Genomics and Clinical Virology

Viral genome sequencing and sequence-dependent detection methods have
been applied to the diagnosis and management of viral infections for
decades.  However, the introduction of next-generation
sequencing (NGS) technologies is transforming how clinical
microbiology laboratories diagnose and manage infectious diseases.
Whole genome sequencing (WGS) of hundreds of microbes can be undertaken
in hours enabling real time genomics for diagnostics, transmission
investigation and infection control.

This exciting new Genomics and Clinical Virology course combines
practical hands-on laboratory and bioinformatics training with faculty
lectures by, and discussions with, leaders in this crucial and expanding
area.

The course is aimed at virology Clinical Scientists and Specialist
Registrars who are planning to implement NGS in clinical diagnostic
laboratories. Researchers (PhD, postdoc or more senior level) who have an
interest in learning how to carry out NGS of viral genomes are also
welcome to apply. The course will concentrate on the application of
cutting edge genomic techniques that can be implemented now and explore
new approaches that will enter practice in the near future.

The practical parts of the course will include laboratory
sessions focusing on the preparation of
sequencing libraries
for metagenomics and PCR-based approaches. Particular emphasis will be
placed on how to improve the efficiency of viral NGS by
undertaking
variations in library preparation techniques – such as target
enrichment
by probe hybridization.

Participants will also gain hands-on
experience in
bioinformatics analysis of the output data, with focus
on
reference mapping and de novo assembly approaches as well as
downstream
analyses such as phylogenetic inference, epitope
identification and drug
resistance identification.

There will also be lectures and demonstrations of
the
potential applications of NGS in clinical laboratories, limitations
and
pitfalls of the techniques and clinical case studies e.g. in
infection
control.

Please Note: Limited bursaries are available for
clinical and academic applicants from anywhere in the world to attend
this course. In addition, CPD accreditation will be
sought from the Royal College of Pathologists.

Learning Outcomes
After attending the course, participants should be able to:

• Carry out NGS including wet lab preparation and bioinformatic analysis of real samples
• Create sequencing libraries and analyse samples derived from patients with viral infections (e.g. HIV, HCV, EBOV, Zika)
• Evaluate how to improve the efficiency of NGS by carrying out variations in library preparation technique (e.g. target enrichment)
• Evaluate the pitfalls of NGS interpretation in clinical viral diagnostics
• Evaluate potential future applications of NGS in clinical diagnostic laboratories and appreciate the limitations of the technique

The course will cover a wide range of cutting-edge viral WGS laboratory
techniques and bioinformatics analysis in practical classes,
demonstrations or lectures.  The areas and issues to be addressed
will include:

• Background to viral WGS approaches
• Sample handling and preparation
• Library preparation techniques
• Target enrichment methods e.g. probe-based sequence capture or PCR-based
• Viral metagenomics
• Technique discrimination –  the appropriate technique to use in different scenarios
• Next generation and third generation sequencing platforms
• Bioinformatics analysis including different viral genome assembly approaches
• Data interpretation
• Validation and accreditation of viral WGS diagnostic service
• Case studies in outbreak investigation and infection control

Learning Outcomes
After attending the course, participants should be able to:

• Carry out NGS including wet lab preparation and bioinformatic analysis of real samples
• Create sequencing libraries and analyse samples derived from patients with viral infections (e.g. HIV, HCV, EBOV, Zika)
• Evaluate
  how to improve the efficiency of NGS by carrying out variations in
  library preparation technique (e.g. target enrichment)
• Evaluate the pitfalls of NGS interpretation in clinical viral diagnostics
• Evaluate
  potential future applications of NGS in clinical diagnostic
  laboratories and appreciate the limitations of the technique

Lead instructors
Judith Breuer University College London, UK
Tamyo Mbisa Public Health England, UK
Emma Thomson MRC-University of Glasgow
Centre for Virus Research, UK

Guest speakers
Nick Loman University of Birmingham, UK
Karin Metzner University Hospital Zurich,
Switzerland
Oliver Pybus University of Oxford, UK

Additional guest speakers will be confirmed shortly.

Prerequisites
The course is aimed at virology Clinical Scientists and Specialist
Registrars who are planning to implement NGS in clinical diagnostic
laboratories.
Researchers (PhD, postdoc or more senior level) with an
interest in
learning how to carry out NGS of viral genomes are also
welcome to apply.

Please note: Bioinformatic training will include the use
of UNIX/Linux command-line analysis and familiarity with these resources
is recommended. There are numerous online introductory tutorials to the
UNIX/Linux operating system and commad line, including:
http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

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
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.