NGS bioinformatics quality control and variant annotation for cancer diagnosis

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

Overview

Cutting-edge technologies, like next-generation-sequencing (NGS) applied to gene panels, combined with the development of targeted therapies are now revolutionizing 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 clinicians and professionals from clinical labs working with NGS data, to improve their skills for performing quality controlled-filtering of variants and annotating true somatic variants. This interactive course will consist of lectures alternating with hands-on using publicly-available tools.

Programme

I. Clinical NGS

• Introduction with tumor board context
• Introduction to NGS

II. Quality control

• Overview of a bioinformatics analysis pipeline
• Basic QC
• Hands-on: filtering variants

III. Variant annotation

• Clinical significance: pathogenicity and actionability
• From variant to gene, assessing functional impact with bioinformatics
• Literature and other public databases: essentials and extras
• Hands-on: variant annotation

Audience

Priority will be given to members of clinical institutions in Switzerland with some experience in NGS.

Learning objectives

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

• Participants improve their skills in NGS variant filtering and 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.

Prerequisites

Knowledge / competencies

Some experience in NGS variant analysis.

Technical

This course will be streamed, you are thus required to have your own computer with an internet connection.

Application

Registration is free of charge for HUG staff (valid HUG email required). Registration fees are 60 CHF for academics and 300 CHF for for-profit companies.

Deadline for registration and free-of-charge cancellation is set to 01/03/2021. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

Venue and Time

This course will be streamed.

The course will start at 9:15 CET and end around 17:15 CET. Precise information will be provided to the participants on due time.

Additional information

• Participation to this course is recognized by SSPath with 7 credits of continuing education
• The course will be taught in English.
• Teachers: Dr. Yann Christinat (HUG Molecular Pathology), Dr. Aitana Lebrand (SIB Clinical Bioinformatics).
• Scientific responsibility: Prof. Thomas McKee (Head HUG Molecular Pathology).
• Hospital contributor: Dr. Yann Christinat (HUG Molecular Pathology).
• Course coordinators: Dr. Aitana Lebrand (SIB Clinical Bioinformatics) and Dr. Monique Zahn (SIB Training).

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.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.