Clinical features, genetics, and pathology in a large series of movement disorder cases: a retrospective multi-ancestry brain bank cohort study

GP2 ❤️ Open Science 😍

Last updated: November 2025

Summary

This repository contains code for the analyses conducted in "Clinical features, genetics, and pathology in a large series of movement disorder cases: a retrospective multi-ancestry brain bank cohort study".

The aim of the study is to assess clinico-pathological correlation in individuals carrying disease-associated and risk genetic variants, the frequency of clinical misdiagnosis and the impact of co-pathology.

Data Statement

• Data used in the preparation of this article were obtained from the Global Parkinson’s Genetics Program (GP2; https://gp2.org). All MDGAP/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 clinical and genetic data is available via the GP2 website (https://gp2.org). Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.3.5), publicly available on GitHub.
• In this analysis we used GP2 Release 10 data (10.5281/zenodo.15748014).
• Pathological staging and co-pathology data is included in the GP2 Release 11 (10.5281/zenodo.17753486)

Helpful Links

• GP2 Website
  • GP2 Cohort Dashboard
• Introduction to GP2
  • Other GP2 Manuscripts (PubMed)

Citation

(pending publication)

Repository Orientation

• The analyses/ directory includes all analyses discussed in the manuscript

 THIS_REPO/ 
  ├── analyses/ 
  |     └── 01_Sensitivity_Specificity.R
  |     └── 02_Copathologies.R
  |     └── 03_Genes_Extraction.R
  |     └── 04_Path_Stages.R
  |     └── 05_Ancestry.R
  └── README.md 

Analysis Notebooks

Languages: R, bash

Directory	Scripts	Description
analyses/	01_Sensitivity_Specificity.R	Compare clinical and pathological diagnoses to assess diagnostic accuracy
analyses/	02_Copathologies.R	Association analyses between clinical characteristics and co-pathologies
analyses/	03_Genes_Extraction.R	Extract genes of interest
analyses/	04_Path_Stages.R	Visualizations; analyze associations between pathological staging and genetic variants
analyses/	05_Ancestry.R	Associations between genetically defined ancestry and pathology

Software

Software	Version(s)	Resource URL	RRID	Notes
R Project for Statistical Computing	4.5.1	(http://www.r-project.org/)	RRID:SCR_001905	tidyverse; dplyr; tidyr; ggplot; data.table; used for general data wrangling/plotting/analyses
PLINK	2.0	(https://www.cog-genomics.org/plink/2.0/)	RRID:SCR_001757	used for genetic analyses
samtools (bcftools)	1.9	(https://samtools.github.io/bcftools/)	RRID:SCR_002105	VCF maniplulation