Topic outline

  • General

    NGS bioinformatics quality control and variant annotation for cancer diagnosis

    Bern, 12 November 2019

    This page is addressed to registered participants. To access course description and application form, please click here. For any assistance, please contact
  • Detailed program and venue

    Venue: University of Bern, Hochschulstrasse 4, main building, classroom 028 (ground floor)
    Schedule: from 9h15 to 17h15, with a lunch break and 2 coffee breaks.


    09:15-10:30 - Why are we doing this?
    - Overview of a bioinformatics analysis pipeline:

    • FASTQ and PHRED scores
    • Reference genome, alignment concepts, and the BAM file format
    • Sequencing depth, coverage
    • VCF, BED formats
    • Variant annotation (from DNA to HGVS)

    - QC throughout the NGS pipeline
    - Variant-level QC: common measures and thresholds for IonTorrent and Illumina

    10:30-10:45 Coffee break

    10:45-11:15 Example study case presented on OncoBenchTM

    11:15-12:15 Hands-on: Spotting data artifacts among true variants (in groups of 2-3 people, 2 patients)

    12:15-12:45 Presentation/Discussion of the results

    12:45-13:45 Lunch break



    - Clinical significance: pathogenicity & actionability
    - Annotation using literature and other public databases: essentials and extras
    - From variant to gene, assessing functional impact:

    • Existing tools and when (not) to use them
    • Variant effects on the protein
    • Genes, transcripts and HGVS nomenclature

    15:00-15:15 Coffee break

    15:15-16:15 Study case – Annotation using bioinformatics tools and public databases (in groups of 2-3 people, 2 patients)

    16:15-17:00 Presentation/Discussion of the results

    17:00-17:15 Wrap-up of the course and take-home messages

  • Course material

    Download slides below

    Additional reading

  • Hands-on