Alzheimer’s Disease GWAS Summary Data (Wightman)#

The SNP-level association testing summary statistics for Alzheimer’s disease from Wightman et al 2021 Nature Genetics. This file contains the meta-analyzed summary statistics of three cohorts: all individuals, all individuals excluding 23andMe, all individuals excluding 23andMe and UKBB.

Contact#

Oluwatosin Olayinka

Path(s) to summary statistics#

• NIAGADS FTP

  • meta results /ftp_fgc_xqtl/projects/ADGWAS_Wightman_2021_hg38_liftover_meta/wightman_meta_sumstat_hg38_qc.chr*
  • only 23andMe/ftp_fgc_xqtl/projects/ADGWAS_Wightman_2021_hg38_liftover_23andme/wightman_sumstat_hg38_qc.chr*

• CU

  • original data (in GRCh37)
    • all individuals: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.all/PGCALZ2full.txt
    • all individuals excluding 23andMe: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.excluding.23andme/PGCALZ2sumstatsExcluding23andMe.txt
    • all individuals excluding 23andMe and UKBB: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.excluding.23andme/PGCALZ2ExcludingUKBand23andME_METALInverseVariance_MetaAnalysis.txt
    • only 23andMe individuals
      • /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/23andme/alzheimers_matched.dat.gz
      • /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/23andme/v8.2_european_bundle-001.tar (decompressed into all_snp_info.txt, gt_snp_stat.txt, im_snp_stat.txt
      • after formatting: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/23andme/alzheimers_matched.dat_no_NA.formatted.tsv
  • liftover data (in hg38)
    • all individuals: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.all/PGCALZ2full.hg38.txt
    • all individuals excluding 23andMe: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.excluding.23andme/PGCALZ2sumstatsExcluding23andMe.hg38.txt
    • all individuals excluding 23andMe and UKBB: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/sum.stat.excluding.23andme/PGCALZ2ExcludingUKBand23andME_METALInverseVariance_MetaAnalysis.hg38.txt
    • only 23andMe individuals: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230530_Wightman/23andme/all_snp_info.hg38.txt

Path to SuSiE RSS Fine-mapping Objects#

• Li-San Wang FTP: /ftp_fgc_xqtl/projects/GWAS_Finemapping_Results/Wightman/

Download source#

Download source not publicly available

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 & Europe, UK, Norway, Sweden, Iceland, Finland, Spain, Norway, US, EUR

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.