Difference between revisions of "Whole genome association study: Tobacco consumption in the Cohorte Lausannoise"
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'''Students''': [[User:AnneCatherineClerc|Anne Catherine Clerc]] & [[User:ZoeEnderlin|Zoe Enderlin]] | '''Students''': [[User:AnneCatherineClerc|Anne Catherine Clerc]] & [[User:ZoeEnderlin|Zoe Enderlin]] | ||
+ | |||
+ | '''1st meeting''': Fr. 27/2/09 with [[Murielle Bochud]] joint with students from the project [[Whole genome association study: Alcohol 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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[Sven Bergmann]] joint with students from the project [[Whole genome association study: Alcohol 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 | ||
+ | |||
+ | - population stratification | ||
+ | |||
+ | ---- | ||
+ | |||
+ | '''3rd meeting''': date to be fixed between Wed. 11 to Fr. 13/3/09 with [[User:Zoltan|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"]]) | (Project in [[Course: "Solving Biological Problems that require Math"]]) |
Revision as of 18:24, 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 tobacco consumption and related phenotypes. Particular emphasis will be put on SNP tagging taste-specific genes such as the TAS2R.
Mathematical tools: The tool of choice for this project is logistic 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 smoking in the general population and in the context of cardiovascular risks.
Supervisor: Pedro Marques-Vidal & Zoltan Kutalik
References: see Genome Wide Association Studies
Students: Anne Catherine Clerc & Zoe Enderlin
1st meeting: Fr. 27/2/09 with Murielle Bochud joint with students from the project Whole genome association study: Alcohol 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: Alcohol 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
- 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")