Topic outline

  • General

    NGS bioinformatics quality control and variant annotation for cancer diagnosis

    Streamed from Geneva, 15 March 2021

    This page is addressed to registered participants. To access course description and application form, please click here. For any assistance, please contact training@sib.swiss.

    • Detailed program and venue

      Venue: Streamed in Zoom
      Schedule: from 9h15 to 17h15, with a lunch break and 2 coffee breaks.

      PARTS I & II: NGS BIOINFORMATICS PIPELINE & QUALITY CONTROL (QC)

      09:15-09:35 Introduction: tumor board context, example with lung cancer explaining spectrum of detectable alterations. Dr. Timothée Olivier

      09:35-10:05 Introduction to NGS technologies (Dr. Aitana Lebrand)

      10:05-10:45 Overview of a bioinformatics analysis pipeline and basic QC (Dr. Aitana Lebrand)

      10:45-11:00 Break

      11:00-12:30 Hands-on on Galaxy: using Galaxy to filter variants based on quality filters and variant allele frequency. (Dr. Yann Christinat)

      12:30-13:30 Break


      PART III: ANNOTATION

      13:30-14:45 Clinical significance: pathogenicity & actionability. Predict variant effect and impact using bioinformatics tools. Annotation using literature and other public databases. (Dr. Aitana Lebrand)

      14:45-15:00 Break

      15:00-17:00 Hands-on on variant annotation. (Dr. Yann Christinat)

      17:00-17:15 Wrap-up of the course and take-home messages. (Dr. Yann Christinat & Dr. Aitana Lebrand)