CGH-Profiler: data mining based on genomic aberration profiles.
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.


CONCLUSIONS
CGH-Profiler is a useful tool for processing of CGH and CESH data.
Schubert
Falk
F
Theoretical Bioinformatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. f.schubert@dkfz-heidelberg.de
Tausch
Bernhard
B
Joos
Stefan
S
Eils
Roland
R
D002869:Chromosome Aberrations / Q000145:classification*; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D020732:Cytogenetic Analysis / Q000379:methods*; D003625:Data Collection / Q000379:methods; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval; D009693:Nucleic Acid Hybridization; D015203:Reproducibility of Results; D012984:Software