This course type is laboratory

Genomics and Clinical Virology

04 - 09 February 2018Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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
  • Programme

    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
  • Instructors / Speakers

    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.

  • How to Apply

    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 / Bursaries

    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.