Topic outline

  • 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