J Med Genet. 2013 Aug;50(8):529-33. doi: 10.1136/jmedgenet-2012-101497. Epub 2013 May 31.
CNVinspector: a web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts.
SourceDepartment of Neuropediatrics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin D-13353, Germany, email@example.com.
OBJECTIVES:Many genetic disorders are caused by copy number variations (CNVs) in the human genome. However, the large number of benign CNV polymorphisms makes it difficult to delineate causative variants for a certain disease phenotype. Hence, we set out to create software that accumulates and visualises locus-specific knowledge and enables clinicians to study their own CNVs in the context of known polymorphisms and disease variants.
METHODS:CNV data from healthy cohorts (Database of Genomic Variants) and from disease-related databases (DECIPHER) were integrated into a joint resource. Data are presented in an interactive web-based application that allows inspection, evaluation and filtering of CNVs in single individuals or in entire cohorts.
RESULTS:CNVinspector provides simple interfaces to upload CNV data, compare them with own or published control data and visualise the results in graphical interfaces. Beyond choosing control data from different public studies, platforms and methods, dedicated filter options allow the detection of CNVs that are either enriched in patients or depleted in controls. Alternatively, a search can be restricted to those CNVs that appear in individuals of similar clinical phenotype. For each gene of interest within a CNV, we provide a link to NCBI, ENSEMBL and the GeneDistiller search engine to browse for potential disease-associated genes.
CONCLUSIONS:With its user-friendly handling, the integration of control data and the filtering options, CNVinspector will facilitate the daily work of clinical geneticists and accelerate the delineation of new syndromes and gene functions. CNVinspector is freely accessible under http://www.cnvinspector.org.
KEYWORDS:Clinical genetics, Diagnostics, Genetic screening/counselling
- [PubMed - in process]