NGS bioinformatics quality control and variant annotation for cancer diagnosis / Contrôle qualité bioinformatique et annotation de variants NGS pour le diagnostic du cancer

Date 28 September 2017
Fees *academic: 50 CHF   -   for-profit: 0 CHF
Cancellation deadline 11 Sep 2017
City Lausanne
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.


This course is organised by SIB Swiss Institute of Bioinformatics, in collaboration with the Clinical Pathology Division of the University Hospital of Geneva (HUG).

Cutting-edge technologies, like next-generation-sequencing (NGS) applied to gene panels, combined with the development of targeted therapies are now revolutionising clinical practice in oncology. In this context, clinical bioinformatics plays a pivotal role, ensuring that NGS data are converted into clinically relevant knowledge. While bioinformatics analysis pipelines can be automated to some extent, they still require human expertise to perform robust quality control and annotation/interpretation of somatic variants.

This course therefore aims at deepening the underlying bioinformatics concepts for professionals from clinical labs working on NGS data, to improve their skills for spotting artifacts from NGS data and annotating true somatic variants. This interactive course will consist of lectures alternating with study cases using a bioinformatics pipeline for cancer diagnosis, and group discussions/presentations.



  • Overview of a bioinformatics analysis pipeline: from FASTQ to BAM, VCF and annotation.


  • Quality control throughout the NGS pipeline
  • Variant-level quality control: common measures and thresholds for IonTorrent and Illumina
  • Study case – Spotting data artifacts among true variants


  • Clinical significance: pathogenicity and actionability
  • Literature and other public databases: essentials and extras
  • From variant to gene, assessing functional impact
  • Study case – Annotation with literature and other public databases


Priority will be given to members of clinical laboratories in Switzerland with some experience in NGS somatic variant analysis.

Learning objectives

  • Participants improve their skills in NGS somatic variant annotation through theory and practical hands-on sessions related to their daily clinical practice.
  • Participants share and discuss their own practices, addressing topics from Ion Torrent and Illumina technologies


  • Knowledge / competencies: Some experience in NGS variant analysis.
  • Technical: None. Computers will be provided to participants.


  • Registration is free of charge for HUG staff (valid HUG email required).
  • For other academics, a registration fee of CHF 50.- applies.
  • Participants from non-academic institutions should contact us before application.

Deadline for registration and free-of-charge cancellation is set to 11 September 2017. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions, available at

You will be informed by email of your registration confirmation.


University of Lausanne, exact venue will be communicated to participants in due time.

Additional information

  • The course will be taught in french and teaching material will be provided in english.
  • Teachers: Dr. Walid Gharib (University of Bern & SIB Training) and Dr. Brian Stevenson (SIB Vital-IT).
  • Scientific responsibility: Dr. Thomas McKee (Head HUG Molecular Pathology).
  • Hospital contributor: Dr. Yann Christinat (HUG Molecular Pathology).
  • Course coordinators: Dr. Aitana Lebrand (SIB Clinical Bioinformatics) and Dr. Grégoire Rossier (SIB Training / SIB Vital-IT).

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.