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Methods Mol Biol. 2007;396:255-66.

DNA copy number data analysis using the CGHAnalyzer software suite.


Recently developed microarray-based copy number measurement assays have drastically improved the accuracy and resolution to which DNA copy number alterations can be detected. As with any microarray assay, those designed to measure genome copy number produce large data sets for each sample. Furthermore, many successful studies of genome copy number require the concurrent comparison of many samples. Identifying software packages that provide the proper analytic tools is essential to effectively mine these valuable data. CGHAnalyzer is a freely available, open source software suite designed specifically for the purpose of analyzing multiple-experiment microarray-based genome copy number data. This package can load data from a variety of formats, query large data sets for minimal common regions of gain and loss, integrate other genomic features into analyses (e.g., known/predicted genes), conduct higher order analyses such as hierarchical/k-means clustering and perform statistical tests to identify regions that are differentially altered between classes of samples. Each of these utilities represents common hurdles in approaching microarray copy number data sets. This passage provides an overview of practical, step by step analysis of array-based comparative genomic hybridization data using CGHAnalyzer and demonstrates specific techniques to improve the efficiency and accuracy of analysis.

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