Variants in DNAJC13 and their Association with Parkinson's Disease Across Different Ancestral Backgrounds
GP2 ❤️ Open Science 😍
Last Updated: December 2025
This is the online repository for the manuscript titled "Variants in DNAJC13 Are Not Associated with Parkinson's Disease Across Different Ancestral Backgrounds".
The aim of this study is to explore the association between missense mutations in DNAJC13 and Parkinson's disease (PD) in a large-scale population data derived from Accelerating Medicines Partnership - Parkinson Disease (AMP-PD) and Global Parkinson’s Genetics Program (GP2) initiatives consisting from PD cases and controls representing various ancestral groups, based on previously identified mechanisms in DNAJC proteins playing a role in neurodegeneration1, familial and individual case reports of DNAJC13 disease-causing variants2,3,4,5,6, and functional studies7,8,9 supporting gene-disease relationship.
- All GP2 data are hosted in collaboration with the Accelerating Medicines Partnership in Parkinson's Disease (AMP-PD) and are available via application on the website. The GP2 PD case and control data are available via the GP2 website (https://gp2.org; release 11: 10.5281/zenodo.17753486).
- All data used from the AMP-PD v4 are available via application on the website (https://www.amp-pd.org/).
- Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.0.0), publicly available on GitHub
- The
analyses/directory includes all analyses discussed in the manuscript
analyses/
├── GP2_R11/
│ ├── VWB_01_DNAJC13_GP2_R11.ipynb
└── AMP_PD_R3/
├── 01_DNAJC13_AMP_PD_R3_EUR.ipynb
└── 02_DNAJC13_AMP_PD_R3_AJ.ipynb
- Languages: Python, bash, and R
| Directory | Notebooks | Description |
|---|---|---|
| GP2_R11/ | VWB_01_DNAJC13_GP2_R11 | Full pipeline (subset, annotate, association, gene burden) for GP2 dataset |
| AMP_PD_R3/ | 01_DNAJC13_AMP_PD_R3_EUR | Full pipeline (subset, annotate, association, gene burden) for AMP-PD EUR dataset |
| 02_DNAJC13_AMP_PD_R3_AJ | Full pipeline (subset, annotate, association, gene burden) for AMP-PD AJ dataset |
| Abbreviation | Ancestry |
|---|---|
| AAC | African American |
| AFR | African |
| AJ | Ashkenazi Jews |
| AMR | Admixed American/Latin American |
| CAS | Central Asian |
| EAS | East Asian |
| EUR | European |
| MDE | Middle Eastern |
| SAS | South Asian |
| Software | Version(s) | Resource URL | RRID | Notes | |
|---|---|---|---|---|---|
| Python Programming Language | 3.8 and 3.9 | 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 | |
| RVTests | v2.1.0 | http://genome.sph.umich.edu/wiki/RvTests | RRID:SCR_007639 | Burden analyses |