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Bioinformatics Advance Access published online on January 31, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm030
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CGHcall: calling aberrations for array CGH tumor profiles

Mark A. van de Wiel a,b,c,*, Kyung In Kim d, Sjoerd J. Vosse a, Wessel N. van Wieringen c, Saskia M. Wilting a and Bauke Ylstra a

a Department of Pathology and b Department of Biostatistics, VU University Medical Center, PO Box 7057, 1007MB Amsterdam, The Netherlands, c Department of Mathematics, Vrije Universiteit, Amsterdam, The Netherlands, d Department of Mathematics, Technische Universiteit, Eindhoven, The Netherlands

*to whom correspondence should be addressed. Mark van de Wiel, E-mail: mark.vdwiel{at}vumc.nl


  Abstract

Summary: CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. The algorithm is validated for simulated and verified real array CGH data. By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information.

Availability: An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html.

Supplementary information: Supplementary information is available at Bioinformatics online

Associate Editor: Chris Stoeckert

Received on December 15, 2006; revised on January 23, 2007; accepted on January 23, 2007

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