Pan African Bioinformatics Network for H3Africa

Introduction to Genetic Epidemiology - TrypanoGEN

Workshop venue: Victoria Falls Resort, Livingstone, Zambia 

Workshop dates: 4th May to 6th May, 2015 

Workshop organisers: Lucio Marcello, Bruno Bucheton, Tabitha Kabayo (TrypanoGEN), supported by H3ABioNet 

Workshop Applications open: 3rd March, 2015 

Workshop Applications close: 27th April, 2015 

Workshop Selection notification date: 30th April, 2015 

Link to workshop application form: https://docs.google.com/forms/d/1CJaFPbPe71WG_r7W7Aty034CAhWxY0Canx_TkSzpUKg/viewform?c=0&w=1 

Workshop Sponsors: TrypanoGEN 

Workshop Overview: As the TrypanoGEN network is becoming more established within the H3Africa consortium, this is an opportunity for the whole network to gain relevant skills in genomic epidemiology, which lies at the heart of our endeavours to conduct a Genome-wide Association Studies (GWAS) analysis to identify traits associated with Human African Trypanomiasis (HAT) resistance. The course will be held over two days, providing both theoretical and methodological approaches to the subject.  On the third day, with the insights gained from the course, an update on HAT will be given, and there will be an opportunity for newly recruited PhD students within the network to outline their projects (see Presentation sessions in timetable below) and for each project to be discussed, strengthening communication across the network. 

Intended Audience: This workshop is aimed primarily at TrypanoGEN project members who will be involved in the design and analysis of experiments based on the epidemiological data collected across the network. PhD students in particular are encouraged to attend and present their projects. 

Participation: Open application for TrypanoGEN members and partners (with no selection), with a potential to extend to H3Africa members (with selection). Priority will be given to those who can demonstrate the need for this training. The maximum participant number is set at 15. 

Syllabus and Tools: Participants will learn about Genomic epidemiology, population genetics, genome wide association studies and candidate gene testing. They will be introduced to the use of PLINK software to conduct some basic association analysis. 

Trainers and support staff:  Alexandre Alcaïs, Bruno Bucheton, Lucio Marcello 

Workshop Application: All potential applicants must complete the application form and upload a motivation letter from their supervisor. The successful applicants for the workshop will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and they will be given the H3ABioNet workshop policy.

Workshop Program: 

This course will deliver theoretical lectures, research examples and hands-on computer training on concepts and tools used in the study of Human genetics and genetic epidemiology of infectious diseases. 

1- Introduction to Human genetics and genetic epidemiology of infectious diseases (1 hour)

2- Overview of existing methods in genetic epidemiology: the survival tool kit (2 hours)

Objective: To give the participant an overview of the different methods to study the link between inter individual variability of phenotypic traits and genetic variation and how to choose the most appropriate one, given the trait under study, previous knowledge, epidemiological/cost constraints.

 3- Association between genetic variants and binary phenotypes (4 hours)

Objective: To introduce statistical testing of different inheritance modes and interpretation (Type 1 errors, causal polymorphisms versus polymorphisms in LD, population stratification…) and how to choose a set of variant to best capture genetic information at a given locus/gene. 

4- Introduction to Genome Wide Association Studies (4 hours)

Objective: Give the participants an overview of GWAS analysis methods focusing on their advantages and pitfalls. Train the participants to PLINK through two practical sessions on data sets containing false positive or true association signals. 

5- Do it yourself (2 hours)

Objective: to give participants a hands-on experience of an actual laboratory situation. Participants will be given a dataset and will carry out analysis themselves with the help of trainers. 


Provisional Timetable

Below is a provisional timetable: 


Day 1 

Day 2 

Day 3 - TrypanoGEN 

09:00 – 10:00

Introductory lecture:  

Genetic epidemiology 


Introduction to GWAS 

HAT update 

10:00 – 12:30




Presentation session 1 

12:30 – 14:00




14:00 – 16:00


Association studies 1 



Presentation session 2 

16:00 – 18:00

Association studies 2 

Do it yourself


Cost Estimate for a participant




Total (USD)


Accomodation (3rd, 4th and 5th at $190 per a night)





Meals (dinner on the 3rd, lunch and dinner 4th and 5th)









Service charge (10%)




Total Cost per participant