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Microarray is a type of nucleic acid sample (target) to a very large set of oligonucleotide probes, which are attached to a solid support, to determine sequence or to detect variations in a gene sequence or expression or for gene mapping (MeSH).
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Scope and Importance
A microarray is a pattern of ssDNA probes which are immobilized on a surface (called a chip or a slide). The probe sequences are designed and placed on an array in a regular pattern of spots. The chip or slide is usually made of glass or nylon and is manufactured using technologies developed for silicon computer chips. Each microarray chip is arranged as a checkerboard of 105 or 106 spots or features, each spot containing millions of copies of a unique DNA probe (often 25 not long). Like Southern & northern blots, microarrays are likely use hybridization to detect a specific DNA or RNA in a sample. Similarly, Southern blot uses a single probe to search a complex DNA mixture, a DNA microarray uses a million different probes, fixed on a solid surface, to probe such a mixture.
The right sequence of the probes at each feature/location on the chip is known. If somewhere the sample DNA hybridizes to the probe in a particular spot, the hybridization can be detected because the target DNA is labeled (and unbound target is washed away). So that one can determine which of the million different probe sequences are present in the target.
Microarrays are enough to detect single base differences, mutations, or SNPs (single nucleotide polymorphisms). This makes them useful for a wide range of applications, for example: identifying strains of viruses; identifying contamination of food products with cells from other plants or animals; detecting a panel of mutations in a patient’s cancer cells that can cause the disease’s response to treatment.
Recently exceptionally efficient deep sequencing technologies became available at highly competitive prices. Measuring clone frequencies in bead libraries has the potential to replace or complement chip based fluorescence based transcript imaging in the future. One advantage of this approach is the possibility to detect any genomic transcript of an organism, provided the genome is available. Today many aspects of next-generation sequencing (NGS) remain to be solved. Although data generation can be fast, depending on the technology, the data analysis and processing have currently no user friendly solution, especially when multiple samples and conditions are part of the experiment. In addition, sample preparation is complex and certainly a source for artifacts which is reminiscent to the early days of microarray technology. Finally, the poor concordance of chip based transcript profiling experiments and NGS is inadequately understood in the research community . In summary, I consider the use of microarrays is still the method of choice for routine experiments or studies that are carried out under GLP (good laboratory practice) regulations. The availability of user friendly commercial data analysis packages allows fast, robust and user-friendly data analysis and integration.
Microarrays were developed and commercialized in the eighties. Since then, market has offered tremendous growth and hence has seen an influx of players vying fiercely for a share or this market. The Global DNA & Gene Chip (microarray) market was valued at $760 million in 2010 and is expected to reach $1,425.2 million by 2015 growing at a CAGR of 13.4%. Major players in this market include Affymetrix, Inc. (U.S.), Illumnia, Inc. (U.S.), Agilent Technologies, Inc. (U.S.), Roche NimbleGen (U.S.), Sequenom Inc, (U.S.), and others.
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