CNV-catalog A database of published association results examining copy number variants and their effect on clinical phenotypes

Project Description

An easy toolkit to store and manage published association results for Copy Number Variants (CNVs). The database comes packaged with info on 485 CNV loci, from 53 papers describing 48 different phenotypes.

  • Add and curate data from papers through R shiny interface
  • Data stored in local SQLite Database
  • Create lists of CNV variants based on filters such as phenotype, p-value, OR etc.
  • Compare phenotype and frequency association between multiple loci
  • Examine relationship between studies included
  • View meta-analysis for a given CNV loci

CNV Catalog

Asides from a positive family history, rare copy number variants (CNVs) comprise the most severe risk factor for psychiatric illness. Data from SNP-microarray technology has helped establish strong associations between specific CNV loci and psychiatric illness, cognitive and/or morphological features. CNVs are highly pleiotropic, and yet cause impairment to specific cognitive domains (as well as brain structures) in both affected and healthy carriers.

The literature describing CNV effects is growing, but there is currently no central resource that compiles this knowledge in a structured manner. The lack of a structure in complex information creates barriers and prevents effective utilisation of this valuable resource. Here we present a solution to this problem, through the development of a structured database loaded with CNV association results from the published literature.

We constructed a structured SQLite database schema to hold information on: loci positions, association results, phenotypes, sample size, and inter study relation. The data source is tables from published articles, which are loaded into the database via a function that integrates overlapping loci. Along with the database, we present a set of interactive graphical visualisations using the R Shiny package to help query CNV effects in an easy manner.

CNV Database

The database presented here allow researchers to perform efficient meta-analysis, cross querying, and annotation of local datasets, in addition we provide tools needed to upload additional data alongside running database updates provided by our lab. This resource may be valuable for researchers as well as clinical geneticists who seek to compare their practice with the lasted published literature. The database and applications will soon be made available for download.