Thursday, August 23, 2007

Microarrays more sensitive then qPCR

In the recent paper, "Microarray multiplex assay for the simultaneous detection and discrimination of hepatitis B, hepatitis C, and human immunodeficiency type-1 viruses in human blood samples" a research team at the FDA found their combination of multiplex PCR and oligonucleotide microarray was more sensitive than reported multiplex PCR assays and 14-fold more sensitive than gel electrophoresis analysis. That is exciting, typically the reports we read is nothing is more sensitive than the "gold standard" qPCR. But what the paper shows, which is even more important, is the simultaneous detection and discrimination of these multiple viruses on a single 20 spot microarray...WOW...only 20 spots! The specificity of microarray hybridization, when oligos are properly designed, never ceases to amaze me. Although there are micro spotting pins that make smaller spots, the CMP7 micro spotting pins used to make the microarray in the paper print ~2nl of volume with each touch off. With this spot volume, a single 200nMole synthesis of each oligo at a cost of less than $1K, is enough for the high throughput manufacture of thousands of microarrays. With proven long shelf life and simple room temperature storage, spotted microarrays represent a highly cost effective solution for NAT. To further reduce cost, current microarray tools make it possible hybridize least 48 microarrays of 20+ spots on a single bar coded microscope size substrate, this making the surface chemistry cost for this test less than 20 cents per patient. With proven long shelf life and simple room temperature storage, spotted microarrays represent a highly cost effective solution for NAT. With recent improvements in the miniaturization of PCR, costs for dyes and the labeling reactions, costs are coming down even further. As the authors describe, some more work is required to automate and streamline the protocol, but the foundation is there and the authors clearly hit a home run....especially given the global health problems that these viruses represent. With Hamilton recently announcing automation for microarray labeling preparation (read press release) and papers like this one, it clear microarray is making major headway to improve nucleic acid testing.