An overview of custom array sequencing.
An overview of custom array sequencing.
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DOI：
10.1002/0471142905.hg0717s61
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发表时间：
2009-04
影响因子：
--
通讯作者：
Rehm HL
中科院分区：
文献类型：
--
作者：
Kothiyal P;Cox S;Ebert J;Aronow BJ;Greinwald JH;Rehm HL
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.
