title: CopywriteR: DNA copy number detection from off-target sequence data.
abstract: Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. t.kuilman@nki.nl.
authors.forename: Thomas
authors.initials: T
authors.lastname: Kuilman
authors.affiliation: Central Genomic Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands. a.velds@nki.nl.
authors.forename: Arno
authors.initials: A
authors.lastname: Velds
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. k.kemper@nki.nl.
authors.forename: Kristel
authors.initials: K
authors.lastname: Kemper
authors.affiliation: Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK. mr10@sanger.ac.uk.
authors.forename: Marco
authors.initials: M
authors.lastname: Ranzani
authors.affiliation: Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands. l.bombardelli@nki.nl.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Bombardelli
authors.affiliation: Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands. m.hoogstraat@nki.nl.
authors.forename: Marlous
authors.initials: M
authors.lastname: Hoogstraat
authors.affiliation: Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands. e.nevedomskaya@nki.nl.|Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. e.nevedomskaya@nki.nl.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Nevedomskaya
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. g.xu@nki.nl.
authors.forename: Guotai
authors.initials: G
authors.lastname: Xu
authors.affiliation: Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands. j.d.ruiter@nki.nl.|Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. j.d.ruiter@nki.nl.
authors.forename: Julian
authors.initials: J
authors.lastname: de Ruiter
authors.affiliation: Center for Personalized Cancer Treatment, Amsterdam, The Netherlands. M.Lolkema@erasmusmc.nl.
authors.forename: Martijn P
authors.initials: MP
authors.lastname: Lolkema
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands. b.ylstra@vumc.nl.
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
authors.affiliation: Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands. j.jonkers@nki.nl.
authors.forename: Jos
authors.initials: J
authors.lastname: Jonkers
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. s.rottenberg@nki.nl.|Vetsuisse Faculty, Institute of Animal Pathology, University of Bern, Bern, Switzerland. s.rottenberg@nki.nl.
authors.forename: Sven
authors.initials: S
authors.lastname: Rottenberg
authors.affiliation: Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands. l.wessels@nki.nl.
authors.forename: Lodewyk F
authors.initials: LF
authors.lastname: Wessels
authors.affiliation: Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK. da1@sanger.ac.uk.
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. d.peeper@nki.nl.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Peeper
authors.affiliation: Division of Molecular Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. o.krijgsman@nki.nl.
authors.forename: Oscar
authors.initials: O
authors.lastname: Krijgsman
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations / Q000235:genetics*; D059472:Exome / Q000235:genetics*; D005091:Exons / Q000235:genetics; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA