Topic outline

  • General

    Genetic Diseases - genome-wide association and exome sequencing studies

    Lausanne, 7-10 April 2014

    Overview

    Participants will learn about the genome-wide analysis of variation including GWAS, next generation sequencing (NGS) and how to identify and interpret variants in exomes. The fourth day of the course will introduce techniques to extend GWAS using NGS data, and how to analyse cancer exomes.

    Objectives

    After four days of lectures and practical exercises, participants should have a clear understanding of genome variation, how to perform GWAS and exome analyses, and how to apply these techniques in translational research.

    Requirements

    Skill requirements: Participants should have a good understanding of command-line UNIX (UNIX Fundamentals self-learning module) in order to perform the practical exercises.
    Material requirements: A WiFi-equipped laptop with 3-4GB of RAM, 60GB free hard-disk space and virtualbox installed. You will be given virtual machine images with all softwares and packages needed for this course.

    Application

    Application is now closed. Please note that priority has been given to PhD students members of the Staromics doctoral program.

    Deadline for registration and cancellation is set to the 28th of March 2014.

    Location

    Genopode Building

    Additional information

    For administrative questions, please contact staromics@cuso.ch
    For technical and scientific questions, please contact training@isb-sib.ch

    • Teachers

      AM           Aurélien Macé (Statistical Genetics group (IUMSP/CHUV/UNIL/SIB)
      BS            Brian Stevenson (Vital-IT group (SIB)
      SP            Sylvain Pradervand (LGTF/Vital-IT (UNIL/SIB))
      SR            Sina Rüeger (Statistical Genetics group (IUMSP/CHUV/UNIL/SIB)
      ZK            Zoltán Kutalik (Statistical Genetics group (IUMSP/CHUV/UNIL)

      • Monday 7 April 2014

        09:00 – 11:00                         GWAS - basics (ZK)
        11:30 – 12:00                         GWAS - advanced (ZK)
        13:30 – 17:00                         Practical (ZK)

        GWAS - Basics (slides)

        GWAS - Advanced (slides)

        Practical

        • Tuesday 8 April 2014

          09:00 – 12:00                         Exome Sequencing: From DNA sample to variants file (SP)
          12:00 – 14:00                          “Social lunch” @ Indian resto
          14:00 – 17:00                         Practical (SP + BS)

          Exome Sequencing: From DNA sample to variants file (slides)

          Practical

          VCFS.zip

          • Wednesday 9 April 2014

            09:00 – 10:30                         PacBio Amplicon analysis (SP)
            11:00 – 12:30                         Analysis of cancer samples (SP)
            14:00 – 15:30                         Variant pooling tests & CNVs (ZK + AM)
            15:30 – 17:00                         Rare variant association Practical (SR)

            Sequencing amplicons with PacBio (slides)

            Identification of somatic mutations (slides)

            GWAS - Rare Variants (slides)

            Analysis of rare variants (slides) - Practical

            CNVs detection (slides)

            • Thursday 10 April 2014

              09:00 – 10:30                         Variant annotation and prioritization (part 1) (BS)
              11:00 – 12:30                         Variant annotation and prioritization (part 2) (BS)
              14:00 – 17:00                         Practical (BS + SP)

              Variant annotation and prioritization (slides)

              Practical