An improved method for detecting and delineating genomic regions with altered gene expression in cancer

Björn Nilsson¹^,2^,3 , Mikael Johansson⁴ , Anders Heyden⁵ , Sven Nelander⁶ and Thoas Fioretos¹

¹Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden

²Department of Transfusion Medicine, Lund University Hospital, SE-221 85 Lund, Sweden

³Imaging Platform, Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA

⁴Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden

⁵Department of Applied Mathematics, Malmö University, Malmö, SE-205 06 Malmö, Sweden

⁶Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

author email corresponding author email

Genome Biology 2008, 9:R13doi:10.1186/gb-2008-9-1-r13


Published:	21 January 2008

Subject areas: Bioinformatics, Cancer, Genome studies

Additional files

Additional file 1:

Complete set of ROC curves from the simulation study

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Additional file 2:

Complete set of breakpoint distribution plots from the simulation study

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Additional file 3:

High-resolution versions of the expression maps for each of the ALL cases in the Ross et al data set, as reconstructed by the proposed algorithm. Gray: Original gene scores from the Ross data set. Blue solid: Segmented gene scores. Each row represents one case, except for the bottom row which displays the average segmentation result and DNA copy number profiles (orange) across each leukemic subtype.

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Additional file 4:

Additional information about the proposed segmentation algorithms, including pseudocode.

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Additional file 5:

Additional data illustrating that the use of the default method parameters for CGHseg is appropriate.

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