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  : CGHPRO – a comprehensive data analysis tool for array CGH

Chen, W., Erdogan, F., Ropers, H.-H., Lenzner, S., & Ullmann, R. (2005).: CGHPRO – a comprehensive data analysis tool for array CGH. BMC Bioinformatics, 6(1), 1471-2105. doi:10.1186/1471-2105-6-85.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8698-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8699-9
Genre: Journal Article
Alternative Title : BMC bioinformatics

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 Creators:
Chen, Wei1, Author              
Erdogan, Fikret1, Author              
Ropers, Hans-Hilger1, Author              
Lenzner, Steffen2, Author
Ullmann, Reinhard3, Author              
Affiliations:
1Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433549              
2Max Planck Society, ou_persistent13              
3Molecular Cytogenetics (Reinhard Ullmann), Dept. of Human Molecular Genetics (Head: Hans-Hilger Ropers), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479645              

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 Abstract: Background Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test and reference DNA onto arrays of genomic BAC clones, cDNAs or oligonucleotides, and after correction for various intervening variables, loss or gain in the test DNA can be indicated from spots showing aberrant signal intensity ratios. Now that this technique is no longer confined to highly specialized laboratories and is entering the realm of clinical application, there is a need for a user-friendly software package that facilitates estimates of DNA dosage from raw signal intensities obtained by array CGH experiments, and which does not depend on a sophisticated computational environment. Results We have developed a user-friendly and versatile tool for the normalization, visualization, breakpoint detection and comparative analysis of array-CGH data. CGHPRO is a stand-alone JAVA application that guides the user through the whole process of data analysis. The import option for image analysis data covers several data formats, but users can also customize their own data formats. Several graphical representation tools assist in the selection of the appropriate normalization method. Intensity ratios of each clone can be plotted in a size-dependent manner along the chromosome ideograms. The interactive graphical interface offers the chance to explore the characteristics of each clone, such as the involvement of the clones sequence in segmental duplications. Circular Binary Segmentation and unsupervised Hidden Markov Model algorithms facilitate objective detection of chromosomal breakpoints. The storage of all essential data in a back-end database allows the simultaneously comparative analysis of different cases. The various display options facilitate also the definition of shortest regions of overlap and simplify the identification of odd clones. Conclusion CGHPRO is a comprehensive and easy-to-use data analysis tool for array CGH. Since all of its features are available offline, CGHPRO may be especially suitable in situations where protection of sensitive patient data is an issue. It is distributed under GNU GPL licence and runs on Linux and Windows.

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Language(s): eng - English
 Dates: 2005-04-05
 Publication Status: Published in print
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 Identifiers: eDoc: 269093
DOI: 10.1186/1471-2105-6-85
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Title: BMC Bioinformatics
  Alternative Title : BMC bioinformatics
Source Genre: Journal
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Pages: - Volume / Issue: 6 (1) Sequence Number: - Start / End Page: 1471 - 2105 Identifier: ISSN: 1471-2105