Module 2: Metabolome-wide genome-wide association study

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  • Title: "Metabolome-wide genome-wide association study or how to link genotypes to metabolites"
  • Paper to be examined: “Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links”, PLoS Genet10(2): e1004132. [1]
  • Key claim of the paper: "Genetic variants that correlate with any of the measured metabolome features in a large set of individuals generate a signature that facilitates the identification of the metabolite whose concentration is most likely affected by these variants."
  • Data: will be distributed by the tutors
  • Contents:
    • General introduction to the paper/motivation
    • Write code to import the data and inspect them
    • Run regression analyses between SNP and metabolite features. Plot significance profiles.
    • Matbomatching (sing the PhenoMenal portal: [2]
    • Wrap-up & evaluation
  • Key bioinformatics concept of this module: "Molecular traits as substrate for GWAS. Data in- and export. Regression. Multiple hypotheses testing."