Large-scale Genetic Characterization of Parkinson’s disease in the African and African admixed Populations
GP2 ❤️ Open Science 😍
Last Updated: December 2024
This repository contains all analyses for the manuscript titled "Large-scale genetic characterization of Parkinson’s disease in the African and African admixed populations". This study represents the largest sequencing-based characterization of potentially disease-causing protein-altering and splicing mutations in 710 cases and 11,827 controls from genetically predicted African or African admixed populations.
- Results were generated using
- GP2 data release 8 (controlled-tier access; DOI 10.5281/zenodo.13755496)
- All of Us (AoU) genomic data release 7 (controlled-tier access)
| Dataset | Release / Version | Resource URL | Notes |
|---|---|---|---|
| All of Us | Release 7 | https://allofus.nih.gov/ https://workbench.researchallofus.org/ |
Controlled-tier data used in this study |
| GP2 | Release 8 | https://gp2.org/the-components-of-gp2s-8th-data-release/ | Access-controlled data used in this study |
| BLAACPD | . | https://www.blaacpd.org/DJYD/ | Cohort focusing on African / African admixed populations with PD |
analyses/
├── 00_Annotation_AFR_PDexome.ipynb
├── 01_GP2_AfricanPD.ipynb
└── 02_Characterization of PD genes in All of Us.ipynb
Languages: Python and bash
| Notebook(s) | Description |
|---|---|
00_Annotation_AFR_PDexome.ipynb |
Annotation of variants identified in GP2 WGS African ancestry cohort and in PD GENEration clinical exomes. |
01_GP2_AfricanPD.ipynb |
Analysis of PD genes in GP2 cases and controls of African and African admixed ancestries (release 8). Includes extracting individuals, recoding VCFs, and evaluating the intronic rs3115534-G variant. |
Characterization of PD genes in All of Us.ipynb |
Extraction of African/admixed PD cases and controls from All of Us WGS data (release 7), recoding VCFs, and analysis of the intronic GBA rs3115534-G variant. |
Note: For more details on each notebook’s usage, refer to the introduction and documented code sections contained within each respective
.ipynb.
| Software | Version(s) | Resource URL | RRID | Notes |
|---|---|---|---|---|
| ANNOVAR | 2020-06-08 | http://www.openbioinformatics.org/annovar/ | RRID:SCR_012821 | Genetic annotation software |
| BCFtools | 1.17 | https://samtools.github.io/bcftools/bcftools.html | RRID:SCR_002105 | Used for variant calling file (VCF) manipulation |
| GBA Gauchian Caller | 1.0 | https://github.com/Illumina/Gauchian | . | Used for specialized GBA analyses |
| PLINK / PLINK2 | 1.9 & 2.0 | https://zzz.bwh.harvard.edu/plink/plink2.shtml https://www.cog-genomics.org/plink2 |
RRID:SCR_001757 | Used for genetic analyses |