Alzheimer's Disease GWAS Summary Data (Kunkle)

Alzheimer’s Disease GWAS Summary Data (Kunkle) #

The SNP-level association testing summary statistics for Alzheimer’s disease from Kunkle et al 2019 Nature Genetics. Position values were converted from hg19 to hg38 using liftOver.

Contact #

Oluwatosin Olayinka

Path(s) to summary statistics #

  • NIAGADS FTP, /ftp_fgc_xqtl/projects/ADGWAS_Kunkle_2019_hg38_liftover/kunkle_sumstat_hg38_qc.chr*
  • CU
  • original data (in GRCh37)
  • stage 1: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/'Kunkle_etal_Stage1_results.txt?file=1'
  • stage 2: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/'Kunkle_etal_Stage2_results.txt?file=1'
  • liftover data (in GRCh38):
  • stage 1: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/Kunkle_etal_Stage1_results.txt_file_1_hg38.txt
  • stage 2: /mnt/vast/hpc/csg/data_public/GWAS_sumstats/20231011_Kunkle/Kunkle_etal_Stage2_results.txt_file_1_hg38.txt

Path to SuSiE RSS Fine-mapping Objects #

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

Download source #

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

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
  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 #

  • 46 case-control studies: 21,982 cases + 41,944 controls
  • final sample: 94,437 individuals = 35,274 clinical and autopsy-documented AD cases + 59,163 controls
  • 4 consortia (46 case-control studies in Suppl. Table 2) non-Hispanic Whites (NHW):
  • ADGC: Alzheimer Disease Genetics Consortium
  • CHARGE: Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium
  • EADI: The European Alzheimer’s Disease Initiative
  • GERAD/PERADES: Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer’s Disease Consortium" Supplementary Table 1. Description of the consortium data sets used for Stage 1 discovery, Stage 2 and Stage 3. Discovery
    Alzheimer’s disease cases Controls
    Consortium N Percent female Mean AAO (s.d) N Percent female Mean AAE (s.d)
    ADGC 14,428 59.3 71.1 (17.3) 14,562 59.3 76.2 (9.9)
    CHARGE 2,137 67.3 82.6 (12) 13,474 55.8 76.7 (8.2)
    EADI 2,240 65 75.4 (9.1) 6,631 60.6 78.9 (7.0)
    GERAD 3,177 64 73.0 (0.2) 7,277 51.8 51.0 (0.1)
    N 21,982 41,944
    Stage 2*
    Country N Percent female Mean AAO (s.d) N Percent female Mean AAE (s.d.)
    ————– ——- ————————- ————– – —— ——
    Belgium 878 66.1 78.8 (8.2) 661 59.5 65.7 (14.3)
    Finland 422 68 71.4 (6.9) 562 59.3 69.1 (6.2)
    Germany 972 63.9 73.0 (8.6) 2,378 53.1 69.5 (10.1)
    Greece 256 63.3 73.1 (7.9) 229 34.1 49.3 (16.4)
    Hungary 125 68 78.9 (7.3) 100 69 74.4 (6.5)
    Italy 1,729 66.5 71.5 (8.7) 720 55.7 70.0 (10.4)
    Spain 2,121 66.3 75.0 (8.3) 1,921 55.3 70.2 (10.8)
    Sweden 797 61.7 76.8 (8.1) 1,506 62.8 70.6 (8.7)
    UK 490 67.6 74.6 (8.7) 1,066 29.2 73.8 (6.5)
    USA 572 61.9 83.5 (7.6) 1,340 54 79.3 (6.8)
    N 8,362 10,483
    Stage 3*
    Country N Percent female Mean AAO (s.d) N Percent female Mean AAE (s.d.)
    —— —— —— —— —— —— ——
    Spain (ACE) 932 71 77.7 (7.9) 1,813 68.4 54.7 (12.1)
    UK (Cardiff) 1,902 64.8 77.1 (7.9) 1,047 57.8 73.9 (12.9)
    USA (ADC7) 514 51.3 73.9 (8.3) 790 63.6 72.3 (7.7)
    Spain (GR@ACE) 1,582 74.6 78.5 (8.0) 3,086 48 54.0 (14.0)
    N 4,930 6,736
  • AAO, age at onset; AAE, age at examination.
  • *Stage 2 and Stage 3 datasets were combined for genotyping of 33 replication variants not present on the 2013 custom chip Supplementary Table 2. Demographic description of datasets within each consortium.
    Consortium AD cases Controls
    N % female Mean AA (SD) N % female Mean AAE (SD)
    ADGC ACT 532 62.6 78.8 (12.7) 1,571 55.6 81.7 (5.9)
    ADGC ADC1 1,549 54.3 71.6 (11.0) 512 59.2 76.8 (8.8)
    ADGC ADC2 727 50.8 61.4 (29.5) 156 67.9 75.8 (7.9)
    ADGC ADC3 894 54.7 58.6 (32.8) 586 63 72.8 (17.5)
    ADGC ADC4 304 55.3 73.4 (7.0) 377 63.9 75.7 (8.1)
    ADGC ADC5 286 53.1 73.7 (7.0) 505 65.5 77.6 (9.0)
    ADGC ADC6 213 58.2 73.9 (7.6) 338 66.6 74.6 (9.0)
    ADGC ADNI 268 42.2 75.3 (7.1) 173 40.5 78.6 (5.5)
    ADGC BIOCARD 6 33.3 73.8 (6.1) 112 62.5 68.0 (5.5)
    ADGC CHAP 27 63 84.8 (7.6) 144 52.8 81.8 (6.6)
    ADGC EAS 9 44.4 85.2 (4.9) 141 41.1 84.4 (5.2)
    ADGC GenADA 666 56.9 72.8 (13.5) 712 63.9 74.2 (7.0)
    ADGC MAYO 658 57.4 73.6 (4.8) 1,046 51.1 72.9 (4.4)
    ADGC MIRAGE 491 63.3 69.9 (11.5) 738 58.8 70.8 (12.1)
    ADGC MTC 256 57 73.6 (11.8) 189 61.4 70.9 (9.7)
    ADGC NIALOAD 1,798 65 73.1 (9.3) 1,568 60.2 73.8 (9.3)
    ADGC NBB 80 71.3 74.5 (7.5) 48 56.3 81.5 (9.4)
    ADGC OHSU 132 62.1 85.9 (5.7) 153 54.9 83.9 (7.6)
    ADGC PFIZER 696 53.7 73.7 (5.0) 762 54.1 77.2 (4.9)
    ADGC RMAYO 13 23.1 78.5 (9.0) 233 41.6 79.2 (5.8)
    ADGC ROSMAP 295 70.5 85.6 (6.2) 769 72 82.2 (7.1)
    ADGC ROSMAP2 59 78 81.9 (6.9) 217 76 80.8 (7.2)
    ADGC TARC1 323 61.6 74.0 (7.1) 181 65.2 73.9 (8.2)
    ADGC TGEN2 668 64.8 67.2 (22.9) 365 48.5 80.0 (8.7)
    ADGC UKS 596 57.4 72.2 (6.6) 170 51.2 64.1 (3.0)
    ADGC UMCWRMSSM 1,177 64.5 71.1 (17.4) 1,126 61.3 73.5 (10.6)
    ADGC UPITT 1,255 62.9 66.8 (22.4) 829 63.3 75.5 (6.0)
    ADGC WASHU 339 57.2 69.1 (21.5) 187 60.4 76.9 (8.4)
    ADGC WASHU2 38 57.9 73.4 (7.3) 94 46.8 51.7 (35.2)
    ADGC WHICAP 73 72.6 83.9 (7.8) 560 60.4 81.7 (6.7)
    CHARGE AGES 95 51.6 81.5 (0.1) 2,708 59.2 75.7 (0.1)
    CHARGE ASPS 277 57.8 76.4 (8.3) 169 58 66.4 (10.8)
    CHARGE CHS 450 66 81.9 (5.2) 1,702 60.3 81.1 (5.2)
    CHARGE FHS 330 64 86.1 (7.2) 3,910 49 74.0 (9.5)
    CHARGE ROTTERDAM 985 73.2 83.5 (6.6) 4,985 57.6 78.0 (7.6)
    EADI 2,240 65 75.4 (9.1) 6,631 60.6 78.9 (7.0)
    GERAD   MRC 1,008 70.3 80.9 (6.5) 873 61.6 75.9 (6.3)
    GERAD   ARUK 939 61 76.6 (9.6) 82 59.8 77.9 (7.6)
    GERAD   BONN 551 63.7 72.9 (8.3) 37 64.9 79.5 (3.6)
    GERAD   WASHU 423 56 82.1 (9.0) 156 65.4 78.5 (9.7)
    GERAD   NIMH 127 63 80.1 (6.1) - - -
      GERAD  UCL:PRION 82 59.8 63.6 (9.9) - - -
      GERAD  UCL:LASER 47 74.5 80.6(7.9) - - -
      GERAD  1958BC - - - 5,342 49.8 45.0 (0.0)
    GERAD   KORA - - - 434 49.1 56.0 (7.2)
    GERAD   HNR - - - 353 52.9 54.6 (5.3)
    GERAD   MAYO1 - - - - - -
    TOTALS 21,982 41,944