title: The chemiluminescence based Ziplex automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip expression profiles.
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.
  
  
  CONCLUSIONS
  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.
authors: Department of Human Genetics, McGill University, Montreal, Canada. michael.quinn@mail.mcgill.ca
authors: Michael C J
authors: MC
authors: Quinn
authors: Daniel J
authors: DJ
authors: Wilson
authors: Fiona
authors: F
authors: Young
authors: Adam A
authors: AA
authors: Dempsey
authors: Suzanna L
authors: SL
authors: Arcand
authors: Ashley H
authors: AH
authors: Birch
authors: Paulina M
authors: PM
authors: Wojnarowicz
authors: Diane
authors: D
authors: Provencher
authors: Anne-Marie
authors: AM
authors: Mes-Masson
authors: David
authors: D
authors: Englert
authors: Patricia N
authors: PN
authors: Tonin
mesh_terms: D014408:Biomarkers, Tumor; D045744:Cell Line, Tumor; D015342:DNA Probes; D003627:Data Interpretation, Statistical; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D049449:Luminescence; D008163:Luminescent Measurements / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D010051:Ovarian Neoplasms / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D014408:Biomarkers, Tumor; D015342:DNA Probes