Section outline

  • 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.


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

    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


    PART III: ANNOTATION

    13:45-15:00

    - 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