EMBO Practical Course on Genotype to Phenotype Mapping of Complex Traits


 Monday 28 July Friday 1 August 2014


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application deadline: 

Friday 23 May 2014


Open application with selection


Frank O’Donnell

Registration fee: 


Registration closed


This course will provide researchers with training in the bioinformatics involved in genotype-to-phenotype mapping. Participants will engage in varied activities, including lectures, computer-based practicals, discussion sessions, and problem solving exercises to follow course objectives. The course will be highly interactive and include both theoretical and practical elements. During practicals, participants will have the opportunity to process and analyse data provided by the trainers and/or their own data. Participants will learn how to implement a range of established and cutting-edge Quantitative Trait Loci (QTL) mapping methods across diverse species including bacteria, yeast, flies, plants and worms. This will include major emerging approaches in the field, such as the integration of multi-omics data, e.g from Next Generation Sequencing (NGS) technologies.


This course is aimed at biologists and bioinformaticians who are embarking upon research projects that will involve genotype to phenotype mapping of complex traits. Some of the tools to be introduced on the course will require the use of Unix commands and the IPython notebook. In order to benefit from the course, you will need to familiarise yourself with these free tutorials, which are available from:


Python Scientific Lecture notes:


An introduction to numpy/scipy:


Syllabus, tools and resources

During this course you will learn about:

  • Variation data
  • Population genetics
  • QTL mapping
  • Heritability
  • eQTL analysis


After this course you should be able to:

  • Browse, search and retrieve variation data from widely available public repositories
  • Discuss factors influencing variation data
  • Use widely available bioinformatics tools to implement a range of QTL mapping methods
  • Evaluate a range of approaches for genotype to phenotype mapping

Additional information

AllBio sponsored travel bursaries are available for applicants currently working in EU based institutions on research that is non-human / non-medical in nature. Please fill the relevant boxes within the application if you wish to be considered for a travel bursary.

For scientists based in Singapore additional travel grants are available. Please see the website for more information: http://www.a-star.edu.sg/Research/Funding-Opportunities/Grants-Sponsorship/EMBO-Singapore-Cooperation-Agreement.aspx


Time Topic Trainer
Day 1 - Welcome, Introduction and Variation
12:00-13:00 Registration and lunch  
13:00-13:30 An introduction to the EBI Laura Emery
13:30-14:00 An introduction to the course Oliver Stegle, Christoph Lippert
14:00-15:00 An introduction to variation Adam Eyre-Walker
15:00-15:30 Tea/coffee break  
15:30-17:30 Exploring variation data with Ensembl - Course booklet Emily Pritchard
17:30-18:00 Networking activity Laura Emery
18:00-19:00 Poster Session  
19:30 Dinner at Hinxton Hall  
Day 2 - Population Genetics, Study Design and QTLs
09:00-10:00 Evolution, selection and host pathogen interactions Daniel Wilson 
10:00-10:30 Tea/coffee break  
10:30-12:00 Practical: variation and selection Daniel Wilson
12:00-13:30 Lunch  
13:30-14:15 An introduction to linear models for QTL mapping Practical: Basic QTL mapping I Christoph Lippert
14:15-15:00 Practical: Basic QTL mapping I Christoph Lippert, Oliver Stegle
15:00-15:30 Tea/coffee break  
15:30-16:15 Practical: Basic QTL mapping II Christoph Lippert, Oliver Stegle, Jennifer Listgarten
16:15-17:15 Genotype Phenotype Mapping in Arabidopsis thaliana Bjarni Vilhjalmsson
17:15-18:00 Quiz and discussion Speakers of the day
18:00-19:00 Dinner at Hinxton Hall  
Day 3 - 3 QTL Mapping: Methods and Challenges
09:00-09:45 GWAS methods for structured populations Jennifer Listgarten
09:45-10:30 Practical I: QTL mapping for structured populations Christoph Lippert, Oliver Stegle
10:30-11:00 Tea/coffee break  
11:00-12:00 Practical II: QTL mapping for structured populations Christoph Lippert, Oliver Stegle
12:00-13:30 Lunch  
13:30-14:30 Heritability estimation and prediction David Balding 
14:30-15:15 Practical: Heritability estimation I David Balding & Doug Speed
15:15-15:45 Tea/coffee break  
15:45-16:30 Practical: heritability estimation II David Balding & Doug Speed
16:30-18:00 Complex Trait Genetics in Rodents and Plants Richard Mott
18:00 Dinner at Hinxton Hall  
19:00 Quiz night  
Day 4 - QTL Mapping: Methods and Applications
09:00-09:45 Mapping by sequencing in A. thaliana -   Handout
Korbinian Schneeberger
09:45-10:30 Practical: Mapping by sequencing I Leopold Parts & Korbinian Schneeberger
10:30-11:00 Tea/coffee break  
11:00-11:30 Practical: Mapping by sequencing II Leopold Parts & Korbinian Schneeberger
11:30-12:30 Heritability, missing heritability and related problems Leopold Parts
12:30-14:00 Lunch  
14:00-14:45 Missing heritability, rare variants and set tests Christoph Lippert
14:45-15:30 Practical: Missing heritability, rare variants and set tests Jennifer Listgarten, Christoph Lippert, Oliver Stegle
15:30-16:00 Tea/coffee Break  
16:00-17:00 ENCODE/epigenome data Ian Dunham
17:00-18:00 Practical: Variant annotation Graham Ritchie
18:00 An opportunity to work on your own data  
19:00 Dinner at Hinxton Hall  
Day 5 - Mapping, GWAS and beyond
09:00-09:45 Multivariate phenotype modelling, GxE Oliver Stegle & Christoph Lippert
09:45-10:30 Quantitative trait prediction Bjarni Vilhjalmsson
10:30-11:00 Tea/coffee break  
11:00-12:30 Practical: Multivariate phenotype modelling & risk prediction Oliver Stegle, Christoph Lippert, Bjarni Vilhjalmsson
12:30-13:30 Lunch  
13:30-14:30 Epigenetic characterisation of human populations Jordana Bell
14:30-15:30 Epigenome-wide association studies Jennifer Listgarten
15:30-16:00 Tea/coffee break  
16:00-17:00 RNA-Seq processing Simon Andrews 
17:00-18:00 Genetic analysis of molecular traits Oliver Stegle
18:00-18:05 Course Feedback All
18:30 Coach pickup from conference centre  
19:30 College Dinner  
  1 Nights accommodation in Cambridge City Centre