Genetic analyses of eight complex diseases using predicted continuous representations of disease

This repository contains the following contents:

Pooled ancestry summary statistics (used for main comparison analyses)

Case-control regenie outputs.gzip

Predicted (all feature) regenie outputs.gzip

PLINK clumping outputs.zip

Ancestry-specific summary statistics (used for MTAG and PRS)

Ancestry-specific case-control regenie outputs.gzip

Ancestry-specific predicted (all feature) regenie outputs.gzip

PLINK clumping outputs (MTAG analyses).gzip

Other files

Analysis scripts.zip: Additional analysis scripts (e.g., regenie, MTAG, PRS-CSx) that can also be found in the accompanying GitHub repository.

Data and code for figures and tables.zip: Files and code needed to reproduce key figures and tables.

Mendelian randomization results.tsv: IVW and robust Mendelian randomization results for all tested exposure-outcome pairs

MTAG outputs.gzip: MTAG results and summary statistics (IMPORTANT: Trait 2 is the boosted case-control phenotype)

PRS-CSx weights.gzip: Per variant weights for each ancestry

Variant to gene map.pkl: Pickle file mapping all tested variants to genes using Ensembl VEP and Open Targets V2G.

Note

Full summary statistics for sensitivity analyses (e.g., feature ablation) are too numerous to be included here (50 GB limit). Please contact the corresponding author for these files.