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Design and Analysis of Genetic-based Association Studies

22-26 September 2014

Wellcome Trust Genome Campus, Hinxton, Cambridge

The 2014 course is now closed for applications, please email us to join our mailing list.

This Advanced Course aims to give researchers involved in disease studies a firm grounding in the use of the latest statistical methods and software for analysis of genetic association studies. The course will cover both theoretical and practical aspects of the design and analysis of such studies. Each topic will include a lecture followed by a practical session in which state-of-the-art statistical software will be applied to relevant datasets. The practical sessions will illustrate the ideas presented in the lectures. All the software used will be freely available so skills learned can be applied after the course.

Applicants should have a strong quantitative background (including some familiarity with statistics, mathematics or bioinformatics), a reasonable level of computer literacy and should currently be engaged in relevant research. A basic knowledge and understanding of genetics (both molecular genetics and concepts of inheritance/heritability) will be assumed.

Programme

Introduction to genetic association studies
Overview and history of genetic association studies leading up to and including genome-wide association studies.

Basic association analysis
Single marker association tests including Frequentist and Bayesian tests for association. Calculation of Odds Ratios and Relative risks. Logistic regression. Gene-environment and gene-gene interaction.

Quality control and population structure
Data quality control procedures to avoid the generation of spurious false positives in association studies. The confounding effects of population structure on association studies and methods for protecting against these effects. PCA and mixed model approaches.

Haplotype estimation
Methods for inferring haplotypes from genotype data. The use of haplotypes in genetic association studies for detection of disease variants.

Genotype imputation
Methods for genotype imputation using publicly available reference panels. Pre-phasing based imputation. Frequentist and Bayesian methods of testing association at imputed SNPs and indels. Quality control for imputed SNPs. Meta-analysis using imputed data.

Analysis of rare variants
Methods for analysing rare variants from re-sequencing, genotyping and imputation studies via “collapsing approaches”.

Family-based association studies
Testing for association using family-based study designs. Comparison with designs that use unrelated individuals.

Practical Sessions
Lectures are followed by practical sessions using realistic datasets so that students learn how to apply the theory. Students will learn to use the following computer programs during the course: IMPUTE2, SHAPEIT2, SNPTEST2, QCTOOL, META, GENEBPM, and GRANVIL.

Course instructors

Heather Cordell (Institute of Genetic Medicine, Newcastle University, UK)
Andrew Morris (Wellcome Trust Centre for Human Genetics, University of Oxford, UK)
Jonathan Marchini (Department of Statistics, University of Oxford, UK)

Guest speakers

Martin Tobin (University of Leicester, UK)
Nicholas Timpson (University of Bristol, UK)

Feedback from the 2013 course

“One of the most comprehensive and enjoyable courses I have attended. The instructors were very accessible and friendly.”

“This was an excellent course in terms of topics, academic staff and organisation.”

“Great environment for learning! Overall, it was a great course and I enjoyed the interactions with instructors, teaching assistants, and fellow colleagues.”

How to apply

Prerequisites
Applicants should have a strong quantitative background (including some familiarity with statistics, mathematics or bioinformatics), a reasonable level of computer literacy and should currently be engaged in relevant research. A basic knowledge and understanding of genetics (both molecular genetics and concepts of inheritance/heritability) will be assumed.

Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course and there is a registration fee of £695 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £1800.

Bursaries
Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Applications
The 2014 course is now closed for applications, please email us to join our mailing list.

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