Section outline

  • General

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    Exploring common and rare diseases genetics with GWAS and NGS

    Lausanne, 16-19 March 2015

     

    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 course will also introduce techniques to extend GWAS using NGS data.

    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. 

    Deadline for registration and cancellation is set to the 6th of March 2015.

    Location

    Genopode Building. classroom is 2020, except Monday morning, which is Auditorium A.

    Additional information

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

  • Topic 1

  • Virtual machine images

    Before the beginning of the course, you need to have virtualbox installed on your computer.  Please download and install version 4.3.20 for Mac OS X and 4.3.20 for Windows. Then run the virtual image (download link here) to check it works on your computer.

    Please also note that you need a computer with minimum of 4 GB memory. The virtual machine itself requires 2 GB memory. And at least 10 GB free space on your hard disk.

  • 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 16 March 2015

    09:00 – 11:00                         GWAS - basics (ZK)
    11:30 – 12:00                         GWAS - advanced (ZK)
    12:00 – 14:00                          “Social lunch”
    14:00 – 17:00                         Practical (ZK)

    GWAS - Basics (slides)

    GWAS - Advanced (slides)

    Practical

  • Tuesday 17 March 2015

    09:00 – 12:00                         Exome Sequencing: From DNA sample to variants file (SP)
    13:30 – 17:00                         Practical (SP + BS)

    Exome Sequencing: From DNA sample to variants file

  • Wednesday 18 March 2015

    09:00 – 12:30                         New sequencing technologies (slides)
    14:00 – 15:30                         Variant pooling tests & CNVs (ZK + AM)
    15:30 – 17:00                         Rare variant association Practical (SR)

  • Thursday 19 March 2015

    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)