NDLI: Probe selection for high-density oligonucleotide arrays.

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Probe selection for high-density oligonucleotide arrays.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Christians, Fred C. Mittmann, Mike Kaplan, Paul Bekiranov, Stefan Shen, Mei-mei Liu, Wei-min Hubbell, Earl Webster, Teresa A. Fang, Joy Mei, Rui Ryder, Tom Lu, Gang Kulp, David
Description	Author Affiliation: Mei R ( Affymetrix, Inc., Santa Clara, CA 95051, USA. rui_mei@affymetrix.com);
Abstract	High-density oligonucleotide microarrays enable simultaneous monitoring of expression levels of tens of thousands of transcripts. For accurate detection and quantitation of transcripts in the presence of cellular mRNA, it is essential to design microarrays whose oligonucleotide probes produce hybridization intensities that accurately reflect the concentration of original mRNA. We present a model-based approach that predicts optimal probes by using sequence and empirical information. We constructed a thermodynamic model for hybridization behavior and determined the influence of empirical factors on the effective fitting parameters. We designed Affymetrix GeneChip probe arrays that contained all 25-mer probes for hundreds of human and yeast transcripts and collected data over a 4,000-fold concentration range. Multiple linear regression models were built to predict hybridization intensities of each probe at given target concentrations, and each intensity profile is summarized by a probe response metric. We selected probe sets to represent each transcript that were optimized with respect to responsiveness, independence (degree to which probe sequences are nonoverlapping), and uniqueness (lack of similarity to sequences in the expressed genomic background). We show that this approach is capable of selecting probes with high sensitivity and specificity for high-density oligonucleotide arrays.
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	20
Volume Number	100
Language	English
Publisher	National Academy of Sciences
Publisher Date	2003-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Oligonucleotide Array Sequence Analysis RNA Probes Cell Line Models, Molecular Open Reading Frames Multidisciplinary
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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