A major challenge in translating promising mRNA-based expression biomarkers has been the transfer of results from large-scale gene expression assay technologies to clinical laboratories where only specific gene signatures are of interest. In order to validate and advance these biomarker signatures into routine testing for clinical applications, an alterative platform is required that uses different probes for well-defined targets, enables high throughput processing of a large number of biological samples, and faithfully captures the biologically relevant aspects of the signature.
At Axela, we have developed a flow-through microarray system that can facilitate the expression analysis of a discrete number of genes (up to 150 in triplicate) for use in clinical translational research. After RNA sample preparation, the Ziplex® System takes care of the rest, automating each subsequent step in the assay (hybridization, sample incubation, detection and report generation). Altogether, the Ziplex® System acts as an easy to use, “all-in-one” platform suitable for routine analysis of gene expression that is required for today’s translational research.
To demonstrate the capabilities of the Ziplex® System, 93 selected genes relevant to ovarian cancer were successfully translated from a global expression array to a focused flow-through microarray. Alternative oligonucleotide probes where designed to hybridize to the selected set of gene targets on the microarray (TipChip). The expression levels of the 93 genes were then measured on the Ziplex® System with the newly designed probes using 23 different RNA samples from normal and malignant ovarian cells. Comparison of the Ziplex® expression data to that obtained on the global array system for these same set of genes showed a high concordance between then two platforms (see Figure 1).
Figure 1. Direct transfer of ovarian cancer biomarkers from discovery platform to the Ziplex.
Similarly, 43 selected genes identified from global microarrays platforms were verified as expression markers for predicting breast cancer recurrence using an independent sample set and Ziplex® System. As in the above example, Ziplex® hybridization probes were identified that produced maximum signal intensity and minimal cross hybridization. Expression levels of some of the 43 candidate genes from 52 specimens then permitted the prognostic classification on breast cancer patients with statistical differences in disease free and/or overall survival.
Literature on Oncology Translational Research by Axela
- Application Brief: Biomarker Translation from Global Expression Arrays to Focused Arrays
- Whitepaper: Biomarker Translation from Global Expression Arrays to Focused Arrays on the Ziplex® System
- Poster: A 43-gene expression array for profiling clinical samples for development and validation of breast cancer recurrence test
- Article: Michael C.J. Quinn et al. The chemiluminescence based Ziplex® automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip® expression profiles. Journal of Translational Medicine 2009, 7:55 (6 July 2009)