CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics 2010 Apr 09;3:11
Date
04/13/2010Pubmed ID
20380730Pubmed Central ID
PMC2872651DOI
10.1186/1755-8794-3-11Scopus ID
2-s2.0-77950637906 (requires institutional sign-in at Scopus site) 3 CitationsAbstract
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.
Author List
Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HAAuthor
Serdar Bozdag BS,PhD Assistant Professor, Director of Bioinformatics Lab in the Dept. of Mathematics, Statistics and Computer Science department at Marquette UniversityMESH terms used to index this publication - Major topics in bold
AlgorithmsChromosomes, Human
DNA Copy Number Variations
Genomics
Glioma
Humans
Loss of Heterozygosity
Polymorphism, Single Nucleotide
Software Design