17. Next-Generation Sequencing of Bacterial Artificial Chromosome Clones for Next-Generation Physical Mapping

  1. Dr. Matthias Harbers3,4 and
  2. Prof. Dr. Günter Kahl5,6,7
  1. Robert Bogden1,
  2. Keith Stormo1,
  3. Jason Dobry1,
  4. Amy Mraz1,
  5. Quanzhou Tao1,
  6. Michiel van Eijk2,
  7. Jan van Oeveren2,
  8. Marcel Prins2,
  9. Jon Wittendorp2 and
  10. Mark van Haaren2

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch17

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Bogden, R., Stormo, K., Dobry, J., Mraz, A., Tao, Q., van Eijk, M., van Oeveren, J., Prins, M., Wittendorp, J. and van Haaren, M. (2011) Next-Generation Sequencing of Bacterial Artificial Chromosome Clones for Next-Generation Physical Mapping, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch17

Editor Information

  1. 3

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

  2. 4

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

  3. 5

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 6

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

  5. 7

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

Author Information

  1. 1

    Amplicon Express Inc., 2345 NE Hopkins Court, Pullman, WA 99163, USA

  2. 2

    KeyGene NV, 6700 AE Wageningen, The Netherlands

Publication History

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

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • next-generation sequencing;
  • bacterial artificial chromosome clones;
  • next-generation physical mapping;
  • history;
  • WGP


Two of the major challenges in the field of genomics are first to obtain a correct assembly of DNA sequence data and then mapping known markers onto a genome sequence template to obtain an accurate physical map. Traditionally, the efforts of genome sequence assembly and physical mapping were split into two totally different datasets. This was primarily due to the incompatibility of data generated: physical mapping technologies were based on DNA fragment lengths (i.e., SNaPshot, optical mapping, agarose gel, polyacrylamide gel or capillary electrophoresis, restriction digest-based fingerprinting technology), whereas DNA sequence data is comprised of an A, G, C, and T letter code. Herein, we describe whole-genome profiling (WGPTM) – a technology that solves this dilemma. This new application of bacterial artificial chromosome (BAC) cloning in combination with short-read next-generation sequencing (NGS) technology eliminates the incompatibilities between physical mapping datasets and genome sequencing datasets. WGP is a physical mapping technology that uses Illumina NGS reads on systematically pooled BAC clones to create an ultra-high-density physical map of the genome using DNA sequencing data. In this chapter, we will explore what WGP is, how to perform WGP, and compare the advantages and disadvantages of WGP. We will show that WGP is a superior physical mapping technology that can improve the accuracy of any de novo whole-genome sequencing assembly as well as for finding genetic variations in resequencing projects.