This course type is laboratory

Design and Analysis of Genetic-based Association Studies

21 - 25 September 2015Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • 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 / 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.