CNVinspector for the Evaluation of Copy Number Variations
CNVinspector for the Evaluation of Copy Number Variations
Available computer programmes for CNV data analysis can be roughly divided into three groups: (1) programmes with a focus on the (pre)processing of raw data (eg, array-CGH scanning data) and CNV detection, while only rudimentary visualisation functions are offered (eg, CGHPRO, CNV Workshop, MD-SeeGH, or arrayCGHbase); (2) programmes that are suited for sophisticated CNV visualisation without the capability to handle raw data (eg, CNVineta, VAMP, SEURAT, or FISH-Oracle); (3) programmes that combine raw data processing and visualisation capabilities (eg, CAPweb). Most tools integrate gene annotations and allow inspection in a genome browser. However, most applications have to be downloaded for local installation and often require additional software, such as databases, a web-server, or mathematics software.
An issue almost entirely neglected by the available programmes is the comparison of own CNV data against control data. For useful clinical information, CNVs have to be assessed and evaluated for their functional impact and pathogenicity. Changes present in a larger number of healthy subjects would not be regarded as clinically relevant. To our knowledge, only CNV Workshop has integrated public CNVs from the DGV and from CHOP CNV, but requires local installation. CNVineta and an unpublished version of CGHPRO (http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/CGHPRO.html) offer the possibility to compare genetic variations between different groups of patients or between patients and controls, but the users have to provide their own control data.
CNVinspector will serve its purpose best in the common scenario where a clinical geneticist is provided with preprocessed data from a specialised centre and now wants to validate the clinical relevance of certain CNVs. This is achieved by provision of an easy-to-use online resource with a graphic interface for the comparison of own CNV data with database-stored normative data along with their clinical information.
During the last few years, the number of diagnostic tests using array-CGH has risen sharply as every child with unsolved mental retardation and/or dysmorphism would be a possible candidate for such genetic testing. The resulting flood of data needs to be processed, inspected and evaluated. CNVinspector is a new programme that will facilitate the daily work of a clinical geneticist and will help to accelerate the progress in the delineation of new syndromes and gene functions.
Discussion
Available computer programmes for CNV data analysis can be roughly divided into three groups: (1) programmes with a focus on the (pre)processing of raw data (eg, array-CGH scanning data) and CNV detection, while only rudimentary visualisation functions are offered (eg, CGHPRO, CNV Workshop, MD-SeeGH, or arrayCGHbase); (2) programmes that are suited for sophisticated CNV visualisation without the capability to handle raw data (eg, CNVineta, VAMP, SEURAT, or FISH-Oracle); (3) programmes that combine raw data processing and visualisation capabilities (eg, CAPweb). Most tools integrate gene annotations and allow inspection in a genome browser. However, most applications have to be downloaded for local installation and often require additional software, such as databases, a web-server, or mathematics software.
An issue almost entirely neglected by the available programmes is the comparison of own CNV data against control data. For useful clinical information, CNVs have to be assessed and evaluated for their functional impact and pathogenicity. Changes present in a larger number of healthy subjects would not be regarded as clinically relevant. To our knowledge, only CNV Workshop has integrated public CNVs from the DGV and from CHOP CNV, but requires local installation. CNVineta and an unpublished version of CGHPRO (http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/CGHPRO.html) offer the possibility to compare genetic variations between different groups of patients or between patients and controls, but the users have to provide their own control data.
CNVinspector will serve its purpose best in the common scenario where a clinical geneticist is provided with preprocessed data from a specialised centre and now wants to validate the clinical relevance of certain CNVs. This is achieved by provision of an easy-to-use online resource with a graphic interface for the comparison of own CNV data with database-stored normative data along with their clinical information.
During the last few years, the number of diagnostic tests using array-CGH has risen sharply as every child with unsolved mental retardation and/or dysmorphism would be a possible candidate for such genetic testing. The resulting flood of data needs to be processed, inspected and evaluated. CNVinspector is a new programme that will facilitate the daily work of a clinical geneticist and will help to accelerate the progress in the delineation of new syndromes and gene functions.
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