Alzheimer's Disease GWAS Summary Data (Bellenguez)

Alzheimer’s Disease GWAS Summary Data (Bellenguez) #

The SNP-level association testing summary statistics for Alzheimer’s disease from Bellenguez et al 2022 Nature Genetics. This study uses UK Biobank (UKBB) proxy AD samples

Contact #

Oluwatosin Olayinka, Hao Sun and Rui Dong

Path(s) to summary statistics #

  • NIAGADS FTP: /ftp_fgc_xqtl/projects/ADGWAS_Bellenguez_2022/ADGWAS2022.chr*.sumstat.tsv
  • CU
  • meta-analysis results: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/GCST90027158_buildGRCh38.tsv.gz (original data is already in hg38)
  • cohort-specific results are all stored under /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/ (original data is already in hg38)
  • EADB-core (EADB-TOPMed): /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/EADB_core/EADB_core.tsv.gz (original data is already in hg38)
  • EADI: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/EADI/EADI.tsv.gz (original data is already in hg38)

Path to SuSiE RSS Fine-mapping Objects #

  • Li-San Wang FTP: /ftp_fgc_xqtl/projects/GWAS_Finemapping_Results/Bellenguez/
  • CU: /mnt/vast/hpc/csg/xqtl_workflow_testing/susie_rss/output/ADGWAS_finemapping_extracted/Bellenguez/ADGWAS_sumstat

Download source #

This data is derived from summary statistics from the Bellenguez et al. Nature Genetics paper. The cohort-specific data is requested from Rui Dong and got approved in early 2024. The data is uploaded to the cluster in March 2024.

File Schema #

  • chromosome: chromosome ID
  • position: hg38 position
  • ref: hg38 reference allele
  • alt: alternative effect allele
  • variant: variant ID in the form chr${chromosome}_${position}_${ref}_${alt}
  • beta: SNP effect size
  • se: standard error of beta
  • pvalue: p-value of beta estimate
  • maf: minor allele frequency
  • n_cases: number of cases for estimate
  • n_controls: number of controls for estimate
  • original_effect_allele_frequency: allele frequency of the original effect allele
  1. GWAS summary statistics processing: https://github.com/cumc/fungen-xqtl-analysis/blob/main/analysis/Wang_Columbia/GWAS/AD_GWAS_processing.ipynb

Cohorts included in this study #

111,326 clinically diagnosed/proxy AD cases + 677,663 controls

  • Stage I: 39,106 clinically diagnosed AD cases + 46,828 proxy-ADD cases + 401,577 controls
  • Stage II: 25,392 AD cases + 276,086 controls cohorts:
  • EADB: The European Alzheimer & Dementia Biobank (15 European countries). Also refered as EADB-TOPMed and EADB-core. 21,101,680 variants in sum.stats.
  • EADI: European Association of Development Research and Training Institutes. 12,540,914 variants in sum.stats.
  • UKBB
  • GRACE
  • GERAD/PERADES
  • DemGene
  • Bonn
  • the Rotterdam study
  • the CCHS study
  • NxC Supplementary Table 1: Demographic descriptions of the different meta-analyzed GWAS, including a description of EADB per country
    AD or proxy-ADD cases Controls
    N % females Age Age at onset APOE e4 allele frequency N % females Age APOE e4 allele frequency
    DISCOVERY
    EADB-TOPMed 20,301 61.7 72.0±10.4 71.1±10.5 32.6 21,839 57.3 67.0±14.3 13.2
    Belgium 1,230 64.6 78.7±5.9 78.3±5.9 31.6 1,474 61.8 70.1±8.4 13.6
    Bulgaria 164 54.9 65.1±8.6 65.1±8.6 22.9 - - - -
    Switzerland 182 64.3 76.0±6.5 76.9±6.0 19.2 388 55.9 74.8±4.0 10.1
    Czech Republic 183 60.7 75.8±7.8 - 31.7 61 65.6 66.9±7.2 10.7
    Denmark 403 57.1 79.6±7.8 79.6±7.8 33.7 654 54.4 73.1±8.5 15.4
    Spain 3,273 67.0 75.3±9.0 75.2±9.0 27.2 1,685 63.3 69.3±12.0 10.0
    Finland 1,151 64.0 70.9±8.8 69.8±8.5 42.0 1,806 51.4 71.8±7.1 15.9
    France 1,664 60.2 67.4±11.9 63.2±10.8 33.3 3,106 63.8 44.9±15.4 11.5
    Germany 1,628 60.3 74.8±9.4 74.6±9.8 33.1 2,050 56.0 74.2±8.0 12.3
    Greece 614 63.0 73.1±8.0 72.9±7.9 23.8 1,246 57.3 73.1±5.6 9.1
    Italy 3,271 68.1 73.7±8.9 72.2±8.7 25.0 1,317 56.8 72.2±10.5 8.6
    The Netherlands 2,438 55.8 66.2±10.7 65.6±10.5 41.9 2,389 47.5 60.1±12.0 17.9
    Portugal 80 75.0 69.9±9.2 69.2±8.9 30.0 74 75.7 67.2±6.8 17.6
    Sweden 1,533 62.9 72.8±11.2 72.8±11.2 40.7 3,089 61.8 70.6±9.8 15.6
    United Kingdom 2,487 51.1 68.0±10.7 66.4±10.1 34.4 2,500 51.8 74.4±7.2 12.8
    EADB-HRC 163 54.0 71.5±7.9 71.5±7.9 31.8 405 48.1 77.2±2.1 14.1
    EADI 2,400 65.6 74.3±10.1 73.9±10.2 29.4 6,338 60.3 80.0±7.6 10.5
    GERAD 3,030 63.2 78.1±9.3 78.1±9.3 35.1 7,153 52.0 50.7±11.7 15.4
    Bonn 635 65.5 77.8±9.8 77.8±9.8 30.1 1,210 54.8 69.9±9.3 12.6
    RS1 1,165 72.9 83.7±0.2 83.7±0.2 33.4 4,739 56.7 82.8±0.1 12.9
    RS2 141 59.6 82.8±0.6 82.8±0.6 27.1 1,961 54.1 73.3±0.2 14.1
    GR@ACE/DEGESCO 6,497 64.1 81.8±8.8 81.8±8.8 23.0 6,785 49.1 55.9±15.8 11.0
    DemGene 1,693 65.5 72.2±8.8 71.6±8.8 39.5 5,926 47.7 68.5±11.1 18.2
    CCHS 365 68.5 82.7±6.9 82.7±6.9 31.4 6,106 54.3 58.5±13.7 15.8
    NxC 269 72.4 78.7±6.9 78.7±6.9 26.0 675 44.4 51.9±8.9 10.0
    UKBB-P 49,275 57.3 59.3±6.7 - 22.6 338,440 56.0 55.8±8.2 14.0
    REPLICATION
    ADGC 17,141 57.3 78.6±8.1 73.4±8.0 37.7 17,627 58.8 75.8±8.1 14.4
    CHARGE
    CHS 450 66.0 - 81.9±5.2 34.0 1,702 60.0 81.1±5.0 20.0
    FHS 472 68.0 - 84.5±7.3 18.5 3,878 54.0 74.4±10.8 11.0
    FinnGen 7,329 48.8 82.2±7.4* 78.0±7.6 31.6 252,879 56.7 59.3±17.4* 17.8
    *age at death or current age
    total 111,326 677,663