As scientists we are trained to be independent thinkers, and to value the expertise gained on the learning curve of new technologies. When it comes to microarrays, however, outsourcing or collaborating with an expert can accelerate the development process.“There is a serious investment required in assay development for microarrays,” says Stacey Clarken, VP of Commercial Operations for Applied Microarrays Inc. “Our business model is to support customers ranging from those in early stage microarray development requiring assay optimization to clients ramping up production that need a partner with high capacity manufacturing.”
Many of the customers looking for custom setup services are developing diagnostic devices with relatively small, focused microarrays. Clarken agrees that the miniaturization of protein assays has gained momentum in the recent years. Five years ago about 80% of the microarray projects at Applied Microarrays were genomic, and 20% were protein-based. Today about half of the projects are for proteins, says Clarken, with customers transitioning from ELISA or bead-based assays. Publications in academic journals do not correlate with that number, where only about 2% of publications citing microarrays relate use of protein arrays (based on analysis in Highwire Press). The difference in these statistics could be related to a higher use of protein arrays in the diagnostics/technology sector, which contributes a small portion of academic publications. Academic studies that do utilize protein arrays are generally based around core facilities that assist with setup and can print content.
The main driver for adaptation of arrays in the commercial market is certainly cost. The cost savings for microarrays over ELISA technology is significant as numbers of samples and biomarkers increases—the example given by Applied Microarrays for analysis of 20 biomarkers, 10 plates per biomarker, using ELISA (1 biomarker/plate, 200 plates total) or Multiplex Arrays of all 20 biomarkers: $93,000 for reagent and plate costs using ELISA, compared to $8200 for the same analysis performed on microarrays. This cost is for reagents and materials only, not including labor. Comparing bead-based assays to microarrays, beads consume less antibody than ELISAs, but more than microarrays. An example is given for 15ug of antibody used in 4 plates in a bead-based analysis compared to the same amount of antibody covering 64 plate-equivalents in microarray. It could be argued that assay development costs may be more significant for microarrays than for ELISA or bead-based assays. Thus the transition to microarrays may be more justified for highly repeated assays compared to a limited study—pointing again to a broader adaptation of arrays in the diagnostic sector compared to academics.
The greatest cost for arrays, as for other antibody-based diagnostics, is the protein and antibody content. For example, one high-throughput customer recently estimated it cost them $200 in reagents for a single slide assay, not including the cost of the printed content. With that sort of investment there is little tolerance for low-quality reagents or materials, and many researchers seeking ways to conserve costs as their projects expand. Our seals and chambers are designed to minimize the reagents required for hybridizing and staining microarrays, resulting in significant cost savings over some automated systems and better results than simple coverslip hybridization.
At Grace Bio-Labs we have also seen a surge in demand for 
our nitrocellulose film slides for protein microarrays from companies that are rapidly progressing the technology from discovery to diagnostics. Beyond the material costs, there are a number of our customers who work with precious clinical samples which are irreplaceable once spent. Thus minimizing reagent use and obtaining consistent materials and reagents as well as consulting with experts are key requirements to optimize your return on investment in protein arrays.
