Ziplex System Applications

Gene Expression

The Ziplex Automated Workstation has been shown to compare favorably to five commercially available gene expression analysis platforms while offering significant benefits from automation such as ease of use, fast hybridization times, as well as the ability to perform routine assays. In each case, the Ziplex produced expression signals that were either equal or better than those produced on global expression platforms in terms of reproducibility and sensitivity. This performance, along with the design of appropriate TipChip probes for well defined expression signatures, makes the Ziplex an ideal tool for the verification of differential gene expression results obtained from whole genome analysis. For a detailed comparison of the Ziplex System to other systems and an illustration of the migration of data from a global expression platform to Ziplex, see the references below.

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Biomarker Validation

Gene expression signatures are typically discovered with global expression arrays. To advance these signatures to practical and clinically relevant assays the biomarkers are usually validated on a different analytical platform with independent sample sets. The validation platform should use different probes for well-defined targets, faithfully reproduce the results from the global expression platform, enable high throughput processing of large numbers of patient samples, and offer operating simplicity to facilitate eventual implementation in clinical laboratories. Figure 1 illustrates the Ziplex Workstation’s ability to fulfill these tasks in the successful translation of Affymetrics Ovarian Cancer signature.

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Figure 1. Direct transfer of ovarian cancer biomarkers from discovery platform to the Ziplex.

For other examples of describing the use of the Ziplex System in biomarker translation from global expression arrays, refer to the following technical papers and application notes:

Journal articles and whitepapers:

Application Note and Brief:

Posters:

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Infectious Diseases

Direct detection of pathogens often involves traditional immunoassays or the amplification of the pathogen genome by PCR methods. However, these methods are both time consuming and expensive and in some cases not reliable. The Ziplex System provides a microarray platform to enable rapid serological antibody tests that can allow both the detection of a pathogen and information on disease progression. In the figure below, the patient’s serum is incubated on an array of infectious disease antigens and the antibodies that bind to the individual pathogenic antigens are “reported” by labeled secondary antibodies specific for the IgG, IgM, and IgA classes. IgM class antibodies form the dominant first phase (acute) response, while IgG class antibodies form the mature or post-recovery response. This example illustrates one of the benefits of the Flow-Thru array technology, whereby individual results on 17 pathogens are obtained in as little as 30 minutes, with no sample preparation, other than loading the diluted serum, and no operator intervention.

Figure 2. Detection of infectious disease antigens on the Ziplex microarray

For applications of the Ziplex System for infectious disease research see:

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Formalin-Fixed Paraffin Embedded Samples

FFPE samples are an abundant sample resource for the validation of expression-based assays and are well suited for routine clinical testing. Analysis on microarrays enables the analysis of many transcripts from samples with small amounts of RNA. However, mRNA in FFPE sections is degraded and cross-linked, with RNA fragment sizes of a few hundred bases or less, and consequently standard methods of microarray sample preparation are not reliable unless probes are very strongly biased to the 3’ end. With appropriate sample preparation methods the Ziplex System enables the efficient analysis of FFPE derived samples as well as fresh frozen tissues and other biological samples such as serum, CSF, urine, bronchial lavage and aspirates.

For a description of this application see:

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