title: GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data.
abstract: Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.
authors.affiliation: Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway. heidi.lyng@rr-research.no
authors.forename: Heidi
authors.initials: H
authors.lastname: Lyng
authors.forename: Malin
authors.initials: M
authors.lastname: Lando
authors.forename: Runar S
authors.initials: RS
authors.lastname: Brøvig
authors.forename: Debbie H
authors.initials: DH
authors.lastname: Svendsrud
authors.forename: Morten
authors.initials: M
authors.lastname: Johansen
authors.forename: Eivind
authors.initials: E
authors.lastname: Galteland
authors.forename: Odd T
authors.initials: OT
authors.lastname: Brustugun
authors.forename: Leonardo A
authors.initials: LA
authors.lastname: Meza-Zepeda
authors.forename: Ola
authors.initials: O
authors.lastname: Myklebost
authors.forename: Gunnar B
authors.initials: GB
authors.lastname: Kristensen
authors.forename: Eivind
authors.initials: E
authors.lastname: Hovig
authors.forename: Trond
authors.initials: T
authors.lastname: Stokke
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D018628:Gene Dosage; D006801:Humans; D008228:Lymphoma, Non-Hodgkin / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D014178:Translocation, Genetic; D002583:Uterine Cervical Neoplasms / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm