Difference between revisions of "Whole genome association study: Alcohol consumption in the Cohorte Lausannoise"

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1) paper by Firmann et al. describing the CoLaus study: [[Media: Firmann.pdf]]
 
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.doc]]
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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 variable.pdf]]  
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3) the CoLaus codebook (to check names of the variables) [[Media: codage_des_variable.pdf]]  
  
 
4) one paper in French describing the epidemiology of alcohol and tobacco [[Media: tabac_alcool.pdf]]
 
4) one paper in French describing the epidemiology of alcohol and tobacco [[Media: tabac_alcool.pdf]]
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Students who have time are invited to visit lecture by [[Sven Bergmann]] on Thu. 5/3/09 on GWAS in room AAB032 at the EPFL!
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Students who have time are invited to visit lecture [[Media: GWAS_lecture.ppt slides]] by [[Sven Bergmann]] on Thu. 5/3/09 on GWAS in room AAB032 at the EPFL!
  
 
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Revision as of 15:38, 3 March 2009

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


1st meeting: Fr. 27/2/09 with Murielle Bochud

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

- explained how data have been collected

- discussed 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_variable.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 slides 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

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

- basics on regression and GWAS methodology

- population stratification


3rd meeting: date to be fixed between Wed. 11 to Fr. 13/3/09 with Zoltan Kutalik

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

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


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