DNA microarray

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Image:Microarray2.gif A DNA microarray (also commonly known as gene chip, DNA chip, or biochip) is a collection of microscopic DNA spots attached to a solid surface, such as glass, plastic or silicon chip forming an array.

The affixed DNA segments are known as probes (although some sources will use different nomenclature), thousands of which can be used in a single DNA microarray. Microarray technology evolved from Southern blotting, where fragmented DNA is attached to a substrate and then probed with a known gene or fragment. Measuring gene expression using microarrays is relevant to many areas of biology and medicine, such as studying treatments, disease, and developmental stages.

Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Applications of DNA microarrays to the study of gene expression include: profiling of complex diseases such as cancer, analysis of drug effects, and study of transcriptional regulation of genes under various conditions such as signalling activation or inhibition.

1 Fabrication
2 Study of gene expression
- 2.1 Spotted microarrays
- 2.2 Oligonucleotide microarrays
3 Genotyping microarrays
4 Microarrays and bioinformatics
5 List of microarray technology companies
6 External links

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Fabrication

Microarrays can be fabricated using a variety of technologies, including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, ink-jet printing [1], or electrochemistry on microelectrode arrays.

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Study of gene expression

The most common use of microarrays is to quantify mRNAs transcribed from different protein-encoding genes. RNA is extracted from a cell or tissue sample, then converted to cDNA. Fluorescent tags, (usually Cy3 and Cy5) are enzymatically incorporated into the newly synthesized cDNA or can be chemically attached to the new strands of DNA. A cDNA molecule that contains a sequence complementary to one of the single-stranded probe sequences on the array will hybridize, via base pairing, to the spot at which the complementary reporters are affixed. The spot will then fluoresce (or glow) when examined using a microarray scanner. The fluorescence intensity of each spot is then evaluated in terms of the number of copies of a particular mRNA, which ideally indicates the level of expression of a particular gene.

DNA microarrays can be used to detect RNAs that may or may not be translated into active proteins. Scientists refer to this kind of analysis as "expression analysis" or expression profiling. Since there can be tens of thousands of distinct reporters on an array, each microarray experiment can accomplish the equivalent number of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations.

By giving information on the levels of gene expression of thousands of genes at the same time, DNA microarrays allow researchers, for example, to relate the effect of a disease to particular genes. Researchers hope to find molecules that can be targeted for treatment with drugs among the various proteins encoded by disease-associated genes.

The use of microarrays for gene expression profiling was first published in 1995 (Science) and the first complete eukaryotic genome (Saccharomyces cerevisiae) on a microarray was published in 1997 (Science).

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Spotted microarrays

Image:Microarray-schema.gif

In spotted microarrays (or two-channel microarrays), the probes are oligonucleotides, cDNA or small fragments of PCR products corresponding to mRNAs. This type of array is typically hybridized with cDNA from two samples to be compared (e.g. patient and control) that are labeled with two different fluorofores. The samples can be mixed and hybridized to one single microarray that is then scanned, allowing the visualization of up-regulated and down-regulated genes in one go. The downside of this is that the absolute levels of gene expression cannot be observed, but the cost of the experiment is reduced by half.

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Oligonucleotide microarrays

Image:Affymetrix-microarray.jpg In oligonucleotide microarrays (or single-channel microarrays), the probes are designed to match parts of the sequence of known or predicted mRNAs. There are commercially available designs that cover complete genomes from companies such as Affymetrix, or Agilent. These microarrays give estimations of the absolute value of gene expression and therefore the comparison of two conditions requires the use of two separate microarrays.

Long Oligonucleotide Arrays are composed of 60-mers, and are produced by either ink-jet or robotic printing. Short Oligonucleotide Arrays are composed of 25-mer oligos, and are produced by photolithographic synthesis (Affymetrix). More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes. Arrays can contain up to 390,000 spots, from a custom array design.

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Genotyping microarrays

DNA microarrays can also be used to read the sequence of a genome in particular positions.

SNP microarrays are a particular type of DNA microarrays that are used to identify genetic variation in individuals and across populations. Short oligonucleotide arrays can be used to identify the single nucleotide polymorphisms (SNPs) that are thought to be responsible for genetic variation and the source of susceptibility to genetically caused diseases. Generally termed genotyping applications, DNA microarrays may be used in this fashion for forensic applications, rapidly discovering or measuring genetic predisposition to disease, or identifying DNA-based drug candidates.

These SNP microarrays are also being used to profile somatic mutations in cancer, specifically loss of heterozygosity events and amplifications and deletions of regions of DNA. Amplifications and deletions can also be detected using comparative genomic hybridization in conjuction with microarrays.

Resequencing arrays have also been developed to sequence portions of the genome in individuals. These arrays may be used to evaluate germline mutations in individuals, or somatic mutations in cancer.

Genome tiling arrays include overlapping oligonucleotides designed to blanket an entire genomic region of interest. Many companies have successfully designed tiling arrays that cover whole human chromosomes.

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Microarrays and bioinformatics

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Standardization

The lack of standardization in arrays presents an interoperability problem in bioinformatics, which hinders the exchange of array data. Various grass-roots open-source projects are attempting to facilitate the exchange and analysis of data produced with non-proprietary chips. The "Minimum Information About a Microarray Experiment" (MIAME) XML based standard for describing a microarray experiment is being adopted by many journals as a requirement for the submission of papers incorporating microarray results.

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Statistical analysis

The analysis of DNA microarrays poses a large number of statistical problems, including the normalisation of the data.

From a hypothesis-testing perspective, the large number of genes present on a single array means that the experimenter must take into account a multiple testing problem: even if each gene is extremely unlikely to randomly yield a result of interest, the combination of all the genes is likely to show at least one or a few occurrences of this result which are false positives.

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Relation between probe and gene

The relation between a probe and the mRNA that is expected to detect is problematic. On the one hand, some mRNAs may cross-hybridize probes in the array that are supposed to detect another mRNA. On the other hand, probes that are designed to detect the mRNA of a particular gene according to genomic EST information may be wrongly associated to that gene.

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