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Breathing New Life into DNA Microarrays

DNA microarrays are widely used in biological research and were once thought to be a very promising gene discovery tool. However, since the advent of next generation DNA sequencing, the popularity of DNA microarrays has steadily declined. Compared to the sequencing, microarray behavior is uncertain and microarray data processing programs often yield contradictory results.

A team of researchers from the University of Washington, Max Planck Institute (Germany) and Alabama State University has devised a fundamentally new way to design microarray experiments, where each gene sensor – a DNA oligonucleotide probe – is individually calibrated with a simple dilution series of a biological sample. Such calibrated microarrays permit direct measurement of relative or absolute gene expression as well as gene copy number. The new design distinguishes itself from others because the microarray calibration is straightforward, and it alleviates the need for normalization procedures and reference standards. Calibrated microarrays are “truly analytical instruments”, similar to pH meters. This new design breathes new life into biological research that depends on DNA microarrays because they now yield accurate, reliable, and repeatable results that are currently not attainable with next generation sequencing technology.

The software can be downloaded at: http://web.evolbio.mpg.de/~alexander.pozhitkov/microarray123/
The article describing the new microarray experimental design was published in PlosONE on March 11, 2014.

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