Microarray comparative genomic hybridization cgh allows a genome wide screening at a high resolution for the detection of previously cryptic copy number. This technology was first developed as a research tool for the investigation of genomic alterations in cancer. Chromosomal microarray analysis cma also known as comparative genomic hybridization cgh and snp arrays are routine clinical tools for the evaluation of patients with various diseases and congenital malformations. Cgh microarray data analysis, agilent genomic workbench. Comparative genomic hybridization cgh is a molecular cytogenetic method for analysing. These tools assist in automated analysis of array cgh data and. Microarray comparative genomic hybridization cgh and snp array results. Array cgh or acgh uses slides arrayed with small segments of dna as the. The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cdna, and bac clones across the entire genome has triggered and accelerated the use of several platforms for analysis of dna copy number changes, amongst others microarray comparative genomic hybridization arraycgh. Comparative genomic hybridization cgh microarrays from agilent. Microarray comparative genomic hybridization acgh analysis revealed a 1. Using traditional and array cgh, frequent dna copy number gains at 1q, 8q and 20q, and frequent dna copy number losses at 1p, 4q, 8p, q, 16q and 17p have been identified in hcc samples 10 14. Comparative genomic hybridization cgh, also referred to as chromosomal microarray analysis cma, and array cgh acgh, is a method of genetic testing that may identify small deletions and duplications of the subtelomers, each pericentromeric region and other chromosome regions.
Application of arraybased comparative genomic hybridization. This protocol is specifically developed and optimized to enzymatically label dna from blood, cells or frozen tissues. Output files were imported into agilents cgh dataanalysis software, cgh analytics 3. Array based comparative genomic hybridization array cgh has emerged as a powerful tool for detecting gene copy number variants implicated in many disease states. You can also detect genetic variants such as copy number variations cnvs and single nucleotide polymorphism snps from comparative genomic hybridization cgh data. Mathworks is the leading developer of mathematical computing software for engineers and.
Visualize gene and proteinprotein interaction networks using graph theory algorithms. This dramatically reduces the time required for hybridization and analysis. Comparative genomic hybridization cgh, also known as array cgh acgh and chromosomal microarray analysis cma, is a technique used to analyze the human genome to look for abnormalities that commonly lead to a variety of diseases or the failure of a foetus to develop properly. Analysis cma medical policy comparative genomic hybridization cgh chromosomal microarray guidelines this policy does not certify benefits or authorization of benefits, which is designated by each individual policyholder contract. Array cgh comparative genomic hybridisation is a molecular cytogenetic technique for the genome wide detection of chromosomal. Copy number aberration calls are determined entirely. Prenatal diagnosis of chromosomal abnormalities using arraybased comparative genomic hybridization.
Medical policy comparative genomic hybridization cgh. Nov 22, 20 comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations cnvs relative to ploidy level in the dna of a test sample compared to a reference sample. Comparative genomic hybridization cgh, also referred to as chromosomal microarray analysis cma, and array cgh acgh, is a method of genetic testing that may detect aneuploidy, triploidy, as well as deletions and duplications. Comparative genomic hybridization cgh was developed to survey dna copy number variations across a whole genome. Array comparative genomic hybridization also microarray based comparative genomic hybridization, matrix cgh, array cgh, acgh is a molecular cytogenetic technique for the detection of chromosomal copy number changes on a genome wide and highresolution scale.
A method for comparing two sets of chromosomal dna by analyzing differences in the copy number and location of specific sequences. Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations cnvs relative to ploidy level in the dna of a test sample compared to a reference sample, without the need for culturing cells. The competitive hybridization of the test dna to the control dna reveals copy number changes in the patients dna for the chromosomal regions tested. Whilst some of the technical difficulties encountered. Aug 03, 2005 microarray comparative genomic hybridization array cgh data. Comparative genomic hybridization cgh analysis has revolutionized the. Recent advances in array comparative genomic hybridization. Arraybased comparative genomic hybridization reveals. Microarray comparative genomic hybridization detection of. The utility of array comparative genomic hybridization cgh testing in prenatal diagnosis has been recently described 1, 2 with potential advantages, including improved detection of pathogenic chromosomal rearrangements following rapid analysis of uncultured chorionic villi or amniocytes. Loh in the long arm terminal region of chromosome 6, b bone marrow sample after treatment at 165 d with only germline duplication of. With agw, scientists can change filters, thresholds, and other settings to. Chitty3,4,5 1ne thames regional genetics service, great ormond street hospital for children nhs foundation trust, london, uk. The dna samples are differentially labeled and hybridized to an immobilized substrate.
A, initial bone marrow showing the duplication of 8q21. Dec 02, 2015 chromosomal microarray analysis cma also known as comparative genomic hybridization cgh and snp arrays are routine clinical tools for the evaluation of patients with various diseases and congenital malformations. Comparative genomic hybridization cgh is a molecular cytogenetic method for analysing copy number variations cnvs relative to ploidy level in the dna of a test sample compared to a reference sample, without the need for culturing cells. Cancer research 63, 33093316, june 15, 2003 a combined comparative genomic hybridization and expression microarray analysis of gastric cancer reveals novel molecular subtypes1,2 su ting tay, 3siew hong leong, kun yu, amit aggarwal, soo yong tan, chee how lee, keith wong, jaya visvanathan, dennis lim, wai keong wong, khee chee soo, oi lian kon, and patrick tan 4. Highlysensitive 60mer oligonucleotide probes deliver the resolution needed to accurately examine chromosomal changes. Microarray comparative genomic hybridisation cgh profile of the bt474 cell line.
Regardless of the type of probe, the basic methodology for acgh analysis is. For classical cgh, several commercial software packages are. Array comparative genomic hybridization array cgh is a method used to detect segmental dna copy number alterations. Array cgh has been used to survey chromosomal amplifications and deletions in. Cgh analysis is used as a supplemental technique to conventional cytogenetics. With agw, scientists can change filters, thresholds, and other settings to optimize the realtime visualization effects. Comparative genomic hybridization cgh or chromosomal microarray analysis cma is a recent technology development that allows for an entire genome to be analyzed in more detail than is possible using conventional cytogenetics. Array based comparative genomic hybridization array cgh has emerged as a powerful tool for detecting gene copy number variants implicated in many. Software for array cgh visualization and analysis download table. Arraycgh is a technique based on the same principle as cgh, but the hybridization of test and reference dna is shorter and does not take place on metaphase spreads, but on chips containing thousands of loci. In the past two decades, comparative genomic hybridization cgh and array. Yet another popular technique is comparative genomic hybridization cgh, which. Comparative genomic hybridization cgh in genotoxicology.
Validation of microarray comparative genomic hybridization. Assessing large regions of homozygosity related to uniparental disomy or identity by descent. This system is more rapid and convenient than general dnadna hybridization methods and produces a large. Prenatal diagnosis of chromosomal abnormalities using. Microarraybased comparative genomic hybridization acgh. Although conventional microarray analytical procedures have proved adequate in handling mcgh data, data interpretation using these methods is based on a continuous character model in which gene. A new approach for the analysis of bacterial microarray. Comparative genomic hybridization cgh to metaphase chromosome targets 1,2 has significantly contributed to our understanding of the cancer cytogenetics of more complex malignancies such as.
Comparative genomic hybridization using oligonucleotide pnas. Arraycomparative genomic hybridization also cma, chromosomal microarray analysis, microarraybased comparative genomic hybridization, array cgh, acgh, acgh is a technique to detect genomic copy number variations at a higher resolution level than chromosome based comparative genomic hybridization cgh. In addition, acgh has proven to be a powerful tool for the detection of. Agilent oligonucleotide arraybased cgh for genomic dna. Dna is isolated from tissue samples and is labeled with fluorochromes before being hybridized to a microarray of mapped genomic dna clones or probes.
Comparative genomic hybridization cgh was developed to monitor the dna copy number changes on a genomic scale at the resolution of. Comparative genomic hybridization cgh utilizing microarray technology has been used for several years in the clinical diagnosis of children and adults with a suspected genetic syndrome of unknown etiology. The density of oligonucleotide probes available on current microarray platforms is particularly. Oligonucleotide arraybased cgh for genomic dna analysis protocol 1 before you begin procedural notes 8 safety notes 9 agilent oligo cgh microarray kit contents 10 required equipment 15 required reagents 18 required hardware and software 20 make sure that you read and understand the information in this chapter and. For processing ffpe samples, follow the agilent oligonucleotide arraybased cgh for genomic dna analysis uls labeling for blood, cells, tissues or ffpe protocol pn g441090020. Biodiscovery releases imagene 7 microarray image analysis. Simple, robust genomic dna labeling reagents and removal of free dye and nucleotides are two of the most critical components determining array cgh experiments performance. Microarray based comparative genomic hybridization array cgh has been applied for a decade to screen for submicroscopic dna gains and losses in tumor and constitutional dna samples. Microarraybased comparative genomic hybridization array cgh is a revolutionary platform that was recently adopted in the clinical laboratory. Chromosomal microarray analysis, or comparative genomic. With easytouse catalog products for a variety of cgh applications and the industrys most affordable and flexible custom content program, agilents cgh solution provides.
Aug 14, 2015 array comparative genomic hybridization also cma, chromosomal microarray analysis, microarray based comparative genomic hybridization, array cgh, a cgh, acgh is a technique to detect genomic copy number variations at a higher resolution level than chromosome based comparative genomic hybridization cgh. Tool for comprehensive analysis of genomic aberrations in tumor samples. Microarrays have an advantage over conventional cgh in that the evaluation of the green or red fluorescence is simple and easily automated with a computer and software. The density of oligonucleotide probes available on current microarray platforms is particularly wellsuited. Cghexplorer is a program for visualization and statistical analysis of microarraybased comparative genomic hybridization. All our samples, except one premalignant lesion, presented alterations, ranking from 1287 alterationstotal targets in the array in a premalignant lesion to 175287alterations in the cell line rova. Comparative genomic hybridization an overview sciencedirect. Agilent cgh microarray platform combines sensitivity, flexibility and coverage, allowing scientists to finely view chromosomal variations and elucidate their relationship to disease susceptibility. Array cgh detects gains or losses of dna, also called dna dosage alterations. Array comparative genomic hybridization thermo fisher. A survey of analysis software for arraycomparative genomic. Simple, robust genomic dna labeling reagents and removal of free dye and nucleotides are two of the most critical components determining array cgh experiment s performance. Microarray cgh is the comparative, competitive hybridisation of test patient and reference genomic dna to probes arrayed onto a glass slide microarray this allows robust detection of copy number imbalance loss or gain of genetic material across the entire genome at a very high. Hybridization signals are then digitized and analyzed using software that.
Gene expression and genetic variant analysis of microarray data. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations. Surprisingly, the extent of variation in copy number in the human genome outnumbers the heterogeneity in sequence variation. This technology later evolved so that the dna targets are hybridized to microarrays containing cdna fragments or bacterial artificial. Recommendations are made for hardware and software capabilities that will permit a level of performance of comparative genomic hybridization cgh analysis on metaphase chromosomes that is.
Comparative genomic hybridization cgh medical clinical. Comparative genomic hybridisation cgh is a technique that permits the detection of. Comparative genomic hybridization cgh chromosomal microarray analysis cma conventional cytogenetic tests identify known genetic abnormalities when a specific clinical syndrome is suspected. Microarraybased comparative genomic hybridization mcgh has been used to characterize the extensive intraspecies genetic diversity found in bacteria at the wholegenome level. Cgh microarray data analysis, agilent genomic workbench agilent. Vantage agilent comparative genomic hybridization arrays cgh. Comparative genomic hybridization wikipedia republished.
Arraybased comparative genomic hybridisation acgh is a powerful method used to detect and. Arraybased comparative genomic hybridization array cgh, also called microarray analysis, is a new cytogenetic technology that evaluates areas of the human genome for gains or losses of chromosome segments at a higher resolution than traditional karyotyping. Cgh microarray service cd genomics has cgh microarray service for a number of species, including human, mouse, rat, and chicken, and custom cgh arrays for other species are also available. Currently, ivf1 uses a system that allows us to get results in 24 hours. Comparative genomic hybridization cgh measures dna copy number differences between a reference genome and a test genome. Cd genomics has cgh microarray service for a number of species, including human, mouse, rat, and chicken, and custom cgh arrays for other species are also available microarray comparative genomic hybridization cgh allows a genome wide screening at a high resolution for the detection of previously cryptic copy number imbalance deletions and duplications. A new approach to species determination for yeast strains. Array comparative genomic hybridization thermo fisher scientific. Dec 05, 20 array comparative genomic hybridization also cma, chromosomal microarray analysis, microarray based comparative genomic hybridization, array cgh, acgh, or virtual karyotype is a technique to detect genomic copy number variations at a higher resolution level than chromosomebased comparative genomic hybridization cgh. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. Mesh 20 array comparative genomic hybridization acgh. The agilents cgh microarrays enable the scientist to confidently characterize chromosomal aberrations associated with developmental abnormalities, disease susceptibility, and differential drug responses. Arraybased comparative genomic hybridisation acgh is a powerful.
Introduction to array cgh analysis 10810, cmb lecture 11 eric xing tumor cell chromosomes of tumor cell. Microarray based comparative genomic hybridization array cgh is a revolutionary platform that was recently adopted in the clinical laboratory. Analysis of comparative genomic hybridization data on cdna. In early cgh experiments, the dna targets were hybridized to metaphase chromosome spreads in fluorescent in situ hybridization fish assays. Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations cnvs relative to ploidy level in the dna of a test sample compared to a reference sample. Microarraybased comparative genomic hybridization arraycgh has been applied for a decade to screen for submicroscopic dna gains and losses in tumor and constitutional dna samples.
It allows for a highresolution evaluation of dna copy number alterations associated with chromosome abnormalities. Agilent oligonucleotide arraybased cgh for genomic dna analysis. Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. More than 70 disorders are known to be associated with birth defects or developmental problems that are. Microarraybased comparative genomic hybridization arraycgh is a technique by which variations in copy numbers between two genomes can be analyzed using dna microarrays. Using a fluorescence microscope and computer software, the differentially. Recently, advances in this technology have enabled highresolution examination. Comparative genomic hybridization cgh is a molecular testing method for detecting copy number changes throughout the genome 172174. Prenatal diagnosis of chromosomal abnormalities using array. Arraybased comparative genomic hybridization cgh measures. Paramount applies coding edits to all medical claims through coding logic software. Genomic dna from the test and control samples are differentially labeled with fluorescent dyes and patient hybridized to the ayarr.
Cghpro a comprehensive data analysis tool for array cgh. Array comparative genomic hybridization also microarraybased. To interpret microarray performance, cgh analytics generates a set of quality metrics including. The aim of this technique is to quickly and efficiently compare two genomic dna samples arising from two sources, which are most often closely related, because. A bacterialphage artificial chromosome polymerase chain reaction representations were used as probe dnas spotted on to the glass slide. Array comparative genomic hybridization array cgh analysis. Cgh microarray solutions for genomewide genetic analysis. Comparative genomic hybridization cgh is a hybridization method used to identify. Agilent cgh microarrays are widely recognized as the industry standard for genomewide chromosomal analysis. This method has become increasingly flexible with the integration of new biological resources generated by genome sequencing projects.
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