title: Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Source code and sample data are available at http://bioinfo-out.curie.fr/projects/freec/.
authors.affiliation: Institut Curie, INSERM, U900, Paris, France. freec@curie.fr
authors.forename: Valentina
authors.initials: V
authors.lastname: Boeva
authors.forename: Andrei
authors.initials: A
authors.lastname: Zinovyev
authors.forename: Kevin
authors.initials: K
authors.lastname: Bleakley
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Vert
authors.forename: Isabelle
authors.initials: I
authors.lastname: Janoueix-Lerosey
authors.forename: Olivier
authors.initials: O
authors.lastname: Delattre
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D000465:Algorithms; D001482:Base Composition; D045744:Cell Line, Tumor; D003596:Cytosine / Q000032:analysis; D056915:DNA Copy Number Variations; D023281:Genomics / Q000379:methods*; D006147:Guanine / Q000032:analysis; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D012984:Software
chemical_list: D006147:Guanine; D003596:Cytosine