Immunophenotyping: Generation and Analysis of Immunological Datasets

19–25 February 2017

Wellcome Genome Campus, Hinxton, UK


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.


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 and 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



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

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