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Updated: Jun 2, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Targeted sequencing using Affymetrix CustomSeq Arrays.

Polakit Teekakirikul¹, Stephanie Cox, Birgit Funke

¹Harvard Medical School, Boston, Massachusetts, USA.

Current Protocols in Human Genetics

|April 12, 2011

Summary

This summary is machine-generated.

This protocol details oligo hybridization sequencing on Affymetrix arrays for targeted genome resequencing up to 300 kilobases. It covers array design, experiments, data analysis, and mutation detection, primarily substitutions.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Oligo hybridization-based sequencing offers a targeted approach for genomic analysis.
The Affymetrix GeneChip CustomSeq Resequencing Array platform provides a specific tool for this technology.

Purpose of the Study:

To provide a comprehensive protocol for oligo hybridization-based sequencing using the Affymetrix GeneChip CustomSeq Resequencing Array.
To detail the entire workflow from array design to data analysis and base-calling.

Main Methods:

Array design considerations for targeted resequencing.
Experimental protocols for sample preparation and hybridization.
Data management strategies and base-calling algorithms specific to the platform.

Main Results:

The protocol is optimized for sequencing targeted genomic regions up to 300 kilobases.
The technology is effective for detecting substitution mutations.
InDel detection is possible with the addition of targeted indel probes.

Conclusions:

This unit establishes a foundational protocol for utilizing Affymetrix CustomSeq arrays for targeted genome resequencing.
The described methods facilitate efficient mutation detection, particularly substitutions, within defined genomic regions.