Alzheimer's Disease GWAS Summary Data (Wightman)

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:
  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.
    Dataset Population Cases Controls Imputation panel
    Included in Jansen et al. (2019) ｜ ｜ ｜ ｜
    IGAP* US & Europe 21982 41944 1000G phase 1
    UKB (Proxy) UK 46613 318246 HRC, 1000G, UK10k
    DemGene Norway 1638 6059 HRC
    TwinGene Sweden 224 6321 HRC
    STSA Sweden 320 750 HRC
    deCODE (partially included) Iceland 7002 181573 deCODE
    Total - 77779 554893 -
    Not included in Jansen et al. (2019)
    Finngen* Finland 1798 72206 SISu v3
    GR@CE Spain 4120 3289 HRC
    HUNT Norway 1156 7157 HRC+HUNT
    BioVU US 600 36059 HRC
    23andMe US 3807 359839 1000 Genomes Phase 3, UK10K, HRC
    Gothenburg H70 Birth Cohort Studies and Clinical AD from Sweden (Gothenburg) Sweden 712 2523 HRC
    ANMerge EUR 366 259 HRC
    Total - 12559 481332 -
    Grand total - 90,338 1,036,225
    *=publically available