UNIT 7.17 An Overview of Custom Array Sequencing
Published Online: 1 APR 2009
Copyright © 2001 John Wiley & Sons, Inc. All rights reserved.
Lab Protocol Title
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.
- Published Online: 1 APR 2009
- 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;
- sequence-specific hybridization;
- mutation detection