Module 2: Metabolome-wide genome-wide association study

• 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."

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

• Data: https://drive.switch.ch/index.php/s/ujkIB2cSeH4OvMb

• Code and answers: https://tinyurl.com/y8bymagn

• 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."

• You will be asked to perform an analysis using the software Metabomatching which is available here: https://public.phenomenal-h2020.eu/?tool_id=metabomatching&version=1.0.0&__identifer=4sdrz9hhfus

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