Metabolomics Data and Methods

This page provides information about the data and methods used to generate the Metabolomics evidence presented in Agora.

The Metabolomics evidence for a specific gene can be viewed on the Evidence/Metabolomics tab of that gene’s page in Agora. You can navigate to a gene’s page using search, from the Nominated Targets list, or from the Gene Comparison Tool.

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Data and Methods

Metabolic data for Agora was analyzed using a multi-step process. Metabolite data was obtained from approximately 1,400 samples of the Alzheimer’s Disease Neuroimaging (ADNI) cohorts. Metabolite concentrations from 157 metabolites were obtained in clinical lab tests performed by participating ADNI centers. Sampled metabolites include: 140 from the Biocrates AbsoluteIDQ® P180 platform, 15 from the Biocrates® Bile Acids Kit, as well as concentrations of total triglycerides and total cholesterol.

Metabolite levels were then associated with individual genes by performing a genome- wide association study using metabolite concentrations as phenotype (mGWAS). This mGWAS analysis yielded 15,401 significant gene-metabolite pairs. For these pairs, we report the Ensembl GeneID, the Associated Gene Name, ID and full name of the metabolite with the strongest genetic association, the P-value of the association, as well as the gene-wide significance threshold derived from 1000 Genomes Project variants.

For all 157 metabolic readouts, we then used linear regression to compare medication- and covariate-adjusted, centered, and scaled metabolite residuals from cognitively normal elderly controls (CN) with those of participants with clinical Alzheimer’s disease (AD). In this analysis, 26 out of the 157 metabolites had an adjusted P-value <= 0.05.

This content has been provided by the Duke AMP-AD Team led by Rima Kaddurah-Daouk. Learn more about the team.