title: CONAN: copy number variation analysis software for genome-wide association studies.
abstract: 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.
authors.affiliation: Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, 6020 Innsbruck, Austria.
authors.forename: Lukas
authors.initials: L
authors.lastname: Forer
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schönherr
authors.forename: Hansi
authors.initials: H
authors.lastname: Weissensteiner
authors.forename: Florian
authors.initials: F
authors.lastname: Haider
authors.forename: Thomas
authors.initials: T
authors.lastname: Kluckner
authors.forename: Christian
authors.initials: C
authors.lastname: Gieger
authors.forename: Heinz-Erich
authors.initials: HE
authors.lastname: Wichmann
authors.forename: Günther
authors.initials: G
authors.lastname: Specht
authors.forename: Florian
authors.initials: F
authors.lastname: Kronenberg
authors.forename: Anita
authors.initials: A
authors.lastname: Kloss-Brandstätter
mesh_terms: D056915:DNA Copy Number Variations; D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software