There are two major applications for DNA microarray technology: 1) identification of sequence (gene/gene mutation); and 2) determination of expression level (abundance) of genes. There are two variants of the DNA micro­array technology, in terms of the property of arrayed DNA sequence with known identity: i) probe cDNA (500-5,000 bases long) is immobilized to a solid surface such as glass using robot spotting and exposed to a set of targets, either separately or in a mixture. This method is the traditional DNA microarray and it was developed at Stanford University (Stanford, CA, USA); ii) an array of oligonucleotides (20-80-mer oligos) is synthesized either in situ (on-chip) or by conventional synthesis followed by on-chip immobilization (www.gene-chips.com). The array is exposed to labeled sample DNA, hybridized, and the identity/ abundance of complementary sequences are determined. This was developed by Affymetrix (Santa Clara, CA, USA) which sells its photolithographically-fabricated products under the GeneChip® trademark. Many companies manufacture oligonucleotide-based chips using alternative in situ synthesis or depositioning technologies.
Design of a DNA Microarray System. There are several steps in the design and implementation of a DNA microarray system. Many strategies have been investigated at each of these steps: DNA types; chip fabrication; sample preparation; assay; readout; and software (informatics) The aim of the microarray is to provide an insight into gene function and via the relevance of genetic loci to the clinical phenotype. This daunting function was first dem­onstrated by microarray experiments on the full sequence of Arabidopsis thaliana and Caenorhabditis elegans. Microarray technology offers the potential to study the expression of different genes.
Applied to expression analysis, this approach facilitates the measurement of RNA levels for the complete set of transcripts of an organism. Applied to genotyping, microarrays provide a possibility to determine the alleles at hundreds of thousands of loci from hundreds of DNA samples, allowing the association studies to determine the genetic contribution to complex polygenic disorders. Applied to mutation screening of disease genes with pro­nounced allellic heterogeneity, the use of microarrays is likely to move the possibility of genetic testing for disease susceptibility of individuals or entire populations.
The two array-based technologies, cDNA and oligo­nucleotide arrays, allow one to study expression levels in parallel [1], thus providing static information about gene expression [in which tissue(s) the gene is expressed] and dynamic information (how the expression pattern of one gene relates to that of others). The high degree of digital data extraction and processing of these techniques permits use of a variety of samples or experimental conditions.