This course type is laboratory

Immunophenotyping: Generation and Analysis of Immunological Datasets

19 - 25 February 2017Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    Across all biological sciences, technological advances result in more
    ambitious projects and larger data sets. Launched in 2016, this
    practical, laboratory-based course will demonstrate how to take common
    immunological techniques to the next level by combining them with
    semi-automated and automated analysis methods and using appropriate
    statistical analysis pipelines. The course is aimed at PhD students and
    postdocs who would like to get more out of the experiments they perform
    and make sure their data analysis has a sound basis.

    This course is conducted in collaboration with the Wellcome
    Trust Sanger Institute Mouse Genetics Project
    (MGP) and the Infection and
    Immunity Immunophenotyping
    (3i) consortium.

    Participants will receive training in immunological phenotyping and will
    gain hands-on experience in a number of immunological techniques suitable
    for large-scale phenotyping. Using the data generated during the course,
    we will explore manual, semi-automated and automated analysis approaches
    and relevant statistics for different data sets and discuss benefits and
    challenges. All experiments will be conducted on samples from a knockout
    mouse strain which the participants will identify at the end of the

    The programme will cover a number of
    tests that are conducted routinely
    by 3i under high-throughput
    conditions and discuss the best way to
    analyse and interpret the data.

    Feedback from the inaugural 2016 course

    • Read one participant’s course blog here.
    • Extremely well organized course!
    • This was an excellent course and I am happy I had the opportunity to attend!
    • Thanks to all instructors and course organisers. The course exceeded my expectations – I learned a lot.
    • Thank you to all the organisers, instructors and speakers for a fantastic experience.
    • Overall, the course was a fantastic experience and was very interesting and scientifically useful. Considering the course was in its first year I was impressed by the level of organisation.
    • The course was really well organised and I profited a lot from it, especially due to the interactions with other people, both with participants and instructors!

    Scientific and collaborative background to the course

    MGP generates and phenotypes knockout mice, most of which were generated
    by the International Knockout Mouse Consortium. For each mutant line,
    groups of seven male and seven female mice move through a standard
    analysis pipeline aimed at detecting traits that differ from healthy
    C57BL/6N mice. The pipeline collects many measurements of viability,
    fertility, body weight, infection, hearing, morphology, haematology,
    behaviour, blood chemistry and immunity and compares them to wild type
    controls. An overview over the first 250 lines has been published in Cell
    by White and al. (
    Currently, MGP phenotypes 160 knockout lines a year.

    Given the large number of immune-related phenotypes, it was decided to
    subject these 160 knockout lines to an immunological phenotyping and the
    3i consortium was formed to this end in 2013. 3i conducts an in-depth
    immunological screen in the steady state and under challenge. The
    consortium analyses the immune cell compartments of spleen, mesenteric
    lymph nodes, bone marrow, blood and serum in order to identify genes
    regulating the immune system in the absence of challenge. Furthermore 3i
    investigates responses to chemical stress (DSS colitis) and to viral,
    bacterial and nematode infections (Salmonella, influenza and Trichuris
    Data from both the MGP and the 3i screen are open-access and are publicly
    available on the 3i website ( and the website of
    the International Mouse Phenotyping Consortium (,
    an overarching international initiative.

  • Programme

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

    Laboratory techniques:

    • Detection of antinuclear antibodies in serum
    • CD8 degranulation assay
    • 12-colour panel design for various immune cell populations
    • Flow-cytometric analysis of blood, spleen, lymph nodes and bone marrow
    • Microscopic analysis of the immune compartment in mouse skin

    Analysis techniques:

    • Analysis of 2D microscopic images with a macro
    • Analysis of 3D microscopy data with ImageJ and Velocity
    • Analysis of multidimensional flow data with automated and semi-automated approaches
    • Use of appropriate statistical techniques to analyse the generated datasets

    Learning outcomes
    After having attended this course, participants will be able to:

    • measure antinuclear antibodies in serum
    • assess degranulation of cytotoxic cells
    • prepare and stain skin samples for use on a confocal microscope
    • use basic algorithms to analyse 3D confocal data in different software programmes
    • employ a high-throughput approach to large-scale sample preparation of blood, spleen, and bone marrow for flow-cytometric analysis
    • analyse and interpret high-dimensional flow cytometry data
    • use appropriate statistical tests to analyse data generated during the course
    • explain how sources of variation can impact data
    • manage sources of variation through experimental design
    • assess when multiple testing will lead to false positives
    • develop a work plan for analysing mice at their home institution
  • Instructors / Speakers

    Course instructors
    King’s College London, UK
    Wellcome Trust Sanger Institute, UK
    King’s College London, UK
    Wellcome Trust Sanger Institute, UK
    Natasha Karp (AstraZeneca UK)
    King’s College London, UK
    King’s College London, UK

    Confirmed 2017 guest speakers
    University of Dundee, UK
    Jacobs Jr.
    Einstein College of Medicine, USA
    Kevin Maloy
    University of
    Oxford, UK
    Trinity College Dublin, Ireland
    Melanie Wencker Inserm, France

  • How to Apply

    The course is aimed at PhD students, postdocs or clinicians conducting
    relevant research. Please note: The
    course assumes
    participants will have some basic experience and knowledge of
    including fundamentals of flow cytometry and FlowJo analysis.


    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 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.


    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

    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

  • Cost / Bursaries

    course is subsidised by the Wellcome Genome Campus Advanced Courses
    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.

    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

    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,
    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

    Overseas Courses (held outside of the UK)
    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.
    will be notified of a bursary award along with their place on
    course, usually within one month of the application deadline. The
    decision of the selection committee is