Alzheimer's Disease GWAS Summary Data (Jansen)

Alzheimer’s Disease GWAS Summary Data (Jansen) #

The SNP-level association testing summary statistics for Alzheimer’s disease from Jansen et al 2021 Nature Genetics. This study uses proxy AD individuals from UK Biobank.

Contact #

Oluwatosin Olayinka

Download source #

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

Path(s) to summary statistics #

  • Li-San Wang FTP: /ftp_fgc_xqtl/projects/ADGWAS_Jansen_2019_hg38_liftover/jansen_sumstat_hg38_qc.chr*
  • CU
  • original data: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230620_Jansen/AD_sumstats_Jansenetal_2019sept.txt (GRCh37)
  • liftover to hg38: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20230620_Jansen/AD_sumstats_Jansenetal_2019sept.hg38.txt (hg38)

Path to SuSiE RSS Fine-mapping Objects #

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

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
  • Neff: effecting sample size
  1. Summary statistics preprocessing: https://github.com/cumc/fungen-xqtl-analysis/blob/main/analysis/Zhang_BU/summary_stat_qc_all.nb.html

Cohorts included in this study #

  • 455,258 individuals of European ancestry = 71,880 (proxy) cases + 383,378 (proxy) controls
  • Phase 1: 79,145 individuals (Nsum; Neff=72,500) = 24,087 clinically diagnosed LOAD cases + paired with 55,058 controls.
  • Phase 2: 376,113 individuals of European ancestry from UKB with parental AD status = 47,793 proxy cases + 328,320 proxy controls" “79145 from phase 1:
  1. Alzheimer’s disease working group of the Psychiatric Genomics Consortium (PGC-ALZ) – 17477
  2. the International Genomics of Alzheimer’s Project (IGAP) – 54162
  3. the Alzheimer’s Disease Sequencing Project (ADSP) – 7506 individuals = 4343 cases + 3163 controls Supplementary Table 1. Overview of cohorts for meta-analysis
  • Note: AD = Alzheimer’s disease; GWAS = genome-wide genotype data; WES = whole exome sequencing data; 1000G = Thousand Genomes; HRC = Haplotype Reference Consortium. * The PGC-ALZ summary statistic have been meta-analyzed with the other 3 main cohorts, but PGC-ALZ sub-cohort specific demographics are also displayed. The ‘age of onset’ and ‘age of last contact’ of the UKB samples, refers to the age of the UKB participants (so not of the parents). For the controls of the DemGene cohort, mean age was based on 2382 individuals for which this information was available. Proxy cases and controls only refers to the UKB cohort, all other cohorts are clinical case-control cohorts.
    Cohort Sub-cohort Geographic origin N cases: N Age of onset % female controls: N Age last contact % female Phenotype Data Type Imputation Reference
    1. PGC-ALZ* a. DemGene Norway 9703 2066 77.0 62.9 7637 58.8 48.0 AD GWAS 1000G Phase 3
    b. TwinGene Sweden 6647 322 79.6 52.5 6325 64.2 52.4 AD GWAS 1000G Phase 3
    c. STSA Sweden 1127 348 80.5 66.4 779 75.5 51.1 AD GWAS 1000G Phase 3
    2. IGAP Europe/US 54162 17008 74.2 61.3 37154 69.8 57.3 AD GWAS 1000G Phase 1
    3. ADSP Europe/US 7506 4343 74.1 55.0 3163 86.5 59.5 AD WES 1000G Phase 3
    4. UKB UK 376113 47793 59.1 56.5 328320 56.4 53.6 by proxy AD GWAS HRC