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Identification of novel GWAS genetic risk variants for Parkinson’s disease in East Asian populations

GP2 ❤️ Open Science 😍

License: MIT DOI

Last Updated: March 2026

Summary

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 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. 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

Helpful Links

Repository Orientation

  • 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

Analysis Notebooks

  • 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

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