Teaching 2009-2010

• When does the first class take place?
• Wednesday February 3.
• If you have a laptop, please bring it to the class.
• No other material is necessary. This will be a class to discuss the set-up of the future classes, to discover the background knowledge, to talk about your expectations and wishlist for these classes, and to start with a gentle introduction on some concepts and terms



• When do the next classes take place?
• Click here for an updated course schedule


Updated (19 April !!!)



• Where do the classes take place?
• room F50 (B35)


• What about homeworks?
• Click here for some guidelines


• What if I have additional questions?
• Consult Kristel Van Steen (kristel.vansteen@ulg.ac.be) before or after class or by e-mail. In order for the mail not to get lost, please mention "epidemiology course" in the header

• Course notes: Chapter 1
• Downloading instructions R and Bioconductor: Follow this link
• In class reading:
• Paper 1
• Paper 2

• Course notes: Chapter 2
• Downloading instructions R and Bioconductor: Follow this link
• Information on using R:
• Part 1: R manuals
• Part 2: Basic Commands !!!
• Part 3: An introduction to R
• Part 4: Advanced
• In class reading:
• Paper 1: History of genetics and sequencing of the human genome
• Paper 2: Genetic Linkage Studies
• Homework assignment:
• HW1: Data exploration
• Pedigree File Family data with basic information and genetic markers
• Phenotype File A continuous trait, measured for all family members
• Conversion R Script Coversion programme in R (remember the easy-to-use Tinn-R) to create a .ped file that can be opened and viewed in Notepad. Change the working directory, according to the location on your computer with the data

• Course notes: Chapter 3
• In class reading:
• Paper 1: Prospects of genetic epidemiology in the 21st century
• Paper 2: The importance of integration of genetics and epidemiology
• Background reading:
• Paper 1: Key concepts in genetic epidemiology
• Paper 2: Basic epidemiology (book)

• Course notes: Chapter 4
• In class reading:
• Paper: Shaking the tree
• Background reading:
• Paper: Genomewide association studies and human disease
• Homework assignment:
• HW2: Population genetics

• Aim of this week:
• Giving you the opportunity to catch up with concepts and to start finding your way in the literature of this field
• Solution to HWE problem from class discussion
• Allowing you to find solutions in an independent way to problems that are common to genetic epidemiology (by starting on the Homework 2 assignment)
• R is new to some of you, hence use the documentation below to try to find those functions within the provided packages, that can help you in completing the Homeworks (1 and 2). The provided packages contain useful quality control options, but were constructed in the light of carrying out a population-based association analysis (Chapter 5)
• About the R Genetics package
• About the R SNPassoc package
• Basic overview of R commands that can be taken as a quick reference of some special commands.
• Read the following papers (marking parts that are unclear or parts you would like to know more about):
• Paper 1: Genetic Association Studies
• Paper 2: What makes a good genetic association study?

Please bring your computer to the class


• Answering any question you might have after last week's self-study / self-exploration
• Course notes: Chapter 5
(as reference material)
• About the R Genetics package
• About the R SNPassoc package
• Basic overview of R commands that can be taken as a quick reference of some special commands.
• Useful conversion code: Click here (Updated April 22!!!)
• Additional R packages
• dgc.genetics
• DGCgenetics
• InClassReading / Background Reading:
• Paper 1: Genetic Association Studies
• Paper 2: What makes a good genetic association study?
• Homework assignment:
• HW3: Population-based association analysis
Updated (10 March !!!)

Please bring your computer to the class


• Course notes: Chapter 6
• Additional R packages (for your information; not for this class)
• GenABEL manual
• GenABEL tutorial
• ProbABEL manual
• InClassReading / Background Reading:
• Families for Genetic Association Studies?

Please bring your computer to the class


• Buffer class: this is your opportunity to ask questions about course notes / homeworks / ...
• Recall: important documentation on R packages
• About the R SNPassoc package
• About the R genetics package
• Basic overview of R commands that can be taken as a quick reference of some special commands.
• Homework assignment:
• HW4: Family-based association analysis

• Homeworks 3 and 4
• Useful conversion code: Click here (Updated April 22!!!)

Please bring your computer to the class for an FBAT session!

_
• Click here to download
• software
• the FBAT toolkit
• the FBAT tour
• Useful conversion code for previous homeworks: Click here (Updated April 22!!!)
• Homework assignment (due May 5):
• HW4: Family-based association analysis
• Prepared genotype data for fbat: pedigree_forfbat.ped
• Prepared phenotype data for fbat: pheno_forfbat.phe (A file with such an extension .phe can be opened in any editor like Notepad for inspection)

Please bring your computer to the class for an "interaction" session!


• Course notes: Chapter 7
• Background Reading:
• Paper: Genomics and Molecular Genetics in Clincal Practice
• Homework assignment (due May 12):
• HW5: Looking for epistatic effects
• General conversion code for fbat input files: Click here


Please prepare this class well: there will be room for asking questions about remaining unsolved issues.

More information about the exam project will be given in this class as well, and posted after May 12. Hence, please keep on consulting this site!

• Homeworks: please send HW 2 - HW 5 electronically to kristel.vansteen@ulg.ac.be with subject title "homework genetic epi"
• Useful conversion code: Click here (Updated May 10!!!)
• data set: one column per marker as result of previous coding
• UPDATED HOMEWORK 4 - extra explanations
• UPDATED HOMEWORK 5 - extra explanations

• Exam project assignment and exam preparations:
• Click here