27. Experimental Design and Quality Control of Next-Generation Sequencing Experiments

  1. Dr. Matthias Harbers5,6 and
  2. Prof. Dr. Günter Kahl7,8,9
  1. Peter A. C. 't Hoen1,2,
  2. Matthew S. Hestand1,3,
  3. Judith M. Boer1,4,
  4. Yuching Lai1,
  5. Maarten van Iterson1,
  6. Michiel van Galen1,
  7. Henk P. Buermans1 and
  8. Johan T. den Dunnen1

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch27

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

't Hoen, P. A. C., Hestand, M. S., Boer, J. M., Lai, Y., van Iterson, M., van Galen, M., Buermans, H. P. and den Dunnen, J. T. (2011) Experimental Design and Quality Control of Next-Generation Sequencing Experiments, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch27

Editor Information

  1. 5

    4-2-6 Nishihara, Kashiwa-Shi, Chiba 277-0885, Japan

  2. 6

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

  3. 7

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 8

    University of Frankfurt am Main Biocenter, Max-von-Lauestraße 9, 60439 Frankfurt am Main, Germany

  5. 9

    Frankfurt Biotechnology Innovation Center (FIZ), GenXPro Ltd, Altenhöferallee 3, 60438 Frankfurt am Main, Germany

Author Information

  1. 1

    Leiden University Medical Center, Center for Human and Clinical Genetics, Postal Zone S4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands

  2. 2

    Leiden University Medical Center, Leiden Genome Technology Center, Postal Zone S4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands

  3. 3

    University of Kentucky, Department of Veterinary Science, Gluck Equine Research Center, 1400 Nicholasville Road, Lexington, KY 40546-0099, USA

  4. 4

    Erasmus Medical Center, Laboratory of Pediatric Oncology, Erasmus MC-Sophia Children's Hospital, room Ee1575, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands

Publication History

  1. Published Online: 23 JAN 2012
  2. Published Print: 14 DEC 2011

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • experimental design;
  • quality control;
  • next-generation sequencing;
  • platform;
  • sequencing depth;
  • perspectives


Next-generation sequencing (NGS) is a powerful, but resource-intensive technology. Spending money on an experiment that cannot give an answer to the research question at hand is a waste. This chapter addresses several issues in the experimental design of tag-based expression profiling and chromatin immunoprecipitation (ChIP-seq) experiments, and provides some practical guidelines for finding the most optimal experimental design. Monitoring of the quality of the different experimental and analytical procedures is also key to the success of NGS experiments. General as well as platform- or application-specific quality control measures and checks are also described.