Difference between revisions of "Whole genome association study: Alcohol consumption in the Cohorte Lausannoise"
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'''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. | '''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]] & [[ | + | '''Supervisors''': [[Murielle Bochud]] & [[User:Sven|Sven Bergmann]] |
| + | |||
| + | '''Presentation''': [[Media:Murielle.ppt]] | ||
| + | |||
| + | '''References''': see [[Genome Wide Association Studies]] | ||
| + | ---- | ||
| + | |||
| + | '''Students''': [[User:ColinCourvoisier|Colin Courvoisier]] & [[User:FrancelineWetter|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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html 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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html 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: - [http://www.nature.com/ng/journal/v38/n8/pdf/ng1847.pdf Principal Component Analysis for gene-chip data], [http://www.mathworks.com/access/helpdesk/help/techdoc/index.html?/access/helpdesk/help/techdoc/ref/textscan.html&http://www.mathworks.com/cgi-bin/texis/webinator/search/ Reading in large text files with Matlab], [http://www.nature.com/nrg/journal/v7/n10/pdf/nrg1960.pdf Relatedness]. | ||
| + | ---- | ||
| + | |||
| + | '''4th meeting''': Fr. 20/3/09 at 13:20 in Bugnon 27, DGM-218 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[User:Zoltan|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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[User:Zoltan|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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[User:Zoltan|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 ([http://serverdgm.unil.ch/bergmann/CBG_location.html directions]) with [[User:Zoltan|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"]]) | (Project in [[Course: "Solving Biological Problems that require Math"]]) | ||
Latest revision as of 09:03, 17 April 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
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")
