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. 2011 Jan 15;27(2):268-9.
doi: 10.1093/bioinformatics/btq635. Epub 2010 Nov 15.

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

Valentina Boeva  1 , Andrei Zinovyev, Kevin Bleakley, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot
Affiliations

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

Valentina Boeva et al. Bioinformatics. .

Abstract

Summary: We present a tool for control-free copy number alteration (CNA) detection using deep-sequencing data, particularly useful for cancer studies. The tool deals with two frequent problems in the analysis of cancer deep-sequencing data: absence of control sample and possible polyploidy of cancer cells. FREEC (control-FREE Copy number caller) automatically normalizes and segments copy number profiles (CNPs) and calls CNAs. If ploidy is known, FREEC assigns absolute copy number to each predicted CNA. To normalize raw CNPs, the user can provide a control dataset if available; otherwise GC content is used. We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs.

Availability: Source code and sample data are available at http://bioinfo-out.curie.fr/projects/freec/.

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Figures

Fig. 1.
Fig. 1.
Normalization of CNPs using only information about average GC content in a window. (A–D) GC content versus RC in 50 kb windows for COLO-829BL (normal diploid genome), COLO-829, NCI-H2171 and HCC1143, respectively. The result of the least-square fit for P-copy regions is shown in black. Curves corresponding to other frequent copy numbers are shown in gray. Values of copy numbers are given at the right of each panel. Chromosomes X and Y were not included. (E–H) GC-content normalized CNPs for chromosome 1 for COLO-829BL, COLO-829, NCI-H2171 and HCC1143, respectively. Automatically predicted copy numbers are shown in black.
See this image and copyright information in PMC

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