UNIT 7.17 An Overview of Custom Array Sequencing

  1. Prachi Kothiyal1,2,
  2. Stephanie Cox3,
  3. Jonathan Ebert1,
  4. Bruce J. Aronow1,2,
  5. John H. Greinwald1,2,
  6. Heidi L. Rehm3,4

Published Online: 1 APR 2009

DOI: 10.1002/0471142905.hg0717s61

Current Protocols in Human Genetics

Current Protocols in Human Genetics

How to Cite

Kothiyal, P., Cox, S., Ebert, J., Aronow, B. J., Greinwald, J. H. and Rehm, H. L. 2009. An Overview of Custom Array Sequencing. Current Protocols in Human Genetics. 61:7.17:7.17.1–7.17.11.

Author Information

  1. 1

    Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio

  2. 2

    University of Cincinnati, Cincinnati, Ohio

  3. 3

    Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts

  4. 4

    Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts

Publication History

  1. Published Online: 1 APR 2009
  2. Published Print: APR 2009


This unit provides an overview of oligo hybridization–based resequencing and a wide range of considerations for implementing the technology and analyzing the resulting data. The specific technology discussed is the Affymetrix GeneChip CustomSeq Resequencing Array platform. Concepts related to array design, experimental protocols, and base-calling using existing algorithms are presented. Details that should be evaluated during development of sequence tiling, target amplification, and PCR protocols are addressed. An overview of the Affymetrix GeneChip Sequence Analysis Software (GSEQ) is provided, along with factors that influence base-calling coverage and accuracy. Also outlined are performance measures that can be used to characterize base-calling with resequencing arrays, as well as factors known to affect their performance. Limitations associated with detection of insertions and deletions (indels) are discussed, with empirical data from our experiments used to outline possible approaches to indel detection. Critical topics in the design, implementation, and analysis of targeted sequencing arrays not previously discussed in detail are highlighted. Curr. Protoc. Hum. Genet. 61:7.17.1-7.17.11. © 2009 by John Wiley & Sons, Inc.


  • resequencing microarrays;
  • CustomSeq;
  • base-calling;
  • sequence-specific hybridization;
  • mutation detection