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_cohort/EADB_core.tsv.gz (original data is already in hg38)
    • EADI: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/EADI_cohort/EADI.tsv.gz (original data is already in hg38)
    • GR@ACE: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/GRACE/GRACE_cohort/AD_4Pcs_TopMedGRACE_Rsq0.3_20200109.tar.gz The summary statistics is in hg38 (imputation with Topmed Rsq>0.3) adjusted by 4PCs.
    • FinnGen (used in Bellenguez paper): /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240200_FinnGen/R6/finngen_R6_G6_AD_WIDE.gz (original data is already in hg38)
    • FinnGen (most recent version until 20240222): /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240200_FinnGen/R10/. All in hg38.
  • another related meta-analysis result of GR@ACE, IGAP and UKB. This one is publicly available in de Rojas 2021, Nature Communications.
    • original: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/GRACE/meta-analysis (GRCh37)
    • liftover to hg38: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20240300_Bellenguez/GRACE/meta-analysis/Sumstats_SPIGAPUK2_20190625.hg38.txt

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

Links to GWAS data analysis notebooks#

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: UK Biobank. We have the genotype and imputed variants ourselves.
• GR@ACE: the Genome Research at Fundació ACE. 61,744,410 variants in sum.stats.
• GERAD/PERADES
• DemGene
• Bonn
• the Rotterdam study
• the CCHS study
• NxC
• FinnGen:
  • R6 includes 147,061 females and 113,344 males, and the one that Bellenguez paper used should be R6/AD_WIDE (N=7,329 cases and N=252,879 controls).
  • R10 is the latest version (until 20240222), including 230,310 females and 181,871 males.

Supplementary Table 1: Demographic descriptions of the different meta-analyzed GWAS, including a description of EADB per country