CONAN: copy number variation analysis software for genome-wide association studies

Background: Genome-wide association studies (GWAS) based on single
nucleotide polymorphisms (SNPs) revolutionized our perception of
the genetic regulation of complex traits and diseases. Copy number
variations (CNVs) promise to shed additional light on the genetic
basis of monogenic as well as complex diseases and phenotypes.
Indeed, the number of detected associations between CNVs and
certain phenotypes are constantly increasing. However, while
several software packages support the determination of CNVs from
SNP chip data, the downstream statistical inference of
CNV-phenotype associations is still subject to complicated and
inefficient in-house solutions, thus strongly limiting the
performance of GWAS based on CNVs. Results: CONAN is a freely
available client-server software solution which provides an
intuitive graphical user interface for categorizing, analyzing and
associating CNVs with phenotypes. Moreover, CONAN assists the
evaluation process by visualizing detected associations via
Manhattan plots in order to enable a rapid identification of
genome-wide significant CNV regions. Various file formats including
the information on CNVs in population samples are supported as
input data. Conclusions: CONAN facilitates the performance of GWAS
based on CNVs and the visual analysis of calculated results. CONAN
provides a rapid, valid and straightforward software solution to
identify genetic variation underlying the `missing' heritability
for complex traits that remains unexplained by recent GWAS. The
freely available software can be downloaded at
http://genepi-conan.i-med.ac.at.