Laboratory

Design and Analysis of Genetic-based Association Studies

September 21st - 25th 2015

Wellcome Genome Campus, Hinxton, UK

Summary

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.

Feedback from previous courses
“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.”

Programme

The programme will include lecture and computer-based practical sessions
covering the following topics:

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.

Instructors and speakers

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
Manj Sandhu (Wellcome Trust Sanger Institute, UK)

Louise Wain (University of Leicester, UK)

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 is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £730 towards board and lodging for non-commercial
applicants. Please contact us for the commercial fee.

Applications
Applications for this course can now be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
This course is now closed. Please contact the course organiser to be
added to our mailing list.

Bursaries

Bursaries
Advanced Courses are subsidised for non-commercial applicants from
anywhere in the world. Limited bursaries are
available (up to 50% of the
course fee) and are awarded on merit. If you would like to apply for a
bursary, please complete the bursary section of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.

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