Fig. 3

Association of Genome-wide significant SNPs across all Biochemical Measures, Meta-Analysis, and ADNI dataset with AD-related Phenotypes. Associations of novel (top) and known (bottom) GWS Index SNPs across all 18 biochemical measures in the Mayo Clinic Brain Bank cohort (n = 441) and results from meta-analysis with AD-related phenotypes in up to 4 cohorts (n = 3707). Meta-analysis was conducted using data from four independent autopsy datasets, namely the AMP-AD Mayo Clinic (n = 344), Mount Sinai Brain Bank (MSBB, n = 267), Rush (ROSMAP, n = 1091) and the Mayo expanded brain bank dataset (n = 2005). Mayo AMP-AD and expanded brain bank datasets were non-overlapping, and latter also included the 441 AD donors from the brain biochemical measures GWAS. Meta-analysis results are fixed effects models adjusted for sex and age at death when appropriate. Rs483082 was not significant after conditioning on rs429358 (APOE-ε4) and so was not carried forward for meta-analysis. Proxy SNPs genotypes were used for rs148028977 and rs116580059 in the Mayo expanded dataset. Note, Thal measures were only available from the expanded Mayo dataset and the AMP-AD Mayo dataset. Rs34805055 was not genotyped in the expanded Mayo dataset, therefore meta-analysis excluded this cohort for this SNP. ADNI associations include amyloid PET (N = 784), CSF amyloid (N = 1154), CSF p-Tau (N = 1151), plasma amyloid (N = 262), and plasma p-Tau (N = 787) adjusted for age and sex. Dot color indicates direction of beta value (blue = positive, red = negative), size of dot indicates absolute beta value. Associations with a p-value ≤2.98E-8 indicated by (***),1E-05 ≤ p-value < 2.98E-8 indicated by (**), and 0.05 ≤ p-value <1E-05 indicated by (*)