Alzheimer's Disease GWAS Summary Data (Kunkle)

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Oluwatosin Olayinka

Source files

The original summary statistics (GRCh37) and a liftover to GRCh38 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 data are derived from the summary statistics of Kunkle et al..

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
• beta: SNP effect size
• se: standard error of beta
• pvalue: p-value of beta

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

• 46 case-control studies: 21,982 cases + 41,944 controls

• final sample: 94,437 individuals = 35,274 clinical and autopsy-documented AD cases + 59,163 controls

• 4 consortia (46 case-control studies in Suppl. Table 2) non-Hispanic Whites (NHW):

• ADGC: Alzheimer Disease Genetics Consortium

• CHARGE: Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium

• EADI: The European Alzheimer’s Disease Initiative

• GERAD/PERADES: Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium

Supplementary Table 1. Description of the consortium data sets used for Stage 1 discovery, Stage 2 and Stage 3. Discovery

Stage 2*

Stage 3*

• AAO, age at onset; AAE, age at examination.
• *Stage 2 and Stage 3 datasets were combined for genotyping of 33 replication variants not present on the 2013 custom chip

Supplementary Table 2. Demographic description of datasets within each consortium.