Immunophenotyping: Generation and Analysis of Immunological Datasets

Across all biological sciences, technological advances result in more
ambitious projects and larger data sets. This 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.

This practical, laboratory-based course is suited to 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.

Participants will receive training in how to set up an immunological
phenotyping experiment 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 strain which the participants will
identify at the end of the course.

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

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.

During the course we will delve hands-on into 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 2017 course

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

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

Please note: The course assumes participants have some
basic experience and knowledge of immunology including fundamentals of
flow cytometry and FlowJo analysis.

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

Course instructors
Adrian
Hayday King’s College London, UK
Simon
Clare Wellcome Trust Sanger Institute, UK
Lucie
Abeler-Dörner King’s College London, UK
Anneliese
Speak Wellcome Trust Sanger Institute, UK
Adam
Laing King’s College London, UK
Dmitry
Ushakov King’s College London, UK

Guest speakers
Ian Humphreys (Cardiff University UK)
William R. Jacobs, Jr. (Albert Einstein College of Medicine, USA)

Prerequisites
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
immunology
including fundamentals of flow cytometry and FlowJo analysis.

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 £775 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. Places are limited
and will be awarded on merit. 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 £775 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.