Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™

Abstract Background Microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes. These normalization approaches are not appropriate for focused arrays with small sets of genes where a... Ausführliche Beschreibung

1. Person: Lambert Iain B verfasserin
Weitere Personen: Dong Hongyan verfasserin; Rowan-Carroll Andrea verfasserin; Zheng Jenny L verfasserin; Zhou Gu verfasserin; Berndt Lynn M verfasserin; Boucher Sherri verfasserin; Williams Andrew verfasserin; Yauk Carole L verfasserin; Douglas George R verfasserin; Parfett Craig L verfasserin
Quelle: In BMC Genomics (01.10.2006)
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Sprache: English
Veröffentlicht: 2006
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  Creative Commons License Source: Directory of Open Access Journals (DOAJ).
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100 0 |a Lambert Iain B  |e verfasserin  |4 aut 
245 1 0 |a Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™  |h Elektronische Ressource 
300 |a Online-Ressource 
520 |a Abstract Background Microarray normalizations typically apply methods that assume absence of global transcript shifts, or absence of changes in internal control features such as housekeeping genes. These normalization approaches are not appropriate for focused arrays with small sets of genes where a large portion may be expected to change. Furthermore, many microarrays lack control features that can be used for quality assurance (QA). Here, we describe a novel external control series integrated with a design feature that addresses the above issues. Results An EC dilution series that involves spike-in of a single concentration of the A. thaliana chlorophyll synthase gene to hybridize against spotted dilutions (0.000015 to 100 μM) of a single complimentary oligonucleotide representing the gene was developed. The EC series is printed in duplicate within each subgrid of the microarray and covers the full range of signal intensities from background to saturation. The design and placement of the series allows for QA examination of frequently encountered problems in hybridization (e.g., uneven hybridizations) and printing (e.g., cross-spot contamination). Additionally, we demonstrate that the series can be integrated with a LOWESS normalization to improve the detection of differential gene expression (improved sensitivity and predictivity) over LOWESS normalization on its own. Conclusion The quality of microarray experiments and the normalization methods used affect the ability to measure accurate changes in gene expression. Novel methods are required for normalization of small focused microarrays, and for incorporating measures of performance and quality. We demonstrate that dilution of oligonucleotides on the microarray itself provides an innovative approach allowing the full dynamic range of the scanner to be covered with a single gene spike-in. The dilution series can be used in a composite normalization to improve detection of differential gene expression and to provide quality control measures. 
700 0 |a Dong Hongyan  |e verfasserin  |4 aut 
700 0 |a Rowan-Carroll Andrea  |e verfasserin  |4 aut 
700 0 |a Zheng Jenny L  |e verfasserin  |4 aut 
700 0 |a Zhou Gu  |e verfasserin  |4 aut 
700 0 |a Berndt Lynn M  |e verfasserin  |4 aut 
700 0 |a Boucher Sherri  |e verfasserin  |4 aut 
700 0 |a Williams Andrew  |e verfasserin  |4 aut 
700 0 |a Yauk Carole L  |e verfasserin  |4 aut 
700 0 |a Douglas George R  |e verfasserin  |4 aut 
700 0 |a Parfett Craig L  |e verfasserin  |4 aut 
773 0 8 |i In  |t BMC Genomics  |g  (01.10.2006)  |w (DE-601)DOAJ000041084  |x 1471-2164 
856 4 0 |u http://dx.doi.org/10.1186/1471-2164-7-266 
856 4 0 |y DOAJ  |u https://doaj.org/article/41626feaf062480b94ae15623623b52a 
856 4 0 |u http://www.biomedcentral.com/1471-2164/7/266 
856 4 0 |u https://doaj.org/toc/1471-2164 
912 |a GBV_DOAJ 
951 |a AR 
952 |j 2006  |b 01  |c 10 

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