Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: Causes of signal variation and false positive signals

Sasaki, D., Kondo, S., Maeda, N., Gingeras, T. R., Hasegawa, Y., Hayashizaki, Y. (2007) Characteristics of oligonucleotide tiling arrays measured by hybridizing full-length cDNA clones: Causes of signal variation and false positive signals. Genomics, 89 (4). pp. 541-551. ISSN 08887543 (ISSN)

URL: http://www.ncbi.nlm.nih.gov/pubmed/17292583
DOI: 10.1016/j.ygeno.2006.12.013

Abstract

An assessment of the hybridization characteristics of oligonucleotide tiling arrays was carried out using 162 full-length sequenced cDNA clones in spike-in experiments. The properties of array probes that influence signal intensity were investigated, and their capability in the detection of the cDNA exons was evaluated. The signal intensities detected in exonic and nonexonic genomic regions were examined by focusing on the features of probe sequences that raise or lower the level of intensity and on the causes of false positive signals found in nonexonic regions. The effectiveness of measures used in published protocols to improve the separation between signal and background intensity distributions, including the use of replicates and threshold parameterization of signal intensity, was assessed. Sensitivity and specificity in the detection of exons were measured using various sets of threshold parameters, and the effects of each parameter on the detection efficiency and the rate of false positives were evaluated. It was also demonstrated that hybridization of full-length cDNA clones is an excellent method to investigate the characteristics of oligonucleotide tiling arrays. © 2007 Elsevier Inc. All rights reserved.

Item Type: Paper
Uncontrolled Keywords: complementary DNA article controlled study DNA hybridization DNA microarray DNA probe exon genome analysis human microarray analysis molecular cloning nonhuman priority journal sensitivity and specificity signal detection signal noise ratio DNA, Complementary False Positive Reactions Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Oligonucleotide Probes
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > annotation > sequence annotation
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 2007
Date Deposited: 08 Mar 2012 16:31
Last Modified: 12 Jul 2013 19:58
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25322

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