Open Access Software

CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations

Yuri Kotliarov1, Serdar Bozdag1, Hangjiong Cheng2, Stefan Wuchty1, Jean-Claude Zenklusen1 and Howard A Fine1*

Author Affiliations

1 Neuro-Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA

2 NCI Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, 2115 E Jefferson St., Rockville, MD 20852, USA

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BMC Medical Genomics 2010, 3:11  doi:10.1186/1755-8794-3-11

Published: 9 April 2010



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.


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.


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.