Introduction to genetic epidemiology
(use 7-Zip to unpack zipped files):
INFORMATION BY CLASS:
Getting started (to be adapted to the new programme)
Molecular genetics: taxonomy
- Course notes: Chapter 2
- Downloading instructions R and Bioconductor: Follow this link
- Information on using R:
- Background reading (series 1):
- Background reading (series 2):
Different faces of genetic epidemiology: a primer
- In-class reading:
- Course notes: Chapter 3
- Downloading instructions R and Bioconductor: Follow this link
- Information on using R: see last class
- 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
- Background reading:
- Code in R as useful examples to homework 1
Population genetics
- Course notes: Chapter 4
- In class reading:
- Preparatory reading for next class:
- Homework assignment:
Population-based genetic association analysis
- Answering any questions you might have wrt reading assignment
- Course notes: Chapter 5
(as reference material)
- Useful conversion code: Click here
- Additional R packages
- Preparatory Reading:
- Homework assignment:
Population-based genetic association analysis - continued (discussion about this subfield of Genetic Epidemiology via key papers):
- InClassReading:
- Homework assignment (last session's homework assignment revisited):
Family-based genetic association studies
- Course notes: Chapter 6
- In Class Reading:
- Additional R packages (for your information; not for this class)
Family-based genetic association studies - continued (discussion about this subfield of Genetic Epidemiology via key papers)
- In Class Reading:
- Click here to download
- software
- the FBAT toolkit
- the FBAT tour
- Homework assignment:
Fitting the genetic epi pieces together
- The following is a collection of the most important course papers/questions, to help you better digest the course note materials:
Genetic epidemiology: an ever expanding discipline
- Homeworks:
- I will first give some solutions to the homeworks and will discuss what the expectations are for the homeworks, the project and the exam.
- Bottomline = DO NOT WORRY!
- The goal of this course is that you understand a few key concepts (we will again go over them during this class - hence ask questions if you do not understand),
that you understand the role of genetic epidemiology for public health policies and that you are able to perform basic genetic association analyses.
- InClassReading:
Travelling a world of "interactions": from linkage analysis to omics integration for better diagnostics and improved health
- Course notes: Chapter 7
- InClassReading:
- Background reading:
NOTES ABOUT HOW THE DATA WERE SIMULATED :
- Exam project assignment and exam preparations:
- Some examplar solutions to homeworks: Click here