; Technologies, applications and data analysis Course 2542 Dr. Martie C.M. Verschuren Avans Hogeschool Research group Analysis techniques in Life Science, Breda Prof. dr. Johan T. den Dunnen Leiden Genome Technology Center, Leiden 1-4 April 2014 Avans Hogeschool Research Group Analysis Techniques in Life Science P.O. Box 90116 4800 RA Breda The Netherlands www.alsavans.nl All rights reserved. No part of this publication may be reproduced or transmitted, in any form or by any means, without permission from Avans Hogeschool Breda
Code 2542 Tuesday April 1, 2014 Next generation sequencing technologies 08.45 Arrival and registration (Dr. Martie Verschuren, Avans Hogeschool) 09.00 General course introduction and NGS overview [B] (Dr. Martie Verschuren, Avans Hogeschool) 09.45 NGS terminology & NGS sample preparation [C] (Dr. Henk Buermans, LUMC, Leiden) 10.25 Lecture: Illumina / Solexa technology platform [E] (Dr. Ies Nijman, Hubrecht laboratory, Utrecht) 10.55 Coffee/Tea 11.10 Lecture: Ion Torrent platform [D] (André Wijfjes, ServiceXS B.V. Leiden) 11.50 Lecture: Single molecule sequencing [F] (Ing. Yavuz Ariyurek, LUMC, Leiden) 12.30 Lunch Next generation sequencing Data analysis 13.30 General Introduction to data analysis [3] 13.50 Lecture: Introduction to Linux [4] 14:10 Lecture: Command line and NGS tools [5] (Ing. Michiel van Galen, LGTC, Leiden) 14.40 break 15:00 Lecture: Connecting to other machines [6] 15.30 Computer practical 1, General tools used in NGS: Command line practice. Splitting on bar codes. Alignment and SNP calling.
(Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 17.30 End of the course day one 18.30 Welcome Diner 20.30 End of day 1
Code 2542 Wednesday April 2, 2014 Next generation sequencing applications 09.00 Welcome coffee and introduction of day 2 09.30 Lecture: Think before you start [G] (Dr. Judith Boer, Human Genetics, LUMC Leiden and Laboratory for Pediatric Oncology, Erasmus MC) 10.15 Lecture: NGS-based mrna profiling: from Tag-based approaches to Fulllength sequencing to investigate transcription, RNA processing and translation [H] (Eleonora de Klerk, LUMC, Leiden) 11.00 Coffee/Thee 11.15 Lecture: mirna profiling [IJ] (Dr. Henk Buermans, LUMC, Leiden) 12.00 Lecture: NGS in DNA diagnostics [TU] (Dr. Jasper Saris Erasmus MC, Rotterdam) 12.45 Lunch 13.45 Computer practical, parallel sessions with Genome browser views on: RNA expression analysis, mirna profiling, DNA diagnostics 16.45 Lecture: De novo sequencing: a tool to discover novel pathways in microorganisms [NO] (Dr. Huub Op den Camp, IWWR, Radboud University Nijmegen) 17.30 End of the course day two
Code 2542 Thursday April 3, 2014 Next generation sequencing applications 09.00 Welcome coffee and introduction day 3 09.30 Lecture: Metagenomics [R] (Dr. Sacha van Hijum, Nijmegen) 10.15 Lecture: DNA methylation sequencing [M] (Dr. Arjen Brinkman, NCMLS, Radboud University Nijmegen) 11.00 Coffee/Thee 11.15 Lecture: Re-sequencing and detection of variants [K] (Dr. Victor Guryev, European Research Institute for the Biology of Ageing (ERIBA) 11.45 Lecture: ChIP-seq [L] (Dr.Wilfred van IJcken, Erasmus MC, Rotterdam) 12.30 Lunch 13.30 Computer practical, parallel sessions with Genome browser views on: Re-sequencing and detection of variants, Chip-seq and DNA methylation sequencing 16.00 Lecture: edna [R] (Kevin Beentjes, Naturalis, Leiden) 16.45 Lecture: NGS single cell analysis (Dr. Thierry Voet, Leuven) 17.30 End of day 3
Code 2542b Friday April 4, 2014 Next generation sequencing data analysis 09.00 Welcome coffee and introduction day 4 09.15 Lecture: Introduction to Nextgene data analysis [PQ] (Fons Elstrodt, Bioke) 09.45 lecture: Introduction to CLCbio data analysis [S] (Sarah Nema, CLCbio) 10.15 Coffee/Thee 10.30 Computer practical: Windows practical: Nextgene data analysis (Fons Elstrodt, Bioke) or Computer practical: Windows practical: CLCbio Workbench (Sarah Nema, CLCbio) 12.30 NGS: other applications and future developments [V] (Prof.dr. Johan den Dunnen, LGTC, Leiden) 13.15 Lunch Data analysis pipelines 14.00 Lecture: NGS Pipelines [7] (Ing. Michiel van Galen, LGTC, Leiden) 14.30 Lecture: Galaxy and GAPSS [8] 15.00 Break 15.30 Computer practical 2, pipelines for complete analysis: Variant calling Expression analysis (CAGE). (Dr. Jeroen Laros and Ing. Michiel van Galen, LGTC, Leiden) 16.30 General discussion (Prof.dr. Johan den Dunnen, LGTC, Leiden)
17.15 Evaluation and official closing of the course 17.30 End of the course Avans Hogeschool reserves the right to modify course materials or substitute speakers without notice.