Alzheimer's Disease GWAS Summary Data (Wightman)

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Oluwatosin Olayinka

Source files

The summary statistics are available from the NIAGADS FTP site. The original data (GRCh37, 23andMe individuals only) and a liftover to hg38 are held on the Columbia University (CU) cluster.

Path to SuSiE RSS Fine-mapping Objects

• AD GWAS fine-mapping models (AD Knowledge Portal): syn69670625
• Additional fine-mapping objects: syn69696846
• Top unified loci summary: syn69865824

AD GWAS–xQTL Integration

AD GWAS–xQTL colocalization results (ColocBoost): syn69865816

AD GWAS–xQTL colocalization models: syn69670630

AD colocalization models (all GWAS studies): syn69670626

Integrated AD Gene-Level Summary

AD risk genes prioritized by xQTL + GVC: syn70095142

AD risk genes prioritized by xQTL + TWAS + GVC: syn70095143

Download source

The download source is not public.

File Schema

• chromosome: chromosome ID
• position: hg38 position (converted from hg19 with liftOver)
• variant: variant ID in the form chr${chromosome}_${position}_${ref}_${alt}
• alt: alternative effect allele
• ref: reference allele
• z - z-score of the SNP effect size
• pvalue: p-value of beta
• N:

Links to GWAS data analysis notebooks

1. Summary statistics preprocessing: https://github.com/floutt/brain-xqtl-analysis/blob/main/analysis/Zhang_BU/susie_rss/summary_stat_qc_all.nb.html

Cohorts included in this study

• 1,126,563 individuals = 90,338 (46,613 proxy) cases + 1,036,225 (318,246 proxy) controls
• 77,779 cases + 554,893 controls from Jansen et al.
• 12,559 cases + 481,332 controls not from Jansen et al: Finngen, GRACE, HUNT, BioVU, 23andme, Gothenburg H70 Birth Cohort Studies and Clinical AD from Sweden (Gothenburg), ANMerge.
• Population: US and Europe (UK, Norway, Sweden, Iceland, Finland, Spain)

Supplementary Table 1: A list of the datasets included in the meta-analysis. The UKB data was generated with a continous phenotype so the case-control values are estimates where the number of individuals with phenotype values <1 are controls and >=1 are cases.