Exploring MAPT-containing H1 and H2 haplotypes in Parkinson's Disease across diverse populations

GP2 ❤️ Open Science 😍 ##Add zenodo DOI

Last Updated: July 2025

Summary

This repository contains the code and data analysis pipelines used for the research project titled "Exploring MAPT-containing H1 and H2 haplotypes in Parkinson's Disease across diverse populations". This study examined two main haplotypes at the 17q21.31 locus, which contains the MAPT gene, and their association to risk of Parkinson’s disease (PD) across diverse ancestry groups.

Citation

If you use this repository or find it helpful for your research, please cite the corresponding manuscript:

Title Authors

Manuscript DOI: coming soon

GitHub DOI: 10.5281/zenodo.15933056

Data Statement

• Data used in the preparation of this analysis were obtained from the Global Parkinson’s Genetics Program (GP2; https://gp2.org). Specifically, we used Tier 2 data from GP2 releases 6 [DOI: https://doi.org/10.5281/zenodo.10962119] and 7 [DOI: https://doi.org/10.5281/zenodo.10962119]. 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.
• Genotyping imputation, quality control, ancestry prediction, and processing were performed using GenoTools (v1.0.0), publicly available on GitHub

Repository Orientation

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

analyses/
├── 00_MAPThaplotypes_rs1052553_release7.ipynb
├── 01_MAPTproject_AAO_regression.ipynb
├── 02_MAPT_Haplotype_freq_plots.R
├── 03_MAPT_Forest-plots.ipynb
├── 04_MAPTproject_Subhaplotypes_analysis.ipynb
├── 05_MAPT_Subhaplo_Plots.R
├── 06_MAPT_GenoML_Analysis.ipynb
├── 07_MAPT_Locus_Zoom_Plots.R

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Analysis Notebooks

• Languages: Python, bash, and R

Notebooks / Scripts	Description
00_MAPThaplotypes_rs1052553_release7.ipynb	Analyses looking at the frequency of haplotypes in PD cases and controls in MAPT using the tagging SNP rs1052553
01_MAPTproject_AAO_regression.ipynb	Adjusted regression for H1/H2 haplotypes in Age at Onset for PD
02_MAPT_Haplotype_freq_plots.R	Bar plots of MAPT H1/H2 haplotype frequencies across multiple populations in PD cases and controls
03_MAPT_Forest-plots.ipynb	Visualization of results from association (adjusted and unadjusted) analysis using forestplots
04_MAPTproject_Subhaplotypes_analysis.ipynb	Analyses looking at the frequency of subhaplotypes in PD cases and controls in MAPT using six tagging SNPs
05_MAPT_Subhaplo_Plots.R	Bar plots of MAPT H1/H2 subhaplotype frequencies across multiple populations in PD cases and controls
06_MAPT_GenoML_Analysis.ipynb	GenoML to rank subhaplotypes by predictive value
07_MAPT_Locus_Zoom_Plots.R	Locus zoom regional association plots for the MAPT locus

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Software

Software	Version(s)	Resource URL	RRID	Notes
Python Programming Language	3.10.12	python.org	RRID:SCR_008394	pandas; numpy; seaborn; matplotlib; Used for general data wrangling and analyses
R Project for Statistical Computing	4.3.0	r-project.org	RRID:SCR_001905	tidyverse; dplyr; tidyr; ggplot; data.table; topr; Used for general data wrangling/plotting/analyses
PLINK	1.9 and 2.0	nitrc.org	RRID:SCR_001757	Used for genetic analyses
GenoML	2	genoml.com	NA	Used for machine learning analysis