional Mapping and Annotation of Genome Wide Association Studies (FUMA) | 1.8.0 | https://fuma.ctglab.nl/ | RRID:SCR_017521 | used for variant annotation |