GP2 ❤️ Open Science 😍
Last updated: June 2026
This is the online repository for the manuscript titled "Association of the GCH1 p.Ser80Asn variant with Parkinson’s disease in East Asian populations". This study focuses on investigating the association of GCH1 p.Ser80Asn variant with PD risk across ancestries.
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 Tier 2 GP2 Release 11 data (https://zenodo.org/records/17753486).
- The
analysis/directory includes all analyses discussed in the manuscript.
| Directory | Notebooks | Description |
|---|---|---|
analyses/ |
00_GCH1_Ser80Asn.ipynb |
To identify GCH1 p.Ser80Asn variant carriers across ancestries and perform halpotype analysis amongst carriers in the EAS cohort |
| Software | Version(s) | Resource URL | RRID | Notes |
|---|---|---|---|---|
| ANNOVAR | d.06.08.2020 | http://www.openbioinformatics.org/annovar/ | RRID:SCR_012821 | Used for variant annotation. |
| Beagle | v.5.4 | https://faculty.washington.edu/browning/beagle/beagle.html | RRID:SCR_001789 | Used for phasing. |
| GenoTools | v.1.2.3 | https://github.com/GP2code/GenoTools | NA | Used for quality control and genetic ancestry inferrence. |
| gnomAD | v.4.1 | http://gnomad.broadinstitute.org/ | RRID:SCR_014964 | Used to retrieve population frequency data. |
| PLINK | v.1.9,v. 2.0 | http://www.nitrc.org/projects/plink | RRID:SCR_001757 | Used for genetic analyses. |
| Python Programming Language | 3.7, 3.8, 3.9, 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 | v.4.2.2 | http://www.r-project.org/ | RRID:SCR_001905 | tidyverse; dplyr; tidyr; ggplot; data.table; Used for general data wrangling/plotting/analyses |