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Category Genomics>Genetic Data Analysis/Tools Abstract CGH Explorer is analysis software for comparative genome hybridization (CGH). This software tool can be used for analyzing two color copy number alteration arrays from multiple platforms, including Agilent Technologies, Illumina, AffyMetrix, NimbleGen, BioRobotics, Combimetrix and others. The software performs raw image analysis and gridding eliminating image biases to significantly improving analysis accuracy. CGH Explorer utilizes genomic DNA from both reference and test genome that are labeled with fluorescent dyes. The genomic samples competitively hybridize with an array of probes arranged on a substrate. The hybridized slide can be scanned evaluating the signal intensity ratio for the two (2) dyes to determine the copy number for each DNA segment. The majority of microarray platforms use short DNA fragments (25–75 base pairs), oligonucleotides, or larger bacterial artificial chromosome (BAC) clones of about 100 kilo-base pair (kbp). Along with the arrays covering chromosome specific regions, there are genome wide arrays used for quick assessment of losses and gains in larger regions. In addition, cDNA arrays, originally designed for gene expression profiling, are used to evaluate the number of copies in coding regions. Note: Array Comparative Genomic Hybridization (CGH) is a technique for identifying genomic regions with copy number alterations. Deletions, duplications, and other types of chromosome instability are associated with genetic diseases and somatic alterations in cancer. Products features/capabilities include: 1) CGH Explorer's 'Recap Window' following data processing permits rapid review of critical analysis and quality control. All panels, such as Raw Image, Quality Control, Feature Statistics, and Log Plot can be evaluated in a single glance. 2) The desired platform (e.g. Agilent Technologies, Illumina, AffyMetrix, etc.) can be chosen in AutoRun. The platform associated parameters for image processing and data analysis are chosen automatically. Parameters can be adjusted to meet an individuals needs, and these parameters are saved. 3) CGH Explorer automatically corrects image biases and filters out all low quality features. Two-channel images are aligned, features are placed into the grid, local adjustments are made, feature quality is assessed and intensities are extracted for each channel. 4) Automatic Gridding -- The grid is determined by design file information. In addition, the position of each cell is automatically adjusted. The low intensity spots that do Not satisfy the statistical model are filtered out. 5) Quality Control -- Quality is evaluated for the whole chip through MA and scatter plots, in addition to displays of control features and other statistics. For each feature several quality score parameters are considered for calculating the overall quality score. Each feature is assigned as Good, Bad, or To Be Checked. 6) Interactive Review -- A double mouse click on a data point of the Log plot brings the user to the corresponding raw image feature, allowing for visual quality evaluation. 7) CGH Explorer interfaces with an integrated genetic database assisting with the quick identification of information such as gene and known Copy Number Variations. Comparative analysis of multiple projects can be conducted. 8) Along with the standard copy number variation report, the statistical and quality information about each array feature is available. The information about each array feature is collected in a table. This includes the statistical parameters, genomic information for the probe, quality control parameters, and the overall quality score. 9) Automated Processing -- Batch processing of several projects can speed up analysis and free up time by minimizing the need for user intervention. The data processing results are saved in project files that can be loaded and evaluated at a later time. System Requirements OS: Windows 98, NT, XP, Vista Processor: 2.8 GHz RAM: 2GB CPU Available hard disk space: 20GB Manufacturer Home office; see web site for international locations.
Suite 235, 200 Innovation Blvd State College, PA 16803 USA Phone: 814-237-9340 or 888-791-1270 Fax: 814-237-9343 Email: Technical Service: tech_support@softgenetics.com Product Sales and Marketing: info@softgenetics.com
Price Contact manufacturer G6G Product Number 20125 G6G Manufacturer Number 102425 |
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