Pan African Bioinformatics Network for H3Africa

  Introduction to Genome Wide Association Studies

 University of the Witwatersrand, Johannesburg 

Sydney Brenner Institute for Molecular Bioscience/Wits Bioinformatics

H3A AWIGEN --- H3ABioNet

Monday 14 April-Thursday 17 April

Genome Wide Association Studies have become a very popular and powerful investigative technique for many genomic studies and has become a widely-used technique to study a range of questions.
This short course will introduce participants to the key concepts required to perform GWAS studies and give a hands-on training course using some of the commonly used tools:

  • Planning a GWAS: types of GWAS, cost versus power
  • Example platforms
  • Quality control
  • Population structure and correcting for population structure
  • Performing association testing
  • Multiple testing
  • Snags and what to look for (principles and practicalities)
  • Annotation of results
  • The Linux command-line

The tools that will be used are plink, admixture, EIGENSTRAT or SNPRelat. Some other key tools will be identified.  The bulk of the course will be platform independent but about half a day will be spent specific tools for the Affymetrix platform, particularly those required for manipulating image files (the principles of what we will cover apply to other platforms). GWAS requires a reasonable level of Linux competence and the course will provide the necessary background.

Applications close on the 12th March, 2014. The number of places are limited and we will make firm offers after the 14th March date in order to help the planning of those who need to travel. There is no fee for the course, but on confirmation of participation, you will be required to give a commitment of attendance.

H3ABioNet is offering 5 travel fellowships to attend this workshop which will cover airfare and accommodation only (meals excluded).

Of these 5 travel fellowships H3ABioNet is offering, there is a possibility of funding an internship from an H3ABioNet Node to remain at the Wits Node for ~ 5 weeks who will work under the supervision an experienced bioinformaticist and will be involved in all aspects of doing a significant population structure and GWAS analysis. There will be an emphasis on hands-on experience with a range of computational tools, and some exposure to high-performance computing environment. We will also give some training in installation of tools.

The selected intern will be expected to arrive in Johannesburg on 11 April for a 5 week period.

To apply to attend the Wits’ GWAS workshop and for an H3ABioNet travel fellowship, please send the following information to: This email address is being protected from spambots. You need JavaScript enabled to view it.



H3ABioNet Funded (Yes / No):

H3Africa Project associated to:




If student or postdoc, please give name and email of supervisor:

Applying for an H3ABioNet Travel Fellowship (Yes / No):

Applying for an H3ABioNet Internship at the Wits Node (Yes / No):

Linux command line experience:

GWAS experience:

Planned involvement with GWAS:

To apply for an H3ABioNet internship in GWAS at the Wits Node please:

    1). Complete and submit the application details above
    2). Request an motivational letter from This email address is being protected from spambots. You need JavaScript enabled to view it.
    3). Obtain a motivational letter from your supervisor / PI
    4). Complete the internship application form at: http://surveys.h3abionet.org/internship

The date for H3ABioNet Wits’ GWAS internship application closes on the 12th of March, 2014