The chemiluminescence based Ziplex® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip® expression profilesReport as inadecuate

The chemiluminescence based Ziplex® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip® expression profiles - Download this document for free, or read online. Document in PDF available to download.

Journal of Translational Medicine

, 7:55

First Online: 06 July 2009Received: 07 April 2009Accepted: 06 July 2009DOI: 10.1186-1479-5876-7-55

Cite this article as: Quinn, M.C., Wilson, D.J., Young, F. et al. J Transl Med 2009 7: 55. doi:10.1186-1479-5876-7-55


BackgroundAs gene expression signatures may serve as biomarkers, there is a need to develop technologies based on mRNA expression patterns that are adaptable for translational research. Xceed Molecular has recently developed a Ziplex technology, that can assay for gene expression of a discrete number of genes as a focused array. The present study has evaluated the reproducibility of the Ziplex system as applied to ovarian cancer research of genes shown to exhibit distinct expression profiles initially assessed by Affymetrix GeneChip analyses.

MethodsThe new chemiluminescence-based Ziplex gene expression array technology was evaluated for the expression of 93 genes selected based on their Affymetrix GeneChip profiles as applied to ovarian cancer research. Probe design was based on the Affymetrix target sequence that favors the 3- UTR of transcripts in order to maximize reproducibility across platforms. Gene expression analysis was performed using the Ziplex Automated Workstation. Statistical analyses were performed to evaluate reproducibility of both the magnitude of expression and differences between normal and tumor samples by correlation analyses, fold change differences and statistical significance testing.

ResultsExpressions of 82 of 93 88.2% genes were highly correlated p < 0.01 in a comparison of the two platforms. Overall, 75 of 93 80.6% genes exhibited consistent results in normal versus tumor tissue comparisons for both platforms p < 0.001. The fold change differences were concordant for 87 of 93 94% genes, where there was agreement between the platforms regarding statistical significance for 71 76% of 87 genes. There was a strong agreement between the two platforms as shown by comparisons of log2 fold differences of gene expression between tumor versus normal samples R = 0.93 and by Bland-Altman analysis, where greater than 90% of expression values fell within the 95% limits of agreement.

ConclusionOverall concordance of gene expression patterns based on correlations, statistical significance between tumor and normal ovary data, and fold changes was consistent between the Ziplex and Affymetrix platforms. The reproducibility and ease-of-use of the technology suggests that the Ziplex array is a suitable platform for translational research.

List of abbreviations usedRNAribonucleic acid

mRNAmessenger ribonucleic acid

UTRuntranslated region

Rcorrelation coefficient

MAQCMicroArray Quality Control

RT-PCRreverse transcription polymerase chain reaction

NOSE cellsnormal ovarian surface epithelial cells

TOVovarian tumor

EOCepithelial ovarian cancer

BLASTBasic Local Alignment Search Tool

NCBINational Centre for Biotechnology Information

RINRNA integrity number

HRPhorseradish peroxidase

SNRsignal to noise ratio

SIsignal intensity.

Electronic supplementary materialThe online version of this article doi:10.1186-1479-5876-7-55 contains supplementary material, which is available to authorized users.

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Author: Michael CJ Quinn - Daniel J Wilson - Fiona Young - Adam A Dempsey - Suzanna L Arcand - Ashley H Birch - Paulina M Woj


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