LRRK2 mutation spectrum and association study in a multi-ethnic cohort of Malaysian Parkinson’s Disease patients
GP2 ❤️ Open Science 😍
Last updated: April 2026
This is the online repository for the manuscript titled "LRRK2 mutation spectrum and association study in a multi-ethnic cohort of Malaysian Parkinson’s Disease patients".
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; GP2 Release 11 (10.5281/zenodo.17753486)). Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.0.0), publicly available on GitHub.
THIS_REPO/
├── analysis/
| ├── 01_PC_selection.ipynb
| ├── 02_annotation.ipynb
| ├── 03_assoc.ipynb
| ├── 04_burden_and_kernel_test.ipynb
| ├── 05_haplotype_analysis.ipynb
| └── 06_concordance_check.ipynb
├── LICENSE
└── README.md - Languages: Python, bash, and R
| Directory | Notebook | Description |
|---|---|---|
| analysis/ | 01_PC_selection.ipynb | Selecting number of PCs for association study |
| analysis/ | 02_annotation.ipynb | Annotating data with annovar |
| analysis/ | 03_assoc.ipynb | Running association for all variants |
| analysis/ | 04_burden_and_kernel_test.ipynb | Running rare variant burden and kernel test |
| analysis/ | 05_haplotype_analysis.ipynb | Generate haplotype and run haplotype association for LRRK2 gene |
| analysis/ | 06_concordance_check.ipynb | Checking the concordance of variant genotype between the sequencing technology |
| Software | Version(s) | Resource URL | RRID | Notes |
|---|---|---|---|---|
| Python Programming Language | 3.10 | http://www.python.org/ | RRID:SCR_008394 | pandas; numpy; seaborn; matplotlib; statsmodel; rpy2; used for general data wrangling/plotting/analyses |
| R Project for Statistical Computing | 4.4.2 | http://www.r-project.org/ | RRID:SCR_001905 | tidyverse; dplyr; tidyr; ggplot2; car; cowplot; grid; RColorBrewer; forestmodel; survival; used for general data wrangling/plotting/analyses |
| PLINK | 1.9 and 2.0 | http://www.nitrc.org/projects/plink | RRID:SCR_001757 | used for genetic analyses |
| RVTests | v.2.1.0 | http://genome.sph.umich.edu/wiki/RvTests | RRID:SCR_007639 | Used for burden analyses. |
| ANNOVAR | d.06.08.2020 | http://www.openbioinformatics.org/annovar/ | RRID:SCR_012821 | Used for variant annotation. |