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Tips & tricks

Tips & tricks. Christian Gilissen ( c.gilissen@antrg.umcn.nl ). What we do. Find genetic cause for rare Mendelian disorders Exome sequencing of patients / parents Find a single nucleotide change among thousands Only collaborative projects. How we do it. 3x SOLiD 4. 2x 5500xl.

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Tips & tricks

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  1. Tips & tricks Christian Gilissen (c.gilissen@antrg.umcn.nl)

  2. What we do • Find genetic cause for rare Mendelian disorders • Exome sequencing of patients / parents • Find a single nucleotide change among thousands • Only collaborative projects

  3. How we do it 3x SOLiD 4 2x 5500xl 50Mb Agilent SureSelect, 8 barcoded samples per run About 20 samples per week Completed >400 to date

  4. How bioinformatics • 10 Node cluster running bioscope 1.3 • Custom analysis pipeline • Annotation • Statistics & QC • Variant prioritization • “User friendly” • One for all!

  5. How we do • Revisited projects from last year (100 exomes) • 10 projects with a dominant disorder • 6 new genes identified • Found mutations in 3 known genes • 14 projects with a recessive disorder • 8 new genes identified • A success rate of ±60%

  6. Why did we fail? • Gene is not in the enrichment kit • Lack of sequence coverage • Bioinformatic variant calling issues • Bioinformatic annotation issues • Mutation is not within the coding sequences. • Clinical heterogeneity or wrong diagnosis • Not a SNV • Others publish first

  7. Tips & Tricks exome sequencing • Better be too strict than too relaxed • Reanalyze your data • Focus your efforts where it matters most • Make your life easy: automate, keep uniformity • If at first you don’t succeed, use your common sense • Be independent

  8. Current bioinformatics setup • Common programming language • IDE: Eclipse • Code repository • Ticket system • Automated build scripts • Automated testing • Release procedures • Common coding framework

  9. Bioinformatics • All bioinformaticians in a single room • Shared framework • Write easy reusable code • Good collaboration with lab • “Protected” from individual collaborators

  10. New developments • 5500xl instrument + lifescope • Pooled samples • Different enrichments • RNASequencing • IonTorrent • Diagnostics

  11. Acknowledgements Next generation sequencing team - Genomic Disorders Group: Bioinformatics Jayne Hehir-Kwa Joep de Ligt Nienke Wieskamp Marisol del Rosario Eugene Verwiel Lab Alexander Hoischen Lisenka Vissers, Kornelia Neveling Peer Arts, Bart van Lier, Marloes Steehouwer, Petra de Vries, Irene Janssen, Joris A Veltman http://genomicdisorders.nl

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