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Bioinformatics Advance Access published online on February 22, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn067
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms

Weil Lai 1, Vidhu Choudhary 1 and Peter J Park 1,2,*

1Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA
2Informatics Program, Children's Hospital, Boston, MA, USA

*To whom correspondence should be addressed. Prof. Peter J Park, E-mail: peter_park{at}harvard.edu


  Abstract

Summary: Accurate estimation of DNA copy numbers from array comparative genomic hybridization (CGH) data is important for characterizing the cancer genome. An important part of this process is the segmentation of the log-ratios between the sample and control DNA along the chromosome into regions of different copy numbers. However, multiple algorithms are available in the literature for this procedure and the results can vary substantially among these. Thus, a visualization tool that can display the segmented profiles from a number of methods can be helpful to the biologist or the clinician to ascertain that a feature of interest did not arise as an artifact of the algorithm. Such a tool also allows the methodologist to easily contrast his method against others.

We developed a web-based tool that applies a number of popular algorithms to a single array CGH profile entered by the user. It generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. The clickable heatmap can be moved along the chromosome and zoomed in or out. It also displays the time that each algorithm took and provides numerical values of the segmented profiles for download. The web interface calls algorithms written in the statistical language R.We encourage developers of new algorithms to submit their routines to be incorporated into the website.

Availability: http://compbio.med.harvard.edu/CGHweb.

Contact: peter_park{at}harvard.edu

Associate Editor: Prof. Keith Crandall

Received on November 23, 2007; revised on January 21, 2008; accepted on February 15, 2008

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