GIMAP6_CVD_Analysis

Code and analysis for the association of GIMAP6 variants with cardiovascular disease in the All of Us cohort, as described in Chen, X. et al., 2025.

Project Overview

This repository contains the code used to perform the statistical analyses and generate the figures for the human cohort data presented in Figure 6 of our manuscript. The analysis was conducted within the secure All of Us Researcher Workbench. Due to patient privacy restrictions, the individual-level raw data cannot be shared. However, this code is provided to ensure full transparency of our methodology.

System Requirements

• Python 3.9
• All required packages are listed in the requirements.txt file.

"All of Us" Data Requirements

• Dataset: All of Us Controlled Tier Dataset v8 [C2024Q3R5]
• Phenotypes: The specific SNOMED and ICD concept IDs used to define Coronary Artery Disease (CAD), Heart Failure (HF), and Hypercholesterolemia (HChol) are provided in data/phenotype_concept_ids.csv.
• Variants: The primary variant of interest is GIMAP6 p.Val65Ile (chr7:150628405 C>T). All other variants used for comparison are listed in the analysis scripts.

Instructions for Use

To replicate this analysis, an approved researcher on the All of Us Researcher Workbench should:

1. Create a new workspace using the specified dataset version.
2. Upload the scripts from the /scripts folder.
3. Run the scripts in the following order:
   • 01_define_cohort.py: To query the database and create the initial analysis cohort.
   • 02_run_associations.py: To perform the logistic regression and other statistical tests.
   • 03_generate_figures.py: To generate the final plots.

Expected Output

The scripts will generate the figures found in Figure 6 and the summary-level data tables located in the /results folder.