Clinical bioinformatics for microbial genomics and metagenomics - ESCMID, CHUV, SIB

Date 9 - 12 September 2019
Fees *academic: 750 CHF   -   for-profit: 750 CHF
Cancellation deadline 10 Jul 2019
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

There were many more applications for this course than expected. It is full with a waiting list.

Overview

Next generation sequencing (NGS) is being increasingly used and implemented at clinical microbiology laboratories, heavily relying on bioinformatics for data processing, analysis and interpretation.

This course aims at providing participants with the essential tools to understand the output of bioinformatics analysis pipelines, interpret the results for making better-informed clinical recommendations, recognise the main challenges and limitations when using NGS bioinformatics analysis pipelines in clinical settings, and acquire a common language to foster multidisciplinary discussions of results with clinical bioinformaticians in their team. It will cover the essential bioinformatics concepts on NGS data management and processing for typing and phylogenetics, resistance and virulence prediction, and metagenomics-based taxonomic classification.

Audience

This course is addressed to clinical microbiologists and other professionals working in the field with little or no programming background.

Learning objectives

At the end of the course, the participants are expected to:

  • Identify when NGS analyses could be useful for their clinical practice.
  • Describe the general bioinformatics pipelines and software for genomics and metagenomics applications.
  • Understand and interpret results from genomics and metagenomics bioinformatics analyses.
  • Recognise the main challenges and limitations when setting up and using NGS bioinformatics analysis pipelines in clinical settings.

Faculty Members

  • Claire Bertelli, Lausanne, Switzerland
  • Stefan Boers, Leiden, Netherlands
  • David Dylus, Lausanne, Switzerland
  • Adrian Egli, Basel, Switzerland
  • Gilbert Greub, Lausanne, Switzerland
  • Hassan Hartman, London, United Kingdom
  • Aitana Lebrand, Geneva, Switzerland
  • John W. A. Rossen, Groningen, Netherlands
  • Etienne Ruppé, Paris, France
  • Helena Seth-Smith, Basel, Switzerland
  • Sandra Reuter, Freiburg, Germany
  • Mirko Rossi, Parma, Italy
  • Opota Onya, Lausanne, Switzerland
  • Andrew Page, Norwich, United Kingdom

Application

Registration Fee

  • EUR 600 for ESCMID members
  • EUR 750 for all others

The fee includes the course, tea and coffee during the course, lunch during the 4 days, a dinner on Monday evening and the social event. Travel and accommodation are not included.

There were many more applications for this course than expected. It is full with a waiting list.

Schedule

You will find the schedule in the following link.

Venue

University of Lausanne Campus Dorigny Internef building

Accreditation

This course has been granted the following accreditations: EACCME® (18 credits), Swiss Society of Microbiology (22 credits) and FAMH (22 credits). It is equivalent to 0.75 ECTS credits.

Additional information

Organizing Committee:

  • Adrian Egli, Basel, Switzerland
  • Gilbert Greub, Lausanne, Switzerland
  • Aitana Lebrand, Geneva, Switzerland
  • Jacob Moran-Gilad, Beit Kama, Israel
  • Patricia Palagi, Lausanne, Switzerland
  • John W. A. Rossen, Groningen, Netherlands

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact William Caddy william.caddy@escmid.org.