Alzheimer's Disease GWAS Summary Data (Jansen)

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Oluwatosin Olayinka

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The data are derived from the summary statistics of Jansen et al..

Source files

The summary statistics are held on the Columbia University (CU) cluster.

Path to SuSiE RSS Fine-mapping Objects

• AD GWAS fine-mapping models (AD Knowledge Portal): syn69670625
• Additional fine-mapping objects: syn69696846
• Top unified loci summary: syn69865824

AD GWAS–xQTL Integration

AD GWAS–xQTL colocalization results (ColocBoost): syn69865816

AD GWAS–xQTL colocalization models: syn69670630

AD colocalization models (all GWAS studies): syn69670626

Integrated AD Gene-Level Summary

AD risk genes prioritized by xQTL + GVC: syn70095142

AD risk genes prioritized by xQTL + TWAS + GVC: syn70095143

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

Links to GWAS data analysis notebooks

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.

The 79,145 individuals in phase 1 come from three sources:

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.