Methodology

The chemiluminescence based Ziplex^® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip^® expression profiles

Michael CJ Quinn¹ , Daniel J Wilson² , Fiona Young² , Adam A Dempsey² , Suzanna L Arcand³ , Ashley H Birch¹ , Paulina M Wojnarowicz¹ , Diane Provencher^4,5,6 , Anne-Marie Mes-Masson^4,6 , David Englert² and Patricia N Tonin^1,3,7

¹  Department of Human Genetics, McGill University, Montreal, H3A 1B1, Canada

²  Xceed Molecular, Toronto, M9W 1B3, Canada

³  The Research Institute of the McGill University Health Centre, Montréal, H3G 1A4, Canada

⁴  Centre de Recherche du Centre hospitalier de l'Université de Montréal/Institut du cancer de Montréal, Montréal, H2L 4M1, Canada

⁵  Département de Médicine, Université de Montréal, Montréal, H3C 3J7, Canada

⁶  Département de Obstétrique et Gynecologie, Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada

⁷  Department of Medicine, McGill University, Montreal, H3G 1A4, Canada

author email corresponding author email

Journal of Translational Medicine 2009, 7:55doi:10.1186/1479-5876-7-55

Published:	6 July 2009

Abstract

Background

As 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.

Methods

The 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.

Results

Expressions 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.

Conclusion

Overall 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.