title: CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations.
abstract: BACKGROUND
  Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance.
  
  
  RESULTS
  We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool.
  
  
  CONCLUSIONS
  Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment.
authors.affiliation: Neuro-Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Kotliarov
authors.forename: Serdar
authors.initials: S
authors.lastname: Bozdag
authors.forename: Hangjiong
authors.initials: H
authors.lastname: Cheng
authors.forename: Stefan
authors.initials: S
authors.lastname: Wuchty
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Zenklusen
authors.forename: Howard A
authors.initials: HA
authors.lastname: Fine
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human; D056915:DNA Copy Number Variations; D023281:Genomics / Q000379:methods*; D005910:Glioma / Q000175:diagnosis / Q000235:genetics / Q000628:therapy; D006801:Humans; D019656:Loss of Heterozygosity; D020641:Polymorphism, Single Nucleotide; D012985:Software Design