DNA microarray: Difference between revisions

Revision as of 00:08, 24 November 2022

Revision as of 07:25, 23 December 2022

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{{short description|Collection of microscopic DNA spots attached to a solid surface}}

{{Use dmy dates|date=December 20132022}}

[[File:From_spit_to_DNA-sample.webm|thumb|''How to use a microarray for genotyping.'' The video shows the process of extracting genotypes from a human spit sample using microarrays. Genotyping is a major use of DNA microarrays, but with some modifications they can also be used for other purposes such as measurement of gene expression and epigenetic markers.]]

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|Double-stranded B-DNA microarrays

|Right-handed double-stranded B-DNA microarrays can be used to characterize novel drugs and biologicals that can be employed to bind specific regions of immobilized, intact, double-stranded DNA. This approach can be used to inhibit gene expression.<ref name="Gagna 895–914">{{Cite journal|title = Novel multistranded, alternative, plasmid and helical transitional DNA and RNA microarrays: implications for therapeutics|journal = Pharmacogenomics|date = 2009-05-01|issn = 1744-8042|pmid = 19450135|pages = 895–914|volume = 10|issue = 5|doi = 10.2217/pgs.09.27|first1 = Claude E.|last1 = Gagna|first2 = W. Clark|last2 = Lambert}}</ref><ref name="Gagna 381–401">{{Cite journal|title = Cell biology, chemogenomics and chemoproteomics -– application to drug discovery|journal = Expert Opinion on Drug Discovery|date = 2007-03-01|issn = 1746-0441|pmid = 23484648|pages = 381–401|volume = 2|issue = 3|doi = 10.1517/17460441.2.3.381|first1 = Claude E.|last1 = Gagna|first2 = W.|last2 = Clark Lambert|s2cid = 41959328}}</ref> They also allow for characterization of their structure under different environmental conditions.

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|Double-stranded Z-DNA microarrays

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[[File:Microarray printing.ogv|thumb|A DNA microarray being printed by a [[robot]] at the [[University of Delaware]] ]]

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,<ref>J Biochem Biophys Methods. 2000 Mar 16;42(3):105-10105–10. DNA-printing: utilization of a standard inkjet printer for the transfer of nucleic acids to solid supports. Goldmann T, Gonzalez JS.</ref><ref>{{cite journal|journal=Genome Biology | title=POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer| author=Lausted C| volume = 5 | pages=R58 | doi=10.1186/gb-2004-5-8-r58 | pmid=15287980 | date=2004| issue=8| pmc=507883|display-authors=etal}}</ref> or [[electrochemistry]] on microelectrode arrays.

In ''spotted microarrays'', the probes are [[oligonucleotide synthesis|oligonucleotide]]s, [[cDNA]] or small fragments of [[Polymerase chain reaction|PCR]] products that correspond to [[mRNA]]s. The probes are [[oligonucleotide synthesis|synthesized]] prior to deposition on the array surface and are then "spotted" onto glass. A common approach utilizes an array of fine pins or needles controlled by a robotic arm that is dipped into wells containing DNA probes and then depositing each probe at designated locations on the array surface. The resulting "grid" of probes represents the nucleic acid profiles of the prepared probes and is ready to receive complementary cDNA or cRNA "targets" derived from experimental or clinical samples.

This technique is used by research scientists around the world to produce "in-house" printed microarrays in their own labs. These arrays may be easily customized for each experiment, because researchers can choose the probes and printing locations on the arrays, synthesize the probes in their own lab (or collaborating facility), and spot the arrays. They can then generate their own labeled samples for hybridization, hybridize the samples to the array, and finally scan the arrays with their own equipment. This provides a relatively low-cost microarray that may be customized for each study, and avoids the costs of purchasing often more expensive commercial arrays that may represent vast numbers of genes that are not of interest to the investigator.

Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays,<ref name="TRC Standardization">{{cite journal |date=2005 |title=Standardizing global gene expression analysis between laboratories and across platforms |journal=Nat Methods |volume=2 |pages=351–356 |pmid=15846362 |doi=10.1038/nmeth754 |last12=Deng |first12=S |last13=Dressman |first13=HK |last14=Fannin |first14=RD |last15=Farin |first15=FM |last16=Freedman |first16=JH |last17=Fry |first17=RC |last18=Harper |first18=A |last19=Humble |first19=MC |last20=Hurban |first20=P |last21=Kavanagh |first21=TJ |last22=Kaufmann |first22=WK |first23=KF |first24=L |first25=JA |first26=MR |last27=Li |first27=J |first28=YJ |last29=Lobenhofer |first29=EK |last30=Lu |last31=Malek |first31=RL |last32=Milton |first32=S |last33=Nagalla |first33=SR |last34=O'malley |first34=JP |last35=Palmer |first35=VS |last36=Pattee |first36=P |last7=Paules |first7=RS |last38=Perou |first38=CM |last9=Phillips |first39=K |last40=Qin |last41=Qiu |first41=Y |last42=Quigley |first42=SD |last43=Rodland |first43=M |last44=Rusyn |first44=I |last45=Samson |first45= LD|last46= Schwartz|last47=Shi |first47=Y |last48=Shin |last49=Sieber |last50=Slifer |last51=Speer |first51=MC |last52=Spencer |first52=PS |last53=Sproles |first53=DI |last54=Swenberg |first54=JA |last55=Suk|first55= WA |last56=Sullivan |first56=RC |last57=Tian |first57=R |last58=Tennant |first58=RW |last59= Todd |first59=SA |last60=Tucker |first60=CJ |last61=Van Houten |first61=B |last62=Weis |first62=BK |last63=Xuan |first63=S |last64=Zarbl |first64=H |last65=Members Ofof Thethe Toxicogenomics Research |first65=Consortium |issue=5 |author1=Bammler T, Beyer RP |author2=Consortium, Members of the Toxicogenomics Research |last3=Kerr |last4=Jing |last5=Lapidus |last6=Lasarev |last8=Li |first3=X |first4=LX |first6=DA |first8=JL |first9=SO |first5=S |s2cid=195368323 }}</ref> possibly owing to the small batch sizes and reduced printing efficiencies when compared to industrial manufactures of oligo arrays.

In ''oligonucleotide microarrays'', the probes are short sequences designed to match parts of the sequence of known or predicted [[open reading frame]]s. Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by [[oligonucleotide synthesis|synthesizing]] this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the [[Agilent]] design) or shorter (25-mer probes produced by [[Affymetrix]]) depending on the desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture.

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Microarray data is difficult to exchange due to the lack of standardization in platform fabrication, assay protocols, and analysis methods. This presents an [[interoperability]] problem in [[bioinformatics]]. Various [[grass-roots]] [[open-source model|open-source]] projects are trying to ease the exchange and analysis of data produced with non-proprietary chips:

For example, the "Minimum Information About a Microarray Experiment" ([[MIAME]]) checklist helps define the level of detail that should exist and is being adopted by many [[Scientific journal|journals]] as a requirement for the submission of papers incorporating microarray results. But MIAME does not describe the format for the information, so while many formats can support the MIAME requirements, {{as of|lc=y|2007}} no format permits verification of complete semantic compliance. The "MicroArray Quality Control (MAQC) Project" is being conducted by the US [[Food and Drug Administration]] (FDA) to develop standards and quality control metrics which will eventually allow the use of MicroArray data in drug discovery, clinical practice and regulatory decision-making.<ref>[https://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/ NCTR Center for Toxicoinformatics -– MAQC Project<!-- Bot generated title -->]</ref> The [[MGED Society]] has developed standards for the representation of gene expression experiment results and relevant annotations.

=== Data analysis ===

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== References ==

{{Reflist|30em}}

== External links ==

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* [https://web.archive.org/web/20150924040600/http://www.genome.gov/page.cfm?pageID=10000533 Rundown of microarray technology]

* [http://www.arraymining.net ArrayMining.net]{{snd}}a free web-server for online microarray analysis

* [http://www.unsolvedmysteries.oregonstate.edu/microarray_07 Microarray -– How does it work?]

* [http://www.pnas.org/content/103/44/16063.extract PNAS Commentary: Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data]

* [http://learn.genetics.utah.edu/content/labs/microarray/ DNA microarray virtual experiment]