Monday, December 1, 2014

Special Report: Microarray Not Fade Away

Written by: Lisa Heiden
The microarray, the legacy technology for measuring gene expression, will not go gentle into that good night. True, in some respects, the microarray will be eclipsed by next-generation sequencing (NGS), specifically, whole transcriptome shotgun sequencing. But the microarray will remain indispensible for many applications. Beyond that, the microarray will evolve to complement NGS applications, finding reasons to stay relevant besides the
loyalty of its long-time users.
Microarrays are built upon the concept of hybridization, the binding of cDNA, complementary DNA strands derived from sample RNA, to strands of synthetic DNA. In the prototypic microarray, the synthetic strands are attached to a small, solid support. This support—a biochip—can be manufactured with thousands of probes or capture agents.
Microarray technology evolved from Southern blotting, which was invented by Edwin Southern, Ph.D. at Edinburgh University in 1975. In Southern blotting, DNA fragments are blotted onto a membrane and probed with known sequences to identify specific sequences via probe-target hybridization assays.
At Stanford University in 1995, microarrays were first developed as miniaturized cDNA arrays by Mark Schena, Ph.D., a postdoctoral biochemistry fellow who was later proclaimed the “Father of Microarrays” by DDN. Dr. Schena, now president and chief science officer at Arrayit, remarks that over the past two decades, microarrays have become a deeply rooted and highly developed technology.
In fact, according to Todd Martinsky, founder and executive vice president of Arrayit, the ex situ method (Arrayit U.S. Patent 6.101.946) has enabled all types of biomolecules to be put into microarray formats as capture agents. This includes antibodies, antigens, bacterial components, carbohydrates, DNA/cDNA, lipids, oliogonucleotides, peptides, proteins, and other small molecules as well as whole cells and tissue samples.
After all this development, it may be a good time to reflect on the best uses of microarray technology. Some of these uses are already established; others, such as those complementing NGS, are still emerging.
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