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Open Access Software

CGH-Profiler: Data mining based on genomic aberration profiles

Falk Schubert1*, Bernhard Tausch13, Stefan Joos2 and Roland Eils1

Author Affiliations

1 Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

2 Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany

3 Current address: Research Group Information Systems and Semantic Web, Institute for Computer Science, University of Koblenz-Landau, Universitätsstraße 1 56070 Koblenz, Germany

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BMC Bioinformatics 2005, 6:188  doi:10.1186/1471-2105-6-188

Published: 25 July 2005

Abstract

Background

CGH-Profiler is a program that supports the analysis of genomic aberrations measured by Comparative Genomic Hybridisation (CGH). Comparative genomic hybridisation (CGH) is a well-established, molecular cytogenetic method that allows the detection of chromosomal imbalances in entire genomes. This technique is widely used in routine molecular diagnostics. Typically, chromosomal imbalances are described in a complex syntax based on the International Standard for Cytogenetic Nomenclature (ISCN). This semantic description of chromosomal imbalances hinders a large-scale statistical analysis across different experiments, e.g. for finding aberration patterns associated with a particular disease type or state.

Results

CGH-Profiler circumvents the semantic ISCN description by importing data from different CGH system vendors and by directly transferring the data into a table format that is readily accessible for subsequent statistical analysis. CGH-profiler comes with different consistency checks, calculates various statistics and automatically assigns a median copy number ratio to each chromosomal band.

Import of CGH profiles from different CGH system vendors is already supported; its extension to other systems can be readily achieved through Perl scripts.

CGH profiler can also be used to analyse comparative expressed sequence hybridisation (CESH) data. CESH reveals gene expression patterns according to chromosomal locations in a similar manner as CGH detects chromosomal imbalances.

Conclusion

CGH-Profiler is a useful tool for processing of CGH and CESH data.