Difference between revisions of "Whole genome association study: Alcohol consumption in the Cohorte Lausannoise"
Line 39: | Line 39: | ||
---- | ---- | ||
− | '''2nd meeting''': Fr. 6/3/09 with [[Sven Bergmann]] | + | '''2nd meeting''': Fr. 6/3/09 at 13:00 in Bugnon 27, DGM-328 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[Sven Bergmann]] |
- with all four students (2 for alcohol and 2 for tobacco GWAS). | - with all four students (2 for alcohol and 2 for tobacco GWAS). |
Revision as of 16:31, 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.doc
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 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")