An Overview of Custom Array Sequencing

Prachi Kothiyal1, Stephanie Cox2, Jonathan Ebert3, Bruce J. Aronow1, John H. Greinwald1, Heidi L. Rehm4

1 University of Cincinnati, Cincinnati, Ohio, 2 Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, 3 Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 4 Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 7.17
DOI:  10.1002/0471142905.hg0717s61
Online Posting Date:  April, 2009
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Abstract

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.

Keywords: resequencing microarrays; CustomSeq; base‐calling; sequence‐specific hybridization; mutation detection

     
 
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Table of Contents

  • Introduction
  • CustomSeq Array Overview
  • File Formats and Data Output
  • GSEQ Algorithm Parameters
  • Processing GSEQ Calls for Reducing False Positive Calls
  • Customized Filters and CustomSeq Array Technical Follow‐Up
  • Conclusion
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

   Cutler, D.J., Zwick, M.E., Carrasquillo, M.M., Yohn, C.T., Tobin, K.P., Kashuk, C., Mathews, D.J., Shah, N.A., Eichler, E.E., Warrington, J.A., and Chakravarti, A. 2001. High‐throughput variation detection and genotyping using microarrays. Genome Res. 11:1913‐1925.
   Lipshutz, R., Fodor, S., Gingeras, T., and Lockart, D. 1999. High‐density synthetic oligonucleotide arrays. Nat. Genet. 21:20‐24.
   Ziv, J. and Lempel, A. 1978. Compression of individual sequences via variable‐rate coding. IEEE Trans. Inf. Theory 24:530‐536.
Internet Resources
   http://www.affymetrix.com/products/arrays/specific/custom_seq.affx
  CustomSeq Array Resources provided by Affymetrix.
   http://www.affymetrix.com/support/technical/datasheets/customseq_datasheet.pdf
  GeneChip CustomSeq Resequencing Array Program Data Sheet provided by Affymetrix.
   https://www.affymetrix.com/support/downloads/manuals/gseq_user_guide.pdf
  GeneChip Sequence Analysis Software (GSEQ) User Guide provided by Affymetrix.
   http://www.affymetrix.com/support/technical/technotes/customseq_arraybase_technote.pdf
  Technical note on CustomSeq Resequencing Array Base Calling Algorithm Version 2.0 provided by Affymetrix.
   http://www.affymetrix.com/support/technical/other/customseq_design_manual.pdf
  CustomSeq Resequencing Array Design Guide provided by Affymetrix.
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