Human Copy Number Variants (CNVs) are known to be involved in several diseases such as intellectual disability, autism, schizophrenia and congenital anomalies, generally due to the presence of dosage-sensitive genes. However, CNVs frequently do not target protein-coding genes, thereby hitting interspersed functional DNA regions, with clinical significance that needs to be largely explored.
InCAS allows to comprehensively annotate CNVs using continuously updated information of protein-coding genes, non-coding genes (microRNAs and long non-coding RNAs) and functional elements (microRNA regulatory sites, ultra conserved regions, promoters, enhancer, topologically associated domains, and others) as well as of clinically significant CNVs. The whole framework is implemented in Python and Flask and deployed to a running instance of Nginx. Data are stored in MongoDB and accessible through both a mobile-first web interface and a RESTful interface for programmatic access.
InCAS is a freely available and handy tool for the assessment of the functional effect and clinical significance of CNVs. If you are using InCAS, please cite https://incas.css-mendel.it.