Topic outline

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    Contrôle qualité bioinformatique et annotation de variants NGS pour le diagnostic du cancer

    28 septembre 2017
    Lausanne

  • Programme

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

    09:00-10:15

    - Why are we doing this?

    - Overview of a bioinformatics analysis pipeline

    - QC throughout the NGS pipeline

    - Variant-level QC: common measures and thresholds for IonTorrent and Illumina

    10:15-10:30

    Coffee break

    10:30-11:30

    Introduction to OncoBenchTM and example case

    11:30-12:30

    Study case – Spotting data artifacts among true variants

    12:30-13:30

    Lunch break

    13:30-14:00

    Presentation/Discussion of the results


    PART III: ANNOTATION & INTERPRETATION

    14:00-15:00

    - Clinical significance: pathogenicity & actionability

    - Annotation using literature and other public databases: essentials and extras

    - From variant to gene, assessing functional impact

    15:00-15:15

    Coffee break

    15:15-16:15

    Study case – Annotation using literature and other public databases

    16:15-16:45

    Presentation/Discussion of the results

    16:45-17:00

    Wrap-up of the course and take-home messages

  • Matériel

    SLIDES DU COURS

    Only available to participating students.


    LECTURE ADDITIONNELLE

    The Association for Molecular Pathology together with the American Society of Clinical Pathology and the College of American Pathologists recently released a set of guidelines for the interpretation and annotation of somatic variant in cancer:

    Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer