Alzheimer’s Disease GWAS Summary Data (Kunkle)#

The SNP-level association testing summary statistics for Alzheimer’s disease from Kunkle et al 2019 Nature Genetics. Position values were converted from hg19 to hg38 using liftOver.

Contact#

Oluwatosin Olayinka

Path(s) to summary statistics#

• NIAGADS FTP, /ftp_fgc_xqtl/projects/ADGWAS_Kunkle_2019_hg38_liftover/kunkle_sumstat_hg38_qc.chr*
• CU
  • original data (in GRCh37)
    • stage 1: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/'Kunkle_etal_Stage1_results.txt?file=1'
    • stage 2: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/'Kunkle_etal_Stage2_results.txt?file=1'
  • liftover data (in GRCh38):
    • stage 1: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/Kunkle_etal_Stage1_results.txt_file_1_hg38.txt
    • stage 2: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/Kunkle_etal_Stage2_results.txt_file_1_hg38.txt

Path to SuSiE RSS Fine-mapping Objects#

• Li-San Wang FTP: /ftp_fgc_xqtl/projects/GWAS_Finemapping_Results/Kunkle/
• AD GWAS fine-mapping models (Synapse): 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#

This data is derived from summary statistics from the Kunkle et al. Nature Genetics paper.

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.