title: GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.
abstract: BACKGROUND
  The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multidimensional data analysis and comparison of patient cohorts are needed to assist in the discrimination of clinically relevant CNVs from others.
  
  
  RESULTS
  We developed GenomeCAT, a standalone Java application for the analysis and integrative visualization of CNVs. GenomeCAT is composed of three modules dedicated to the inspection of single cases, comparative analysis of multidimensional data and group comparisons aiming at the identification of recurrent aberrations in patients sharing the same phenotype, respectively. Its flexible import options ease the comparative analysis of own results derived from microarray or NGS platforms with data from literature or public depositories. Multidimensional data obtained from different experiment types can be merged into a common data matrix to enable common visualization and analysis. All results are stored in the integrated MySQL database, but can also be exported as tab delimited files for further statistical calculations in external programs.
  
  
  CONCLUSIONS
  GenomeCAT offers a broad spectrum of visualization and analysis tools that assist in the evaluation of CNVs in the context of other experiment data and annotations. The use of GenomeCAT does not require any specialized computer skills. The various R packages implemented for data analysis are fully integrated into GenomeCATs graphical user interface and the installation process is supported by a wizard. The flexibility in terms of data import and export in combination with the ability to create a common data matrix makes the program also well suited as an interface between genomic data from heterogeneous sources and external software tools. Due to the modular architecture the functionality of GenomeCAT can be easily extended by further R packages or customized plug-ins to meet future requirements.
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Tebel
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.|Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195, Berlin, Germany.
authors.forename: Vivien
authors.initials: V
authors.lastname: Boldt
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.|Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195, Berlin, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Steininger
authors.affiliation: Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, 80937, Munich, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Port
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.|Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195, Berlin, Germany.
authors.forename: Grit
authors.initials: G
authors.lastname: Ebert
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany. reinhard1ullmann@bundeswehr.org.|Institut für Radiobiologie der Bundeswehr in Verb. mit der Universität Ulm, 80937, Munich, Germany. reinhard1ullmann@bundeswehr.org.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Ullmann
mesh_terms: D003198:Computer Simulation; D056915:DNA Copy Number Variations; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D008962:Models, Theoretical; D015203:Reproducibility of Results; D012984:Software
keywords: DNA copy number variants; Integrative visualization; Microarray; NGS