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Genetic Association Course

June 22-26, 2015 Max Delbrueck Center (MDC) for Molecular Medicine Berlin, Germany

The 2015 Course Participants

Course Description

Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.) and with pencil and paper. The emphasis of this course is analysis of population based whole genome and exome data including genotype and sequence data. TOPICS include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; tagSNP selection; controlling population admixture (genomic control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate (FDR).

The Course Organizers and Instructors

Suzanne M. Leal (Baylor College of Medicine, Houston, U.S.A.) and Michael Nothnagel (University of Cologne, Germany)

Data Sets

The data sets used during the computer exercises are available for download below. Due to its size, the data archive for the impute exercise will be available separately from the other data sets. To save the files to your computer, press the right-click button of your mouse (or Strg/Ctrl + mouse-click under MacOS), select 'Save as ..' and then choose an appropriate directory at your local disc.

To unpack the data under Windows, use either the integrated functionality of Windows 7's explorer or one of the following programs: 7-zip, WinZip.

To unpack the data under linux/MacOs, open a shell, change to the directory that contains the archive files and type the following command:
tar -xvzf data.tar.gz
This should create numerous subdirectories containing the exercises-specific data sets.

Software links