View source for 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. [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004132l] 

* 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: [https://public.phenomenal-h2020.eu]
** 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"]]