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Bioinformatics Advance Access published online on November 30, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl608
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received October 9, 2006
Revised November 14, 2006
Accepted November 23, 2006

Applications note

Visualization of genomic aberrations using Affymetrix SNP arrays

André Müller 1, Karlheinz Holzmann 2, and Hans A. Kestler 3 *

1 Internal Medicine I, University Hospital Ulm, Robert-Koch-Str. 8, D-89081 Ulm, Germany
2 Chip Facility/ZKF, University of Ulm, D-89081 Ulm, Germany
3 Internal Medicine I, University Hospital Ulm, Robert-Koch-Str. 8, D-89081 Ulm, Germany; Neural Information Processing, University of Ulm, D-89069 Ulm, Germany

* To whom correspondence should be addressed.
Hans A. Kestler, E-mail: hans.kestler{at}uni-ulm.de


  Abstract

Motivation: DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray based approaches have broadened the knowledge on number and structure of such aberrations. High density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500000 SNPs per genome. Due to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool - IdeogramBrowser - which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data.

Availability: IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/. IdeogramBrowser is a platform independent Java application.

Associate Editor: Martin Bishop
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