AD GWAS Summary Statistics
Access
Controlled access. Request data access on the AD Knowledge Portal; you need a Synapse account. See How to get the data.
| Where | ID | Access | What you get |
|---|---|---|---|
| Synapse | syn69670651 | Controlled | Files described below |
Other Synapse IDs on this page syn69670652 syn69670653 syn69670656 syn69670625 syn69696846 syn69865824
pip install synapseclient
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synapse get -r syn69670651All summary statistics were harmonized to GRCh38 before downstream analysis. The APOE region (chr19:44.4 to 46.5 Mb) was analyzed separately because of its complex LD structure. The LD reference panel was built from 16,571 ADSP whole-genome sequenced samples of European ancestry.
Datasets
The study used eight datasets from four AD meta-analyses: Bellenguez, Wightman, Kunkle and Jansen. They cover clinically confirmed late-onset AD, proxy-based AD cases, and broader dementia phenotypes. Lambert et al. 2013 (IGAP stage 1) is cited as a historical reference and is not one of the eight.
| Dataset | Study | Population | N cases | N controls | Phenotype definition |
|---|---|---|---|---|---|
AD_Bellenguez_2022 | Bellenguez et al. 2022 Nat Genet | European | 111,326 | 677,663 | Clinically confirmed late-onset AD. Primary GWAS, used throughout |
AD_Bellenguez_EADB_2022 | Bellenguez et al. 2022, EADB subset | European | n/a | n/a | n/a |
AD_Bellenguez_EADI_2022 | Bellenguez et al. 2022, EADI subset | European | n/a | n/a | n/a |
AD_Wightman_Full_2021 | Wightman et al. 2021 Nat Genet | European | 90,338 | 1,036,225 | AD and proxy-AD (UK Biobank) |
AD_Wightman_Excluding23andMe_2021 | Wightman et al. 2021, without 23andMe | European | n/a | n/a | AD and proxy-AD (UK Biobank) |
AD_Wightman_ExcludingUKBand23andME_2021 | Wightman et al. 2021, without UK Biobank and 23andMe | European | n/a | n/a | n/a |
AD_Kunkle_Stage1_2019 | Kunkle et al. 2019 Nat Genet | European | 21,982 | 41,944 | Clinically confirmed late-onset AD (ADGC/IGAP) |
AD_Jansen_2021 | Jansen et al. 2019 Nat Genet | European | n/a | n/a | AD and proxy-AD (UK Biobank), meta-analysis with IGAP |
Quality control
Summary statistics passed a QC procedure built around SLALOM. Manual curation then compared single-effect regression with conditional regression outputs and removed suspicious or unstable loci. After QC, 195 AD-associated loci were retained for fine-mapping.
LD reference panel
| Panel | N samples | Population | Build | Synapse ID |
|---|---|---|---|---|
| ADSP WGS | 16,571 | European ancestry | GRCh38 | syn69670651, subfolder EUR/ (syn69670652) |
Data access
| Resource | Description | Synapse ID |
|---|---|---|
| ADSP LD reference (EUR) | LD panel for fine-mapping and colocalization | syn69670652 |
| LDSC reference data | LD scores, munged GWAS, sLDSC annotations | syn69670653 |
| LDSC munged GWAS | Pre-munged AD GWAS summary statistics | syn69670656 |
| AD GWAS fine-mapping models | Fine-mapping outputs per GWAS dataset | syn69670625 |
| AD fine-mapping results | Fine-mapped loci and credible sets | syn69696846 |
| Top loci unified summary | AD_GWAS_finemapping_109_blocks_top_loci_unified_any0.8ANDmin0.5.csv.gz | syn69865824 |
All resources are in the FunGen-xQTL staging folder, syn68872650.
Abbreviations
| Abbreviation | Full name |
|---|---|
| AD | Alzheimer’s disease |
| GWAS | Genome-wide association study |
| ADSP | Alzheimer’s Disease Sequencing Project |
| IGAP | International Genomics of Alzheimer’s Project |
| ADGC | Alzheimer’s Disease Genetics Consortium |
| LD | Linkage disequilibrium |
| WGS | Whole-genome sequencing |
| QC | Quality control |
| sLDSC | Stratified linkage disequilibrium score regression |