EMBO Practical Course on Genotype to Phenotype Mapping of Complex Traits
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Date:
Monday 28 July - Friday 1 August 2014Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication deadline:
Friday 23 May 2014Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£350Registration closed
Overview
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.
Audience
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:
Unix:
http://www.ee.surrey.ac.uk/Teaching/Unix/
Python Scientific Lecture notes:
https://scipy-lectures.github.io/
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
Outcomes
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
Programme
| 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 | ||
In association with
How to apply
Application deadline
23 May 2014
Number of places
30 places
Organisers
Laura Emery
Oliver Stegle
Christoph Lippert - Microsoft, USA
Trainers
Oliver Stegle - EMBL-EBI, UK
Christoph Lippert - Microsoft, USA
Adam Eyre-Walker - University of Sussex, UK
Daniel Wilson - University of Oxford, UK
Jennifer Listgarten - Microsoft Research, USA
David Balding - University College London, UK
Richard Mott - University of Oxford, UK
Leopold Parts - Sanger Institute, UK
Alexis Battle - Stanford University, USA
Korbinian Schneeberger - Max Plank Institute for Plant Breeding, Germany
Nicole Soranzo - Wellcome Trust Sanger Institute, UK
Magnus Nordborg - Gregor Mendel Institute of Molecular Plant Pathology, Austria
Helena Kilpinen - EMBL-EBI, UK
Laura Emery - EMBL-EBI, UK
Emily Perry - EMBL-EBI, UK