Teaching 2009-2010

• When does the first class take place?
• Friday February 12.
• 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 (April 19 !!!)



• Where do the classes take place?
• room 1.123 (B28)


• 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

Updated (February 11)


• Course notes 1: Chapter 1
• Downloading instructions R and Bioconductor: Follow this link
• Course notes 2: Chapter 2
• In class reading:
• Paper: History of genetics and sequencing of the human genome

Updated (February 18)


• Course notes: Chapter 4
• In class reading:
• Paper: Shaking the tree
• Homework assignment: Updated (19 February !!!)
• 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 5
• In class reading:
• Paper 1: Genetic Association Studies
• Paper 2: What makes a good genetic association study?
• Background reading:
• Paper: Statistical Methods for Population-Based Association Studies
• Homework assignment: Updated (15 February !!!)
• HW2: Population Genetics
(Updated 18 March !!!)
• 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.

Important Note:
• The due dates of the homework assignments are indicative
• They give you some structure in catching up with the course note material at a regular basis
• Try to stick to these due dates as much as possible
• A delay of about 2 weeks is still acceptable. However, let me know in advance.

• 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
• 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 of last week to try to find those functions within the provided packages, that can help you in making 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)
• Course notes: Chapter 5
• Go over the course notes (were already posted last week) and consult the Background Paper (last week) to find out more details.
• Carefully write down the parts you do not understand
• Mark the parts you would like more information about
• 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 - Homework 2 due date is postponed to March 26 !!!!


• All the materials for the practical and theoretical aspects of population-based association analysis have been provided
• In this class, we address
• the issues that are raised by you, after having read the two in-class reading papers and after having consulted the course notes,
• practical solutions to relevant problems in population-based association studies (using different R strategies)
• Useful R packages
• dgc.genetics
• DGCgenetics
• SNPassoc
• Homework assignment:
• HW3: Population-Based Association Studies
(Updated 18 March !!!)

• Course notes: Chapter 6
• Background reading / In class reading:
• Paper 1: Family-based designs in the GWA era
• Paper 2: Population-based family studies in genetic epidemiology

Please bring your computer to the class


• Today is a practical session on using R (in particular the package GenABEL) for family-based GWA screening
• Course notes: Chapter 6 ( Updated )
• Supporting documentation:
• GenABEL Manual
• GenABEL Tutorial
• ProbABEL Manual
• Homework assignment:
• HW4: Family-Based Association Studies

• Course notes: Chapter 7

Please bring your computer to the class


• Course notes: Chapter 7
• Background reading / In class reading:
• Paper: A global view on epistasis
• Today we will further explore MDR. Try to already install the software on your computer. A corresponding homework assignment will be part of a discussion in class.
• Prepared genotype data for fbat: pedigree_forfbat.ped
• Prepared phenotype data for fbat: pheno_forfbat.phe
• Revision/correction of the previous homeworks
• Homework assignment:
• HW5: Gene-gene Interaction Association Studies
(Updated 5 May 2010)

• Opportunity to ask questions about the course

• Exam project assignment and exam preparations:
• Click here