GP2code/SouthAfrican_XWAS

This is the online repository for the manuscript titled "Insights into X-Linked Susceptibility to Parkinson’s Disease in the South African Population" # X-Chromosome Wide Association Study of Parkinson's Disease in the South African Population `GP2 ❤️ Open Science 😍` **Last updated:** June 2025 ## Summary This repository contains the code, data workflows, and results associated with the manuscript titled **"X-Chromosome Wide Association Study of Parkinson's Disease in the South African Population"**. This study is an X chromosome wide association (XWAS) analysis for Parkinson’s disease in the South African Study Collection using NeuroBooster array data. ## Data statement Data used in the preparation of this article were obtained from the Global Parkinson’s Genetics Program (GP2; gp2.org) release 7 (GP2 release 7, DOI: 10.5281/zenodo.10962119) and access can be requested through the Accelerating Medicines Partnership in Parkinson’s Disease (AMP-PD) via the online application process (amp-pd.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 (amp-pd.org). For up-to-date information on GP2 data acquisition, access, and policies, visit gp2.org. Tier 1 data can be accessed by completing a form on the Accelerating Medicines Partnership in Parkinson’s Disease (AMP®-PD) website (amp-pd.org). Tier 2 data access requires approval and a Data Use Agreement signed by your institution. ### Helpful Links - GP2 Website - GP2 Cohort Dashboard - Introduction to GP2 - Other GP2 Manuscripts (PubMed) ## Citation *(pending publication)* ## Key analyses: 1. Quality control, file preparation for imputation, and association analysis. a. Autosomal quality control pipeline used: github.com b. X chromosome quality control pipeline used: github.com c. XWAS pipeline used: github.com 5. P-value significance threshold calculations for both sexes. 6. Plotting of …