Whole genome association study: Alcohol consumption in the Cohorte Lausannoise

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Background: The Cohorte Lausannoise (CoLaus) includes more than 6,000 individuals that have been extensively phenotyped for clinical observables related to cardiovascular risk factors and who have been genotyped for about half a million single nucleotide polymorphisms (SNPs).

Goal: The goal of the project is to perform a genome-wide association study that will potentially identify SNPs that are related to “alcohol consumption” and related phenotypes.

Mathematical tools: The tool of choice for this project is regression analysis. The student will learn the basics of regressing a given phenotype to a genotype and how this analysis is implemented on a computer to handle a large number of SNPs. If time permits the student will explore the effect of other phenotypes as covariables and/or environmental interactions.

Biological or Medical aspects: The “biology supervisor” will provide background of the medical significance of alcohol consumption in the general population and in the context of cardiovascular risks.

Supervisors: Murielle Bochud & Sven Bergmann

Presentation: Media:Murielle.ppt

References: see Genome Wide Association Studies


Students: Colin Courvoisier & Franceline Wetter


1st meeting: Fr. 27/2/09 with Murielle Bochud joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- explain how Colaus data have been collected

- discuss which type of phenotypes should be use in the analyses (i.e. how new or corrected phenotypes can be they be constructed from the questionnaire data).

- documents to read:

1) paper by Firmann et al. describing the CoLaus study: Media: Firmann.pdf

2) the CoLaus questionnaire (to see how the phenotypic data was generated) Media: questColaus 1.pdf

3) the CoLaus codebook (to check names of the variables) Media: codage_des_variables.pdf

4) one paper in French describing the epidemiology of alcohol and tobacco Media: tabac_alcool.pdf


Students who have time are invited to visit lecture Media: GWAS_lecture.ppt by Sven Bergmann on Thu. 5/3/09 on GWAS in room AAB032 at the EPFL!


2nd meeting: Fr. 6/3/09 at 13:00 in Bugnon 27, DGM-328 (directions) with Sven Bergmann joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- with all four students (2 for alcohol and 2 for tobacco GWAS).

- basics on regression and Genome Wide Association Studies (GWAS) methodology


3rd meeting: Fr. 13/3/09 at 12:15 in Bugnon 27, DGM-328 (directions) with Sven Bergmann joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- with all four students (2 for alcohol and 2 for tobacco GWAS).

- principal component analysis and population stratification

- Further reading in preparation for Session 4: - Principal Component Analysis for gene-chip data, Reading in large text files with Matlab, Relatedness.


4th meeting: Fr. 20/3/09 at 13:20 in Bugnon 27, DGM-218 (directions) with Zoltán Kutalik joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- "hands on": how to analyze large-scale GWAS data on a computer

- warm-up exercise with "semi-in-silico" data


5th meeting: Fr. 27/3/09 at 12:30 in Bugnon 27, DGM-218 (directions) with Zoltán Kutalik joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- reading in large data sets (in plink format)

- detecting population stratification


6th meeting: Thu. 9/4/09 at 15:00 in Bugnon 27, DGM-218 (directions) with Zoltán Kutalik joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- multiple testing corrections

- QQ-plots


7th meeting: Fri. 17/4/09 at 12:30 in Bugnon 27, DGM-218 (directions) with Zoltán Kutalik joint with students from the project Whole genome association study: Tobacco consumption in the Cohorte Lausannoise

- the alcohol related phenotypes

- CoLaus genotypes


(Project in Course: "Solving Biological Problems that require Math")