title: Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
abstract: BACKGROUND
  Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing.
  
  
  RESULTS
  Here we present ONCOCNV, a method that includes a multifactor normalization and annotation technique enabling the detection of large copy number changes from amplicon sequencing data. We validated our approach on high and low amplicon density datasets and demonstrated that ONCOCNV can achieve a precision comparable with that of array CGH techniques in detecting copy number aberrations. Thus, ONCOCNV applied on amplicon sequencing data would make the use of additional array CGH or SNP array experiments unnecessary.
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Valentina
authors.initials: V
authors.lastname: Boeva
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Popova
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Maxime
authors.initials: M
authors.lastname: Lienard
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Sebastien
authors.initials: S
authors.lastname: Toffoli
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Maud
authors.initials: M
authors.lastname: Kamal
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Christophe
authors.initials: C
authors.lastname: Le Tourneau
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: David
authors.initials: D
authors.lastname: Gentien
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gestraud
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rio Frio
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, 
authors.forename: Philippe
authors.initials: P
authors.lastname: Hupé
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
authors.affiliation: Inserm, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, Inserm, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, Département de recherche translationnelle, Centre de recherche, Next-generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium.
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Laes
mesh_terms: D055028:Comparative Genomic Hybridization; D004273:DNA, Neoplasm / Q000737:chemistry; D059472:Exome; D005260:Female; D018628:Gene Dosage; D052138:Genes, Neoplasm; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm