Genetic Analysis of Population-based Association Studies

Formerly known as Design and Analysis of Genetic-based Association Studies, this advanced course aims to give researchers involved in genetic disease studies a firm grounding in the use of the latest statistical methods and software for analysis of genetic association studies. This includes both small-scale disease-specific studies and large-scale collaborative projects including those that can be used for analysis of multiple complex traits such as UK Biobank.

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 that skills learned can be applied after
the course.

The programme will also include seminars from internationally renowned
researchers from the field of complex disease genetics, along with
opportunities for participants to discuss their own research projects
with course instructors and with each other.

Please note: To ensure participants benefit fully from
the course, applications should include clear evidence of the following
existing knowledge and experience:

• 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)

Feedback from the 2016 course
“Great lecturers, great material.”
“Just wish I had attended before!”
“Outstanding course – catered very well for participants from a wide
range of backgrounds.”
“Excellent course, very well laid out and structured.”
“Excellent course overall. Compressed a large amount of material into a
short timespan and balanced lectures and practicals to maximize the yield
of the presented material.”
“Really exceptional course. This is the best course that I have ever been
on. thank you.”
“I found the course to be excellent and the instructors did a very good
job at teaching.”

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 and meta-analysis

• Single marker association tests (frequentist and Bayesian approaches)
• Calculation of odds ratios and relative risks
• Logistic regression
• Meta-analysis (fixed-effects and trans-ethnic)
• Tests of 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 and genotype imputation

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

Heritability and mixed models

• Concepts of heritability and “missing heritability”
• Use of linear mixed modelling approaches to partition heritability and to adjust for population substructure and relatedness in genome-wide association studies

Analysis of rare variants

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

Post-GWAS interrogation

• Approaches for fine-mapping and follow-up of signals from genome-wide association studies

Practical Sessions
Lectures are followed by practical sessions using realistic datasets so
that students learn how to apply the theory. Students will use a variety
of computer programs during the course including: IMPUTE2, SHAPEIT2,
SNPTEST2, QCTOOL, META, EPACTS, GCTA, FaST-LMM, PLINK.

Learning outcomes
On completion of the course, participants can expect to:

• Understand the general principles, assumptions and basic techniques used in genetic association studies
• Read and comprehend scientific articles that present results from candidate-gene and genome-wide association studies
• Analyse genetic data arising from candidate-gene and genome-wide association studies, (including quality control checks, association testing between genotype and phenotype, and post-association fine-mapping of implicated loci to point to likely causal variants, genes and pathways))
• Perform imputation of variants that have not been directly genotyped, using information from genotyped genetic variants
• Perform analysis of common and rare variants, accounting for population structure and family data

Course instructors
Heather Cordell Institute of Genetic Medicine, Newcastle University, UK
Andrew Morris University of Liverpool, UK
Jonathan Marchini Department of Statistics, University of Oxford, UK

Guest speakers
Cecilia Lindgren University of Oxford, UK
Louise Wain University of Leicester, UK

Prerequisites
The course is open to scientists and clinicians engaged in relevant
research. To ensure participants benefit fully from the course,
applications should include clear evidence of the following existing
knowledge and experience:

• 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)

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 £760 towards
board and lodging for non-commercial applicants. Please contact us for
the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
Applications for this course can 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
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a travel visa
application. Note that letters will be provided to confirmed attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

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 £760 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial applicants from
anywhere in the world. Additional, 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.