This course type is laboratory

Genomics and Clinical Virology

23 - 28 February 2020Wellcome Genome Campus, UK
Deadlines (at 23:59 UTC):
  • Application and bursary deadline Closed

This course has now closed
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the 2021 course.

Learn how to apply next-generation sequencing technologies to clinical virology

  • 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 Genomics and Clinical Virology course combines practical hands-on laboratory and bioinformatics work with faculty lectures by, and discussions with, leaders in this crucial, exciting, and expanding area. The course is aimed at virology researchers at PhD, postdoc or more senior level who have an interest in learning how to carry out NGS of viral genomes, and Clinical Scientists and Specialist Registrars who are planning to implement NGS in clinical diagnostic laboratories. 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 course is aimed at virology Clinical Scientists and Specialist Registrars who are planning to implement NGS in clinical diagnostic laboratories.Virology researchers at PhD, postdoc or more senior level who have an interest in learning how to carry out NGS of viral genomes are also encouraged to apply.

    What will I learn?

    The practical part of the course will provide laboratory sessions that will focus on the preparation of sequencing libraries for metagenomics and PCR-based approaches with particular emphasis 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 gain practical experience in bioinformatics analysis of the output data with focus on reference mapping and de novo assembly approaches, and downstream analyses such as phylogenetic inference, epitope identification and drug resistance identification. There will 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.

    CPD Accreditation
    The course is approved annually for CPD accreditation by the Royal College of Pathologists (43 credits in 2019).

    PLEASE NOTE: bursaries are available for clinical and academic applicants from anywhere in the world to attend this course. Please see the “Cost / Bursaries” tab below for more information.

     

  • 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

     

    *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/

  • Instructors and speakers

    Lead instructors

    Judith Breuer

    Judith Breuer
    University College London, UK

    Nick Loman

    Nick Loman
    University of Birmingham, UK

    Tamyo Mbisa

    Tamyo Mbisa
    Public Health England, UK

    Emma Thomson

    Emma Thomson
    MRC-University of Glasgow Centre for Virus Research, UK

    Module Leads (Wet Lab and Bioinformatics)

    Ana Da Silva Filipe

    Ana Da Silva Filipe
    MRC-University of Glasgow Centre for Virus Research, UK

    Carmen Manso

    Carmen Manso
    Public Health England, UK

    Sunando Roy

    Sunando Roy
    University College London, UK

    Sreenu Vattipally

    Sreenu Vattipally
    MRC-University of Glasgow Centre for Virus Research, UK

    Guest speakers

    Andrew Leigh Brown

    Andrew Leigh Brown
    University of Edinburgh, UK

    Karin Metzner

    Karin Metzner
    University Hospital Zurich, Switzerland

    Oliver Pybus

    Oliver Pybus
    University of Oxford, UK

  • Cost and bursaries
    Cost Accommodation / meals
    *Course fee £800 This is a residential course and the fee includes all accommodation and meals.

    *The course fee is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and applies to non-commercial applicants. Please contact us for the commercial fee.

    Bursaries
    Limited bursaries are available (up to 50% reduction on 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.

    Where there are many bursary applications, the selection committee may issue smaller amounts.

    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.

    Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.

    Additional funding opportunities
    Visit our support page for additional financial support currently available.


    Accommodation services phishing scam – please be vigilant. More information.

  • 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.Virology researchers at PhD, postdoc or more senior level who have an interest in learning how to carry out NGS of viral genomes are also encouraged 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/

    CPD Accreditation
    The course is approved annually for CPD accreditation by the Royal College of Pathologists (43 credits in 2019).

    How to Apply
    Please click the Apply button above to begin the online application process. 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, line manager 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
    Successful applicants will be provided with a support letter for their visa application, if required.

    Please visit the following websites for further information on visiting the UK:

  • Testimonials

    Feedback from the 2019 course:

    “It was an excellent course, brilliantly organized and executed.”

    “The course was excellent. Very well organized and great teachers and teaching. Thank you.”

    “Many thanks for a great course.”

    “The small class size of course and the great atmosphere while learning was one the highlights of the course. The instructors were always on hand and ready to clarify any doubts which was another great aspect of the course.”

    “Very well organised. High calibre instructors”

    “I really enjoyed the whole course and thought that the balance between practical and theory and laboratory techniques and biofiormatics was very well judged.”