H3ABioNet

Pan African Bioinformatics Network for H3Africa

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Introduction to Genome-Wide Association Studies (GWAS) for complex diseases

The African Institute for Mathematical Sciences (AIMS) Ghana and the H3ABioNet Node of the Noguchi Memorial Institute for Medical Research (NMIMR) University of Ghana, are organizing a five-day intensive workshop on GWAS for complex diseases.

Venue of workshop: Conference Room - Noguchi Memorial Institute for Medical Research, Ghana
Dates for the workshop: 12th to 16th June 2017
Registration opens: 28th April, 2017
Registration closes: 19th May, 2017
Notification date: 23th May, 2017
Registration: All interested applicants must complete the application form at the following URL: https://docs.google.com/forms/d/e/1FAIpQLSccskI0-Hbm-pbGRNRtCfGHUU3ItxRASQWSS9M4BrbY0qIWzg/viewform

Proposed workshop objectives:

This workshop is aimed at introducing an interdisciplinary audience to important concepts in genetics and population genetics that are relevant to complex disease association studies and data analysis. Participants will also be introduced to the potential of GWAS and to key strategic considerations in designing and performing association studies for mapping disease genes.  It will cover the fundamental assumptions, showcase recent successes and discuss limitations of current GWAS approaches in the field of complex diseases, and particularly in the case of African populations known for low linkage disequilibrium. It will also provide ‘hands-on’ experience of data analysis.

Syllabus and Tools:

Participants will learn basic genetics and population genetics that is applicable to GWAS analysis, the design and analyses of population data and genome-wide association testing. Hands on data processing, analysis and the interpretation of result
Intended Audience: The target audience includes graduate students, research assistants, postdocs and established and young investigators entering the field of complex trait genetics from a variety of backgrounds such as biological, bioinformatics, statistics, mathematics and computer science.
Prerequisites: Selected participants will need to work through the following resources to enable them to gain the most from the workshop:
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.r-tutor.com/r-introduction
https://www.python.org/

Trainers:
Dr. Gaston K. Mazandu (African Institute for Mathematical Sciences (AIMS), Ghana-South Africa andComputational Biology, University of Cape Town, South Africa)
Dr. Emile R. Chimusa (Human Genetics Division, Department. of Pathology, University of Cape Town, South Africa)
Dr Anita Ghansah (H3ABioNet  Node, (NMIMR), Legon, Ghana)
Dr. Samuel K. Kwofie (Biomedical Engineering Department , University of Ghana, Legon and H3ABioNet  Node, (NMIMR), Legon, Ghana)

Facilitators:
Wisdom Akurugu (H3ABioNet, Node, (NMIMR), Legon, Ghana)
Fiifi Hayford (H3ABioNet, Node, (NMIMR), Legon, Ghana)
Jacquiline Mugo (H3ABioNet, Node (CBIO, Cape Town South Africa)

Workshop program:

Time Topic Trainer
12th June 2017
8:00 Registration and Welcome  
8:30 Introductions and Pre-workshop evaluation  
9:00 Overview on genetics and medical population genetics: Basic genetics and introduction to population genetics Dr. Anita Ghansah
10:30 Tea break  
11:00 Overview on genetics and medical population genetics: introduction to population genetics Dr. Anita Ghansah
12:00 GWAS study design:GWAS versus linkage mapping and power calculation Dr. Chimusa
1:00 Lunch  
2:00 Introduction to population Structure and principal component analysis Dr. Chimusa
3:30 Tea Break  
4:00 Introduction to Admixture Dr. Chimusa
6:00 Workshop End  
13th June 2017
9:00 Advanced Genomic data manipulation with plink Dr Chimusa
10:30 Tea Break  
11:00 Advanced Genomic data manipulation with plink Dr Chimusa
1:00 Lunch  
2:00 Genomic Data Quality Control Dr. Chimusa
3:30 Tea Break  
4:00 Genomic Data Quality Control Dr. Chimusa
6:00 Workshop End  
14th June 2017
9:00 Principal component Analysis and Population structure exercise Dr. Chimusa
10:30 Tea Break  
11:00 Principal component Analysis and Population structure: Introduction to Genesis Jacquiline Mugo
1:00 Lunch  
2:00 Principles of Genome wide Association Studies Dr. Gaston
3:30 Tea Break  
4:00 Genome-Wide Association Studies pipelines with plink Dr. Chimusa and Jacquiline
6:00 Workshop End  
Time Topic Trainers
15th June 2017
9:00 Genome-Wide Association Studies pipelines with plink Dr. Chimusa
10:30 Tea break  
11:00 Genome-Wide Association Studies: Stratification and admixture mapping Dr. Chimusa and Jacquiline
1:00 Lunch  
2:00 Genome-Wide Association Studies pipelines2: Imputation and fine mapping Dr. Chimusa
3:30 Tea Break  
4:00 Genome-Wide Association Studies pipelines2: Imputation and fine mapping Dr. Chimusa
6:00 Workshop End  
16th June   2017
9:00 Genome-Wide Association Studies pipelines3: Enrichment and pathways analysis Dr. Gaston
10:30 Tea Break  
11:00 Genome-Wide Association Studies pipelines3: Enrichment and pathways analysis Dr. Gaston
1:00 Lunch  
2:00 Genome-Wide Association Studies:Ongoing Challenges and opportunities  
3:30 Tea Break  
4:00

Finish exercises and Post-Workshop Evaluation

 
6:00 Workshop End