This course type is laboratory

Design and Analysis of Genetic-based Association Studies

26 - 30 September 2016Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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.

    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 and association between genotype and phenotype)
    • Perform imputation of variants that have not been directly genotyped, using information from genotyped genetic variants

    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 2015 course

    “I would like to thank the instructors and organisation for this
    wonderful course. I’ve learned a lot in this course, this will definitely
    helps me in my further analysis.”

    “Many thanks for all the hard work that went into organising the course.
    It was a great experience in every aspect. The instructors couldn’t have
    been better!”

    “I really enjoyed the course not only for acquired knowledge but also for
    the kindness and superb accommodation. But I especially liked interacting
    with skilled people from prestigious institutions around the world.”

    “I would like to thank all wonderful instructors of the course and their
    assistants to provide such a great opportunity to learn/practice
    genetic-based association studies. Also I would appreciate the course
    organising team for their great support! Thank you all. you are amazing!”

    “I just would like to say that this course will definitely improve a lot
    the way I perform data analysis. It was a great opportunity to learn new
    methods and also to ask questions and discuss my research with real
    specialists. Brilliant team!”

  • 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 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”.

    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 use a variety
    of computer programs during the course including: IMPUTE2, SHAPEIT2,
    SNPTEST2, QCTOOL, META, GRANVIL, GCTA, FaST-LMM, CASSI, PLINK.

    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.

    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 and association between genotype and phenotype)
    • Perform imputation of variants that have not been directly genotyped, using information from genotyped genetic variants
  • Instructors / Speakers

    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

  • 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).

    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 £745 towards board and lodging
    for non-commercial applicants. Please contact us for the commercial fee.

    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

  • Bursaries

    Bursaries
    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.