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42-538: GCOS may refer to: Affymetrix GeneChip Operating Software Global Climate Observing System General Comprehensive Operating System , a family of operating systems oriented toward mainframes, originally called GECOS (General Electric Comprehensive Operating Supervisor) See also [ edit ] GKOS keyboard Geckos Google Chrome Operating System An open source, lightweight operating system that will initially be targeted at netbooks Topics referred to by

84-405: A laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes. Oligonucleotide microarrays often carry control probes designed to hybridize with RNA spike-ins . The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements for

126-416: A biological sample. In this area, Affymetrix was focused on oligonucleotide microarrays, which could be used to address the presence of genes through detection of specific corresponding segments of mRNA . The single-use chips could be used to analyze thousands of genes in a single assay. The company also manufactured machinery for high speed analysis of biological samples, and its GeneChip Operating Software as

168-468: A different condition, and the identity of the feature is known by its position. Many types of arrays exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads: DNA microarrays can be used to detect DNA (as in comparative genomic hybridization ), or detect RNA (most commonly as cDNA after reverse transcription ) that may or may not be translated into proteins. The process of measuring gene expression via cDNA

210-568: A discrete business focusing on wafer-scale genomics to characterize population - variance of genomic markers. In January 2014, the Food and Drug Administration approved Affymetrix's postnatal blood test, CytoScan Dx Assay, looking at whole- genome correlates of congenital abnormalities and other causes of childhood developmental delay. On January 8, 2016, Thermo Fisher Scientific announced its acquisition of Affymetrix for approximately $ 1.3 billion, which closed on March 31, 2016. Affymetrix, Inc.

252-425: A fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy 5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labeled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with

294-538: A genome. Each DNA spot contains picomoles (10 moles ) of a specific DNA sequence, known as probes (or reporters or oligos ). These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA (also called anti-sense RNA) sample (called target ) under high-stringency conditions. Probe-target hybridization is usually detected and quantified by detection of fluorophore -, silver-, or chemiluminescence -labeled targets to determine relative abundance of nucleic acid sequences in

336-402: A probe sequence generate a signal that depends on the hybridization conditions (such as temperature), and washing after hybridization. Total strength of the signal, from a spot (feature), depends upon the amount of target sample binding to the probes present on that spot. Microarrays use relative quantitation in which the intensity of a feature is compared to the intensity of the same feature under

378-412: A silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array. Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions,

420-1035: A system for managing Affymetrix microarray data. Affymetix's competitors in the DNA Microarray business include Illumina , GE Healthcare , Applied Biosystems , Beckman Coulter , Eppendorf Biochip Systems, and Agilent . Prior to its acquisition by Thermo Fisher, and its becoming a line of its products, Affymetrix, Inc. had acquired the technologies of a number of companies. It acquired Genetic MicroSystems for slide-based microarrays and scanners and Neomorphic for bioinformatics , both in 2000, ParAllele Bioscience for custom SNP genotyping , USB /Anatrace for biochemical reagents in 2008, eBioscience for flow cytometry in 2012, and Panomics in 2008 and True Materials to expand its offering of low to mid-plex applications. In 2000, Perlegen Sciences spun out from Affymetrix to focus on wafer-scale genomics for massive data creation and collection required for characterizing population variance of genomic markers and expression for

462-492: 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. The MGED Society has developed standards for the representation of gene expression experiment results and relevant annotations. Microarray data sets are commonly very large, and analytical precision

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504-420: Is called expression analysis or expression profiling . Applications include: Specialised arrays tailored to particular crops are becoming increasingly popular in molecular breeding applications. In the future they could be used to screen seedlings at early stages to lower the number of unneeded seedlings tried out in breeding operations. Microarrays can be manufactured in different ways, depending on

546-777: Is different from Wikidata All article disambiguation pages All disambiguation pages Affymetrix GeneChip Operating Software In 1994, the company's first product under the "GeneChip" Affymetrix trademark, an HIV genotyping chip was introduced, and the company went public in 1996. After incorporation, Affymetrix grew in part by acquiring technologies from other companies, including Genetic MicroSystems (slide-based Microarrays and scanners) and Neomorphic (for bioinformatics ) in 2000, ParAllele Bioscience (custom SNP genotyping ), USB /Anatrace (biochemical reagents ) in 2008, Panomics (low to mid-plex applications) in 2008, and eBioscience ( flow cytometry ) in 2012. Affymetrix spun off Perlegen Sciences in 2000, as

588-427: 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 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

630-406: Is expected to detect is not trivial. Some mRNAs may cross-hybridize probes in the array that are supposed to detect another mRNA. In addition, mRNAs may experience amplification bias that is sequence or molecule-specific. Thirdly, probes that are designed to detect the mRNA of a particular gene may be relying on genomic EST information that is incorrectly associated with that gene. Microarray data

672-419: Is influenced by a number of variables. Statistical challenges include taking into account effects of background noise and appropriate normalization of the data. Normalization methods may be suited to specific platforms and, in the case of commercial platforms, the analysis may be proprietary. Algorithms that affect statistical analysis include: Microarray data may require further processing aimed at reducing

714-543: The National Institutes of Health." The test, known as CytoScan Dx Assay, was designed to diagnose these disabilities earlier to expedite appropriate care and support. DNA Microarray A DNA microarray (also commonly known as DNA chip or biochip ) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of

756-525: 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. One technique used to produce oligonucleotide arrays include photolithographic synthesis (Affymetrix) on

798-431: 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

840-430: The arrays provide intensity data for each probe or probe set indicating a relative level of hybridization with the labeled target. However, they do not truly indicate abundance levels of a gene but rather relative abundance when compared to other samples or conditions when processed in the same experiment. Each RNA molecule encounters protocol and batch-specific bias during amplification, labeling, and hybridization phases of

882-627: The considerations of experimental design that are discussed in the expression profiling article are of critical importance if statistically and biologically valid conclusions are to be drawn from the data. There are three main elements to consider when designing a microarray experiment. First, replication of the biological samples is essential for drawing conclusions from the experiment. Second, technical replicates (e.g. two RNA samples obtained from each experimental unit) may help to quantitate precision. The biological replicates include independent RNA extractions. Technical replicates may be two aliquots of

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924-473: The dimensionality of the data to aid comprehension and more focused analysis. Other methods permit analysis of data consisting of a low number of biological or technical replicates ; for example, the Local Pooled Error (LPE) test pools standard deviations of genes with similar expression levels in an effort to compensate for insufficient replication. The relation between a probe and the mRNA that it

966-483: The drug discovery process. In January 2014, the Food and Drug Administration cleared a first-of-a-kind whole-genome postnatal blood test that can aid physicians in identifying the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children, where it was noted that "[a]bout 2 to 3 percent of U.S. children have some sort of intellectual disability, according to

1008-584: The experiment making comparisons between genes for the same microarray uninformative. The comparison of two conditions for the same gene requires two separate single-dye hybridizations. Several popular single-channel systems are the Affymetrix "Gene Chip", Illumina "Bead Chip", Agilent single-channel arrays, the Applied Microarrays "CodeLink" arrays, and the Eppendorf "DualChip & Silverquant". One strength of

1050-400: The investigator. Publications exist which indicate in-house spotted microarrays may not provide the same level of sensitivity compared to commercial oligonucleotide arrays, 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

1092-447: The level of detail that should exist and is being adopted by many 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 2007 no format permits verification of complete semantic compliance. The "MicroArray Quality Control (MAQC) Project"

1134-568: The measurement of gene expression. The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs . A high number of complementary base pairs in a nucleotide sequence means tighter non-covalent bonding between the two strands. After washing off non-specific bonding sequences, only strongly paired strands will remain hybridized. Fluorescently labeled target sequences that bind to

1176-430: The multiple levels of replication in experimental design ( Experimental design ); the number of platforms and independent groups and data format ( Standardization ); the statistical treatment of the data ( Data analysis ); mapping each probe to the mRNA transcript that it measures ( Annotation ); the sheer volume of data and the ability to share it ( Data warehousing ). Due to the biological complexity of gene expression,

1218-555: The number of probes under examination, costs, customization requirements, and the type of scientific question being asked. Arrays from commercial vendors may have as few as 10 probes or as many as 5 million or more micrometre-scale probes. 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, or electrochemistry on microelectrode arrays. In spotted microarrays ,

1260-663: The only choice in some situations. Suppose i {\displaystyle i} samples need to be compared: then the number of experiments required using the two channel arrays quickly becomes unfeasible, unless a sample is used as a reference. two channel microarray (with reference) This is an example of a DNA microarray experiment which includes details for a particular case to better explain DNA microarray experiments, while listing modifications for RNA or other alternative experiments. The advent of inexpensive microarray experiments created several specific bioinformatics challenges:

1302-524: 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

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1344-405: The probes are oligonucleotides , cDNA or small fragments of PCR products that correspond to mRNAs . The probes are 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

1386-447: The same extraction. Third, spots of each cDNA clone or oligonucleotide are present as replicates (at least duplicates) on the microarray slide, to provide a measure of technical precision in each hybridization. It is critical that information about the sample preparation and handling is discussed, in order to help identify the independent units in the experiment and to avoid inflated estimates of statistical significance . Microarray data

1428-405: The same term [REDACTED] This disambiguation page lists articles associated with the title GCOS . If an internal link led you here, you may wish to change the link to point directly to the intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=GCOS&oldid=1203195058 " Category : Disambiguation pages Hidden categories: Short description

1470-419: The sequence of known or predicted open reading frames . 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 synthesizing this sequence directly onto

1512-484: The sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes. Two-color microarrays or two-channel microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores . Fluorescent dyes commonly used for cDNA labeling include Cy 3, which has

1554-512: The single-dye system lies in the fact that an aberrant sample cannot affect the raw data derived from other samples, because each array chip is exposed to only one sample (as opposed to a two-color system in which a single low-quality sample may drastically impinge on overall data precision even if the other sample was of high quality). Another benefit is that data are more easily compared to arrays from different experiments as long as batch effects have been accounted for. One channel microarray may be

1596-568: The target probes. Although absolute levels of gene expression may be determined in the two-color array in rare instances, the relative differences in expression among different spots within a sample and between samples is the preferred method of data analysis for the two-color system. Examples of providers for such microarrays includes Agilent with their Dual-Mode platform, Eppendorf with their DualChip platform for colorimetric Silverquant labeling, and TeleChem International with Arrayit . In single-channel microarrays or one-color microarrays ,

1638-456: The target. The original nucleic acid arrays were macro arrays approximately 9 cm × 12 cm and the first computerized image based analysis was published in 1981. It was invented by Patrick O. Brown . An example of its application is in SNPs arrays for polymorphisms in cardiovascular diseases, cancer, pathogens and GWAS analysis. It is also used for the identification of structural variations and

1680-488: Was found to be more useful when compared to other similar datasets. The sheer volume of data, specialized formats (such as MIAME ), and curation efforts associated with the datasets require specialized databases to store the data. A number of open-source data warehousing solutions, such as InterMine and BioMart , have been created for the specific purpose of integrating diverse biological datasets, and also support analysis. Advances in massively parallel sequencing has led to

1722-429: Was introduced in 1994 and the company went public in 1996. Affymetrix, Inc. made glass chips for analysis of DNA Microarrays called GeneChip arrays, and sold mass-produced GeneChip arrays intended to match scientifically important parts of human and other animal genomes. Manufactured using photolithography , Affymetrix's GeneChip arrays assisted researchers in quickly scanning for the presence of particular genes in

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1764-556: Was spun-off from Affymax Research Institute by Alex Zaffaroni in 1993, and was eventually based in Santa Clara, California , United States. It began as a unit in Affymax N.V. in 1991 under Fodor and his group. In the late 1980s, that group had developed methods for fabricating DNA microarrays, under the "GeneChip" Affymetrix trademark, using semiconductor manufacturing techniques. The company's first product, an HIV genotyping GeneChip,

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