Welcome to InCAS

InCAS (Integrated Copy number Annotation System) is a tool for the automated functional annotation of human Copy Number Variants using information about protein coding and protein non-coding genes and regulatory regions.

Input Reference Genome

All InCAS annotations and functions are referred to hg19. In order to annotate your CNV/CNV list from other assemblies, an automatic liftover of your CNV coordinates from hg18 and hg38 to hg19 is available.

Window (bp):

This function allows to compare CNVs in your CNV list detecting their percentage of overlap.

Compare the CNV/CNV list of interest with another set of CNV (user defined) or with the Database of Genomics Variants (DGV), detecting the percentage of overlap.

This function calculates how your CNV/CNV list (Query) overlaps to another set of CNVs (Target) considering a minimum reciprocal overlap between query and target (user definable)

This function calculates how your CNV/CNV list (Query) overlaps to another set of CNVs (Target) considering a flanking region (user definable)

Window (bp):
Tissue Description

What is it?

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.