Genome Wide Analysis Workshop

This course is jointly offered by Wits Bioinformatics as part of its NIH H3A Africa Bionet and AWIGEN activities, the Sydney Brenner Institute for Molecular Bioscience, the Wits School of Public Health and related Insituted

Course details

• 28-30 May 2013. Held at Wits: Digital Classroom, School of Public Health.
• On the Education Campus, on the corner of York and Jubilee Road, directly opposite main entrance to the Medical School. See map (next to (H) on the map).
• Prerequisite: familiariy with Linux and the CLI. See details of our Linux course on the 27th.

Course presenter

Matt McQueen is in the Department of Integrative Biology of the Institute of Behavioral Genetics at the University of Colorado, Boulder. His research focus is multi-faceted approach to the investigation of genetic determinants underlying complex disease, with a particular interest in psychiatric, behavioral and neurologic disorders. Recent areas of research include the development and application of statistical and epidemiological methods geared towards large scale genomic analysis in both family-based and population-based samples.

Matt is visiting Wits as part of the WBCA collaboration involving Wits,Brown, and Colorado Universities, and the AAfrican Population and Health Research Centre, Nairobi.

Course description

The workshop is aimed at individuals who would like to gain hands-on experience in using some of the more popular genome-wide software packages for the analysis of genome-wide data.

The post-genomic era has been characterized by the rapid advance of genotyping technology resulting in a wealth of new, high-quality data that may hold promise for the further elucidation of genetic factors underlying complex disease. Without the proper tools and methods, the ultimate utility of such rich data may be limited in scope as the field attempts to process and interpret the growing amount of information being generated. For this workshop, we will adopt a hands-on approach to navigate some of the more popular genome-wide software packages available. A general overview of the topics to be covered is as follows. After a brief introduction on the current state of genetic research, we will begin with a discussion of the key quality assurance and quality control steps that are necessary to any genome-wide analysis. We will then transition to the analysis phase with a focus on genome-wide association using unrelated samples, including an overview of the analysis of gene pathways. Next, we will discuss the use of genome-wide data to estimate heritability followed by an introduction to family-based analysis. Finally, we will conclude with some general thoughts on the analysis of genome-wide gene-by-environment interactions and identify potential future directions.

Material to be covered includes

• Intro to human genetic variation (theory)
• Generating, cleaning and inspecting genome-wide data (theory/tutorial)
• Genome-wide analysis - including multiple testing, covariates, etc. (theory/tutorial)
• Heritability using genome-wide data (theory/tutorial)
• Pathway/system-level approach (theory/tutorial)
• Family-based data, genome-wide GxE, Epistasis, Future directions (theory with minimal tutorial)
• Tools to be covered include plink, GCTA, FBAT and R/RStudio)

To attend

• Please paste the form below into an email, fill in the details and send to gwas2013@bioinf.wits.ac.za.
• There is no charge.
• Numbers are limited. We'll start to make selections on 10 May so applications should be received by 9 May.

Name: 

Organisation/Unit:

Position:

Email:

For students/postdocs -- name and email of supervisor:

Please tick one of the options below (compulsory as this is  prerequisite)

    [  ] I will attend the Linux CLI course on 27 May
    [  ] I already know how to use the Linux CLI


If accepted for the course, I will confirm my attendance. I have Linux
background / will attend Linux course on the 27th.