Analysis of common structural variants in Alzheimer's disease

This repository contains code and source data associated with the publication:

Cao, H., Fu, Y., Zhou, X., Duan, Y. et al. Genome-wide analysis of common structural variants in Alzheimer’s disease identifies a risk-associated regulatory CCG repeat in FAM193B. Nature Neuroscience (2026).
https://doi.org/10.1038/s41593-026-02481-z

Table of Contents

• data_processing: Scripts for processing raw FASTQ/BAM/VCF/PLINK data
• figure: Scripts for reproducing figures

Code details and instructions are provided in the README.md file within each directory.

Directory structure

.
├── data_processing
│   ├── 01.SV_call
│   ├── 02.joint_call
│   ├── 03.SV_annotation
│   ├── 04.genotyping
│   ├── 05.PRS
│   ├── 06.candidate_locus
│   ├── RNAseq
│   ├── WGS
│   └── harmoniSV
└── figure
    ├── input (source data)
    └── output_expected (reproduced figures)

Summary statistics

Due to GitHub file size limits, VCF files and GWAS summary statistics are available only in the Zenodo release.

License

All scripts are distributed under the MIT License. All data are distributed under the CC BY 4.0 License.