Module 2: Metabolome-wide genome-wide association study

• Title: "Metabolome-wide genome-wide association study"

• 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."

• Slides for introduction to GWAS and metabomatching: File:GWASandMetabomatching.pptx

• Data and Code on SWITCH repository: [2]

• Schedule:
  • H1: General introduction to the paper/motivation
  • H2-3: Write code to import the data and inspect them
  • H4-6: Run regression analyses between SNP and metabolite features. Plot significance profiles.
  • H7: QQ-plots
  • H8: Matbomatching (sing the PhenoMenal portal: [3]
  • H9: Wrap-up & evaluation

• Key bioinformatics concept of this module: "Molecular traits as substrate for GWAS. Data in- and export. Regression. Multiple hypotheses testing."

• back to UNIL MSc course: "Case studies in bioinformatics 2017"