title: SG-ADVISER CNV: copy-number variant annotation and interpretation.
abstract: OBJECTIVE
  Copy-number variants have been associated with a variety of diseases, especially cancer, autism, schizophrenia, and developmental delay. The majority of clinically relevant events occur de novo, necessitating the interpretation of novel events. In this light, we present the Scripps Genome ADVISER CNV annotation pipeline and Web server, which aims to fill the gap between copy number variant detection and interpretation by performing in-depth annotations and functional predictions for copy number variants.
  
  
  METHODS
  The Scripps Genome ADVISER CNV suite includes a Web server interface to a high-performance computing environment for calculations of annotations and a table-based user interface that allows for the execution of numerous annotation-based variant filtration strategies and statistics.
  
  
  RESULTS
  The annotation results include details regarding location, impact on the coding portion of genes, allele frequency information (including allele frequencies from the Scripps Wellderly cohort), and overlap information with other reference data sets (including ClinVar, DGV, DECIPHER). A summary variant classification is produced (ADVISER score) based on the American College of Medical Genetics and Genomics scoring guidelines. We demonstrate >90% sensitivity/specificity for detection of pathogenic events.
  
  
  CONCLUSIONS
  Scripps Genome ADVISER CNV is designed to allow users with no prior bioinformatics expertise to manipulate large volumes of copy-number variant data. Scripps Genome ADVISER CNV is available at http://genomics.scripps.edu/ADVISER/.
authors.affiliation: Scripps Health, La Jolla, California, USA.|Scripps Translational Science Institute, La Jolla, California, USA.
authors.forename: Galina A
authors.initials: GA
authors.lastname: Erikson
authors.affiliation: Scripps Health, La Jolla, California, USA.|Scripps Translational Science Institute, La Jolla, California, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Deshpande
authors.affiliation: Scripps Health, La Jolla, California, USA.|Scripps Translational Science Institute, La Jolla, California, USA.
authors.forename: Balachandar G
authors.initials: BG
authors.lastname: Kesavan
authors.affiliation: Scripps Health, La Jolla, California, USA.|Scripps Translational Science Institute, La Jolla, California, USA.|Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA.|Cypher Genomics, La Jolla, California, USA.
authors.forename: Ali
authors.identifier: http://orcid.org/0000-0003-0232-8053
authors.initials: A
authors.lastname: Torkamani
mesh_terms: D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D015894:Genome, Human; D056914:Genomic Structural Variation; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D012984:Software