Section outline

  • Tuesday March 11: Mini symposium

    Genopode building, auditorium A

    9:00
    Welcome address

    9:10-9:50
    Dr. Tiffanie Yael Maoz (Moss)
    Weizmann Institute of Science, Rehovot, Israel
    The New Face of SV Detection and Tool Development

    9:50-10:30
    Prof. Alexandre Reymond
    Center for Integrative Genomics, University of Lausanne, Switzerland
    Large rare variants have a significant burden in general populations

    10:30-11:00
    Coffee break

    11:00-11:40
    Dr. Tobias Rausch
    EMBL Heidelberg, Germany
    Population-based structural variant calling using Delly

    11:40-12:20
    Prof. Bart Deplancke
    Laboratory of Systems Biology and Genetics, EPFL / SIB, Lausanne, Switzerland
    Characterizing genomic variation and assessing its impact on gut immunocompetence in a natural Drosophila population

    12:20-13:40
    Lunch

    13:40-14:20
    Dr. Alexander Schoenhuth     / Dr. Tobias Marschall
    Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
    Discovering and genotyping twilight-zone indels with MATE-CLEVER

    14:20-15:00
    Dr. Valentina Boeva
    Inserm U900 / Institut Curie / Mines ParisTech, France
    Detection of structural and copy number alterations in cancer genomes using different types of sequencing data

    15:00-15:30
    Coffee break


    15:30-16:10
    Mr. Yogesh Paudel
    Wageningen University, The Netherlands
    Copy number variation (CNV) detection method using next generation sequencing (NGS) data

    16:10-16:50
    Prof. Can Alkan
    Bilkent University, Ankara, Turkey
    Characterization of mobile element insertions using NGS

    17:00 Farewell

    Wednesday March 12: Hands-on Workshop

    Genopode building, room 2020

    Analysing structural rearrangement of a genome with Next Generation Sequencing (NGS) data is a difficult task, especially when large insertions and deletions have to be compared to a reference genome. We developed a pipeline to compare the results obtained by various tools and combine them together to a final consensus call. During this workshop we will present our pipeline within a virtual machine (VM) allowing interested researchers to upload their own data in order to detect potential insertions and deletions.

    Organisers: Wai Yi Leung / Hailiang Mei, Sequencing Analysis Support Core, Leiden University Medical Center, NL, Dr. Tiffanie Yael Maoz (Moss) Weizmann Institute of Science, Rehovot, IL, Dr. Alexander Schoenhuth / Dr. Tobias Marschall Centrum Wiskunde & Informatica, Amsterdam, NL, Yogesh Paudel Wageningen University, NL, Dr. Laurent Falquet, University of Fribourg, CH

    (UNIX proficiency is required, as well as a laptop with at least 4 GB RAM, 50 GB free disk space, WIFI and VirtualBox preinstalled)

    9:00 Introduction to the project, SV detection methods, tool selection (Yael, Wai Yi)

    9:30 Introduction to makefiles (Wai Yi)

    10:00 Running the VM and testing it (Wai Yi, Laurent, Tobias, Yogesh, Alex, Yael)

    13:00 Present IGV results (Yael)

    parallel group 1

    14:00 How to load your own data (Wai Yi, Tobias)

    15:00 How to adapt the VM for another software (Wai Yi, Tobias)

    parallel group 2

    14:00 Discussion of projects, current difficulties, issues (Laurent, Yogesh, Alex, Yael)