Analysis Software for Comparative
Genome Hybridization

Array Comparative Genomic Hybridization 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.

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 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 BAC clones of about 100 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.

CGH Explorer™ is an easy-to-use software tool 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.

Simple, user-friendly interface and automation features speed analysis providing final results within a few mouse clicks.

CGH Explorer™ features:

• Multiple Platform Compatibility
• Raw Image Processing improves accuracy and precision
• Comparative Analysis of multiple projects
• Automated parameter setting
• Integrated from raw image processing through final reporting of results
• Batch Processing Capability
• Rapid Analysis performed in minutes
• Easy-to-Use Windows interface
• Multiple Quality Control functions

Recap Window following data processing permits rapid review of critical analysis and quality control. All panels, such as Raw Image, Quality Control, Feature Statistics, Log Plot can be evaluated in a single glance.

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.

Easy Operation	Automatic Gridding
Desired platform can be chosen in AutoRun. The platform associated parameters for image processing and data analysis are chosen automatically. Parameters can be adjusted to meet the individual needs, and these parameters are saved.	The grid is determined by the 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.

Quality is assessed for the whole chip and each feature. Using the control probe intensity the program calculates the uniformity and alignment parameters. Mulitple statistics and charts are available for analysis assesment.

Graphic display are linked,clicking on a individual feature, other windows will scroll to and highlight the appropriate location to allow for easy inspection.

Quality Control	Interactive Review
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.	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.

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.

Integrated Database	Multiple Project Comparison
Clicking on a probe displays the relevant genetic information. The information about known copy number variances (CNVs) is also displayed graphically.	Multiple projects can be loaded to obtain the chromosomal aberrationfrequencies.

Along with the standard copy number variation report, the statistical and quality information about each array feature is available.

Chromosome Alteration Report

Array Features

The information about each array feature is collected in the table. This includes the statistical parameters, genomic information for the probe, quality control parameters, and the overall quality score.

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.